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Helsinki, Finland

The University of Helsinki is a university located in Helsinki, Finland since 1829, but was founded in the city of Turku in 1640 as the Royal Academy of Turku, at that time part of the Swedish Empire. It is the oldest and largest university in Finland with the widest range of disciplines available. Around 36,500 students are currently enrolled in the degree programs of the university spread across 11 faculties and 11 research institutes.As of August 1, 2005, the University complies with the standards of the Europe-wide Bologna Process and offers Bachelor, Master, Licenciate, and Doctoral degrees. Admission to degree programmes is usually determined by entrance examinations, in the case of bachelor degrees, and by prior degree results, in the case of master and postgraduate degrees. Entrance is particularly selective . It has been ranked a top 100 university in the world according to the 2012 QS, Times Higher Education and the Academic Rankings of World Universities.The university is bilingual, with teaching provided both in Finnish and Swedish. Teaching in English is extensive throughout the university at Master, Licentiate, and Doctoral levels, making it a de facto third language of instruction.Remaining true to its traditionally strong Humboldtian ethos, the University of Helsinki places heavy emphasis on high-quality teaching and research of a top international standard. It is a member of various prominent international university networks, such as Europaeum, UNICA, the Utrecht Network, and is a founding member of the League of European Research Universities. Wikipedia.

Mattsson M.,University of Helsinki
Accident Analysis and Prevention | Year: 2014

Since its publication, the Driver Behavior Questionnaire (DBQ) has been used for comparing subgroups of respondents on the constructs formed through factor analyzing the questionnaire items. However, not enough attention has been paid to ascertaining that the instrument actually measures the same constructs in the same way in all respondent groups. I recently published an article (Mattsson, 2012) that aimed to do this for the Finnish 28-item version of the DBQ using the stage-wise factorial invariance approach in the Exploratory Structural Equation Modeling (ESEM) context. de Winter (2013) commented on the publication, arguing that the results were artifacts due to measurement error that too many factors were extracted and that too strict criteria for invariance were applied. In this contribution, I reply to each criticism and suggest methodological approaches for ensuring the measurement invariance of self-report instruments such as the DBQ.© 2013 Elsevier Ltd. All rights reserved.

Teramo K.,University of Helsinki
NeoReviews | Year: 2014

Perinatal morbidity andmortality, congenital malformations, abnormal fetal growth, both spontaneous and iatrogenic preterm birth, hypoxic complications, and trauma during delivery are increased in diabetic pregnancies. Perinatal mortality in diabetic pregnancies is still three to five times higher than the perinatal mortality in the general population. Stillbirths during the last weeks of pregnancy are often considered unexplained, although recent studies indicate that most of these stillbirths are caused by fetal chronic hypoxia. Importantly, perinatal mortality has not changed during the past 3 decades in diabetic pregnancies, which emphasizes the need to find new methods and strategies to improve perinatal outcome. Congenital malformations have decreased in pregestational diabetic pregnancies because of general improvement of glycemic control among diabetic women. However, the rate of fetal malformations is still two to four times higher in type 1 and type 2 diabetic pregnancies than in the general population. Prepregnancy counseling decreases the risk of fetal malformations. Efforts should be made to improve the attendance of diabetic women in prepregnancy clinics. Fetal overgrowth during the last trimester of pregnancy is the most common fetal complication in diabetic pregnancies. Accurate estimation of fetal weight by ultrasound is especially difficult in macrosomic fetuses. Magnetic resonance imaging can be used to assess fetal total volume, shoulder width, and fat amount in addition to obtaining accurate pelvic measurements. More studies on the clinical use of magnetic resonance imaging in obstetrics are urgently needed. Increased fetal erythropoietin (EPO) level is an indicator of fetal chronic hypoxia, which can be detected antenatally by measuring amniotic fluid EPO concentration. Sufficiently large controlled studies are needed before amniotic fluid EPO measurement can be recommended for clinical use. © 2014 by the American Academy of Pediatrics. All rights reserved.

The aim of this study was to clarify the associations between sense of coherence (SOC), dispositional optimism and distress (i.e., anxiety and depression) in cancer patients and their partners. The associations between SOC, dispositional optimism (Life Orientation Test-Revised, LOT-R), depression (Beck Depression Inventory-14, BDI-14) and anxiety (Endler Multidimensional Anxiety Scales, EMAS-State) were studied in 147 cancer couples. The data were collected with self-report questionnaires at the time of diagnosis (2 months) and after 6 months. Path analysis was used to analyse the predictors of follow-up distress and crossover effects in the longitudinal data. Optimistic patients and patients with strong SOC as well as their partners reported fewer symptoms of depression and anxiety than less optimistic subjects and subjects with weaker SOC. Optimism partially explained the effect of SOC on distress and SOC seemed to be an independent factor in predicting distress. Patient and partner distress at baseline and at 8-month follow-up correlated positively. In addition, high partner optimism at baseline seemed to predict low patient anxiety at follow-up. The beneficial effects of SOC seem to include also other elements beyond optimism. In clinical practice, enhancing optimistic expectations of the future and promoting SOC could be expected to reduce distress in cancer patients and their partners.

Heinonen J.S.,University of Helsinki | Kurz M.D.,Woods Hole Oceanographic Institution
Earth and Planetary Science Letters | Year: 2015

The massive outpourings of Karoo and Ferrar continental flood basalts (CFBs) ~180 Ma ago mark the initial Jurassic rifting stages of the Gondwana supercontinent. The origin and sources of these eruptions have been debated for decades, largely due to difficulties in defining their parental melt and mantle source characteristics. Recent findings of Fe- and Mg-rich dikes (depleted ferropicrite suite) from Vestfjella, western Dronning Maud Land, Antarctica, have shed light on the composition of the deep sub-Gondwanan mantle: these magmas have been connected to upper mantle sources presently sampled by the Southwest Indian Ocean mid-ocean ridge basalts (SWIR MORBs) or to high 3He/4He plume-entrained non-chondritic primitive mantle sources formed early in Earth's history. In an attempt to determine their He isotopic composition and relative contributions from magmatic, cosmogenic, and radiogenic He sources, we performed in-vacuo stepwise crushing and melting analyses of olivine mineral separates, some of which were abraded to remove the outer layer of the grains. The best estimate for the mantle isotopic composition is given by a sample with the highest amount of He released (>50%) during the first crushing step of an abraded coarse fraction. It has a 3He/4He of 7.03±0.23 (2σ) times the atmospheric ratio (Ra), which is indistinguishable from those measured from SWIR MORBs (6.3-7.3 Ra; source 3He/4He ~6.4-7.6 Ra at 180 Ma) and notably lower than in the most primitive lavas from the North Atlantic Igneous Province (up to 50 Ra), considered to represent the epitome magmas from non-chondritic primitive mantle sources. Previously published trace element and isotopic (Sr, Nd, and Pb) compositions do not suggest a direct genetic link to any modern hotspot of Indian or southern Atlantic Oceans. Although influence of a mantle plume cannot be ruled out, the high magma temperatures and SWIR MORB-like geochemistry of the suite are best explained by supercontinent insulation of a precursory Indian Ocean upper mantle source. Such a model is also supported by the majority of the recent studies on the structure, geochronology, and petrology of the Karoo CFBs. © 2015 Elsevier B.V.

Malkki L.,University of Helsinki
Terrorism and Political Violence | Year: 2014

School shootings have traditionally been interpreted as non-political acts. Empirical evidence, however, suggests that not all shootings are necessarily so different from political violence, at least in the shooter's own opinion. The article analyses 28 school rampage shootings in Europe, the U.S., and Canada from 1999-2011 to determine common and prevalent political elements in the shootings. The shootings are divided into three categories: shootings with overtly political communication (four cases), shootings with references to previous school rampage shootings (13 cases), and isolated incidents (11 cases). While it is possible to question whether the shootings were genuinely politically motivated, it is clear that the majority of school shooters link their deed to the agenda and beliefs presented by the Columbine shooters, which has created a sense of tradition, continuity, and imagined community among the shooters and their admirers, not unlike in cases of terrorism and political violence that are referred to as leaderless resistance. © 2014 Copyright Taylor and Francis Group, LLC.

Kerola A.M.,University of Helsinki | Kauppi M.J.,Paijat Hame Central Hospital
Clinical Rheumatology | Year: 2014

Only limited evidence exists on the therapeutic potential of biologic agents in the treatment of myositis. We present a brief review of the literature on off-label experiences of biologic agents in myositis, with a special interest in abatacept. Rituximab has been indicated to be beneficial and well tolerated in one large randomized controlled trial and many smaller studies. Initial data on tumour necrosis factor (TNF) inhibitors are conflicting. There are only a few case reports and mechanistic studies on the treatment of myositis with other biologics, including alemtuzumab, anakinra, tocilizumab and abatacept. We report a patient with severe myositis overlap syndrome, manifesting also as rheumatoid arthritis, peripheral vasculitis and interstitial lung disease. Her myositis was refractory to many conventional and biologic therapies but was well controlled with abatacept. This suggests that abatacept might be a beneficial option for the treatment of refractory myositis and that clinical trials are needed to further investigate its efficacy. © 2014 Clinical Rheumatology.

Riihimaki O.,University of Helsinki
Obstetrics and gynecology | Year: 2013

To examine the association between major congenital anomalies and placental abruption. A register-based retrospective case-control study was carried out from 1987 to 2005. Data on baseline characteristics and birth outcomes were collected from three Finnish national health registers: the Medical Birth Register, National Hospital Discharge Register, and Register of Congenital Malformations. The study population consisted of 4,190 women with singleton birth and placental abruption. Three control women without placental abruption were selected for each case, matched by maternal age, parity, year of birth, and hospital district. The main outcome measure of the study was a major congenital anomaly associated with placental abruption. In total, 261 (prevalence 623/10,000) births with placental abruption and 415 (prevalence 330/10,000) control births had major congenital anomalies (odds ratio [OR] 1.92, 95% confidence interval [CI] 1.6-2.52). The association was strongest among births with growth restriction and prematurity. Adjusted analysis revealed a significant association with central nervous system anomalies (OR 2.33, 95% CI 1.29-4.23), anomalies of the eyes and ears (OR 1.82, 95% CI 1.08-3.09), cardiovascular anomalies (OR 1.78, 95% CI 1.34-2.37), respiratory anomalies (OR 3.51, 95% CI 1.56-7.90), gastrointestinal anomalies (OR 3.81, 95% CI 2.27-6.41), genitourinary anomalies (OR 2.55, 95% CI 1.73- 3.74), musculoskeletal anomalies (OR 1.67, 95% CI 1.24-2.24), and anomalies of integument (OR 3.29, 95% CI 1.20-8.98) in births complicated by placental abruption. Major congenital anomalies are twice as common among neonates born from pregnancies complicated by placental abruption compared with control pregnancies without abruption. This observation applies to several organ systems. II.

Savijarvi H.,University of Helsinki
Quarterly Journal of the Royal Meteorological Society | Year: 2014

The nocturnal stable boundary layer (SBL) over snow was studied via 1-D clear-sky simulations at 67oN. Three wind regimes could be identified. A windy SBL was relatively well-mixed, turbulent cooling rates being moderate and long-wave (LW) cooling rates weak as gradients of temperature and moisture (T,q) remained small. In calm and near-calm cases the surface temperature Ts dropped rapidly in the evening, leading to a strong shallow inversion dominated by strong LW cooling. During weak winds (geostrophic wind Vg ∼ 3 m s-1), Ts decreased fairly rapidly in the evening with T2m closely coupled. The nocturnal inversion was moderately strong with strong turbulent cooling in the surface layer. The T,q-profiles induced moderate LW cooling at mid-inversion levels but LW heating in the lowest metres, which resisted the strong turbulent cooling. Thus the heating/cooling rates were fairly sensitive to the wind, especially near the surface. The snow surface was coldest after a calm night and warmer at windy sunrises, whereas the coldest air temperatures were obtained during weak winds, provided that the model's stability functions were of the 'short tails' type. A maximum in the downward sensible heat flux was associated with this. When the model's multilayer snow scheme was replaced by a coarse scheme, the nocturnal Ts and T2m stayed too warm. The use of old snow properties instead of typical snow produced relatively warm nocturnal temperatures whereas fresh snow led to quite cold temperatures. These aspects may have relevance to the SBL warm biases of large-scale models. © 2013 Royal Meteorological Society.

Raheem D.,University of Helsinki
Emirates Journal of Food and Agriculture | Year: 2013

The role of plastics and paper as food packaging materials is reviewed with a brief outlook on the historical background of food packages in general. The inherent properties of these food packages that should be considered by food processors are also discussed. The current efforts in meeting the needs of consumers in ensuring food's quality with prolonged shelf life during storage and distribution were highlighted. This review article also reflects on the emerging trends in technology that address innovations on Modified atmosphere packaging (MAP), Active packaging (AP), Intelligent packaging (IP) and the use of anti-microbial agents to extend the shelf life of foods under storage and distribution conditions. The future of these packaging materials in the food industries and their impacts on the environment and the society at large will continue to receive attention.

Barry R.A.,University of California at San Francisco | Hiilamo H.,University of Helsinki | Glantz S.A.,University of California at San Francisco
Milbank Quarterly | Year: 2014

Context In 2012, Washington State and Colorado legalized the recreational use of marijuana, and Uruguay, beginning in 2014, will become the first country to legalize the sale and distribution of marijuana. The challenge facing policymakers and public health advocates is reducing the harms of an ineffective, costly, and discriminatory "war on drugs" while preventing another public health catastrophe similar to tobacco use, which kills 6 million people worldwide each year. Methods Between May and December 2013, using the standard snowball research technique, we searched the Legacy Tobacco Documents Library of previously secret tobacco industry documents (http://legacy.library.ucsf.edu). Findings Since at least the 1970s, tobacco companies have been interested in marijuana and marijuana legalization as both a potential and a rival product. As public opinion shifted and governments began relaxing laws pertaining to marijuana criminalization, the tobacco companies modified their corporate planning strategies to prepare for future consumer demand. Conclusions Policymakers and public health advocates must be aware that the tobacco industry or comparable multinational organizations (eg, food and beverage industries) are prepared to enter the marijuana market with the intention of increasing its already widespread use. In order to prevent domination of the market by companies seeking to maximize market size and profits, policymakers should learn from their successes and failures in regulating tobacco. © 2014 Milbank Memorial Fund.

Sexual dimorphism in the Arctic tadpole shrimp, Lepidurus arcticus (Pallas, 1793), was examined. Selective forces shape sexes differently. Males fitness increases by successful mate searching, whereas females increase reproductive potential by attaining large sizes. Sexual dimorphism was examined in 331 L. arcticus from Svalbard, Norway. Males were significantly smaller than females and had significantly smaller carapaces, telsons and cercopods. Lepidurus arcticus is an omnivorous, sometimes cannibalistic, predator. Cannibalism potential effects on sexual dimorphism were studied in the field and laboratory. Cannibalism frequency did not differ significantly between populations. Females dominated in all populations. Male L. arcticus searching for females are at greater risk due to increased chance of encounters with predators and cannibalistic females. Male small body size is advantageous against visually hunting predators, while more robust limbs help males search for females effectively and amplex them. In contrast, the significantly larger female carapace protects her and her eggs from predators. © 2015. Published by Brill NV, Leiden.

Herttua K.,University of Helsinki
Epidemiology | Year: 2015

BACKGROUND:: Minimum price of alcohol is one of the proposed set of alcohol policies in many high-income countries. However, the extent to which alcohol-related harm is associated with minimum prices across socioeconomic groups is not known.METHODS:: Using Finnish national registers in 1988–2007, we investigated, by means of time-series analysis, the association between minimum prices for alcohol overall, as well as for various types of alcoholic beverages, and alcohol-related mortality, among men and women aged 30–79 years across three educational groups. We defined quarterly aggregations of alcohol-related deaths, based on a sample including 80% of all deaths, in accordance with information on both underlying and contributory causes of death.RESULTS:: About 62,500 persons died from alcohol-related causes during the 20-year follow-up. The alcohol-related mortality rate was more than threefold higher among those with a basic education than among those with a tertiary education. Among men with a basic education, an increase of 1% in the minimum price of alcohol was associated with a decrease of 0.03% (95% confidence interval = 0.01, 0.04%) in deaths per 100,000 person-years. Changes in the minimum prices of distilled spirits, intermediate products, and strong beer were also associated with changes in the opposite direction among men with a basic education and among women with a secondary education, whereas among the most highly educated there were no associations between the minimum prices of any beverages and mortality. Moreover, we found no evidence of an association between lower minimum prices for wine and higher rates of alcohol-related mortality in any of the population sub-groups.CONCLUSIONS:: The results reveal associations between higher minimum prices and lower alcohol-related mortality among men with a basic education and women with a secondary education for all beverage types except wine. Copyright © 2015 Wolters Kluwer Health, Inc. All rights reserved.

Huttunen S.,University of Oulu | Manninen S.,University of Helsinki
Environmental and Experimental Botany | Year: 2013

The data on Scots pine responses to elevated ozone (O3) mainly come from experimental studies with young seedlings and trees. Based on the 38 experiments reviewed here, Scots pine may be considered as an O3-sensitive conifer species, with mature pines more sensitive than younger trees. This is due to their relatively small proportion of current (c) year needles with the highest photosynthetic capacity. Moreover, young seedlings and trees seem to acclimate to slightly elevated realistic O3 exposures, and hence do not often exhibit growth and biomass reductions in spite of the visible and microscopic needle injuries and changes in needle chemistry. The O3 sensitivity in Scots pine is thought to relate to impaired water status due to the malfunction of stomata and subsequent increase in transpiration. This may lead to reduced wood biomass in the long term, if Scots pines try to maximise the biomass of c needles and root biomass to maintain efficient water and nitrogen (N) supply to support the photosynthesis of c needles. Tree water status also contributes to the spring-time recovery of photosynthesis. We call especially for studies on atmosphere-needle surface interaction that would yield novel information on the impact of O3 on epicuticular waxes and stomatal functioning, which both regulate O3 flux and tree water status and hence also modify photosynthesis. The need for flux-based field studies is especially important in the light of future climatic change, since the risk presented by O3 to Scots pine forests in Northern and Central Europe seems to be equal. © 2012 Elsevier B.V.

Ristola M.,University of Helsinki
Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association | Year: 2012

Nephrin and Neph3 are homologous molecules expressed in the podocyte slit diaphragms that are essential for normal glomerular ultrafiltration. Nephrin and Neph3 genes form a bidirectional gene pair suggesting that they may share key features in their regulation. We investigated if nephrin and Neph3 genes have similar mechanisms in their transcriptional regulation focussing on transcription factor Wilms' tumour 1 (WT1) and nuclear factor-κB (NF-κB) and DNA methylation. Transcriptional regulation of nephrin and Neph3 by WT1 and NF-κB was analysed by overexpression studies, reporter gene assay and chromatin immunoprecipitation using A293 cells and cultured podocytes. The interaction between WT1 and NF-κB was studied by co-immunoprecipitation. The effect of NF-κB activator tumour necrosis factor-α (TNF-α) with or without NF-κB pathway inhibitor (BAY 11-7082) on nephrin and Neph3 messenger RNA (mRNA) expression and on cellular distribution of NF-κB was determined by quantitative polymerase chain reaction (PCR) and immunostaining, respectively. The role of DNA methylation in regulating nephrin and Neph3 genes was studied by demethylating agent (5-aza-2'-deoxycytidine) treatment and quantitative PCR. WT1 and NF-κB interact with nephrin and Neph3 promoter and cooperatively regulate nephrin and Neph3. The cooperation was further supported by the physical interaction between WT1 and NF-κB. TNF-α increased nephrin and Neph3 mRNA expression and this effect was mediated by NF-κB. Furthermore, DNA methylation played a role in silencing nephrin and Neph3 expression in a cell-type and differentiation stage-dependent manner. These results provide novel insights into the transcriptional regulation of nephrin and Neph3 genes and indicate that nephrin and Neph3 share the same mechanisms in their regulation.

Savijarvi H.,University of Helsinki | Maattanen A.,University of Versailles
Quarterly Journal of the Royal Meteorological Society | Year: 2010

Diurnal simulations and sensitivity studies were made with a moist column model at the Mars Phoenix lander site (68°N) for the summer solstice (solar day 30) and for a later date (sol 99), when the LIDAR on board Phoenix detected fog, dust, ice clouds and even snowfall from cloud. The sol 30 simulation reproduces the observed repetitive diurnal 2mtemperature cyclequite well, displaying awell-mixedboundary layer up to 4 km in the afternoon and a strong surface inversion to 500meach night. Weak frost formation peaks atmidnight and a very thin radiation fog appears during the coldest hour. The near-surface water vapour pressure is underestimated during daytime but is close to the thermal and electrical conductivity probe observations during the night. The Prandtl slope wind mechanism produces veering winds in the model as observed by the 'telltale' device while coupled dust evolution implies well-mixed dust to 4 km throughout the sol as observed by the LIDAR. The colder diurnal conditions around sol 99 are also simulated rather well. In these, the morning fog grows up to 800 m height and a water ice cloud forms at 4 km height at about 0300 local time, as observed. The cloud marks the radiatively cooled top of the moist residual boundary layer. Strong ground frost formation peaks in the evening, having a visible impact on the temperatures. The fog and cloud display weak feedbacks to the modelled radiative fluxes. © 2010 Royal Meteorological Society.

Shcherbakova D.M.,Yeshiva University | Shemetov A.A.,Yeshiva University | Kaberniuk A.A.,Yeshiva University | Verkhusha V.V.,Yeshiva University | Verkhusha V.V.,University of Helsinki
Annual Review of Biochemistry | Year: 2015

Genetically encoded optical tools have revolutionized modern biology by allowing detection and control of biological processes with exceptional spatiotemporal precision and sensitivity. Natural photoreceptors provide researchers with a vast source of molecular templates for engineering of fluorescent proteins, biosensors, and optogenetic tools. Here, we give a brief overview of natural photoreceptors and their mechanisms of action. We then discuss fluorescent proteins and biosensors developed from light-oxygen-voltage-sensing (LOV) domains and phytochromes, as well as their properties and applications. These fluorescent tools possess unique characteristics not achievable with green fluorescent protein-like probes, including near-infrared fluorescence, independence of oxygen, small size, and photosensitizer activity. We next provide an overview of available optogenetic tools of various origins, such as LOV and BLUF (blue-light-utilizing flavin adenine dinucleotide) domains, cryptochromes, and phytochromes, enabling control of versatile cellular processes. We analyze the principles of their function and practical requirements for use. We focus mainly on optical tools with demonstrated use beyond bacteria, with a specific emphasis on their applications in mammalian cells. Copyright © 2015 by Annual Reviews. All rights reserved.

Molsa S.H.,University of Helsinki
Veterinary surgery : VS : the official journal of the American College of Veterinary Surgeons | Year: 2010

To (1) report ground reaction forces for healthy Rottweilers at a trot and (2) compare force platform data with values obtained for healthy Labradors. Prospective, clinical study. Adult Rottweilers (n=9) and Labrador Retrievers (12) without orthopedic abnormalities. Dogs were trotted over a force platform at controlled speed and acceleration. Peak vertical and craniocaudal forces, associated impulses, stance time, rising, and falling slopes were analyzed and forces, impulses, and slopes were expressed as percentages of body weight. The effects of weight and anatomic measurements on force platform values were re-evaluated with analysis of covariance (ANCOVA). In Rottweilers, peak vertical forces in thoracic limbs were significantly lower and vertical impulses in thoracic and pelvic limbs were significantly higher than in Labradors. Rising and falling slopes in thoracic and pelvic limbs were significantly smaller in Rottweilers. Body weight and anatomic measurements were significantly larger in Rottweilers. After removing the effect of relative velocity, functional limb length, and body weight by using ANCOVA, there were no significant differences between breeds. Ground reaction forces were significantly different between Rottweilers and Labradors when using standard methods of normalization. Based on ANCOVA differences were attributable to difference in conformation and body weight between breeds. Conformation and body weight have a significant influence on force platform values and this may cause bias when study results are compared.

Niskanen J.A.,University of Helsinki | Machner H.,University of Duisburg - Essen
Nuclear Physics A | Year: 2013

The possibility of η-mesic nuclei remains an open problem in nuclear physics until now. Various calculations give contradictory predictions even for the lightest real nucleus 3He. In this paper we present the connection of the binding energy and width to the complex scattering length for s-states in heavier nuclei than this in the hope that, with knowledge of the final state interaction this could be useful in searches of possible bound states. It is seen that for a consistent analysis also the effective range should be considered. © 2013 Elsevier B.V.

Hakkinen M.,University of Helsinki
Taxon | Year: 2013

The present work is part of a continuing study on Musa taxa by the author. Several molecular analyses support acceptance of only two Musa sections, M. sect. Musa and M. sect. Callimusa. Musa sect. Rhodochlamys is synonymized with M. sect. Musa and M. sect. Australimusa and M. sect. Ingentimusa are treated as synonyms of M. sect. Callimusa. Species lists are provided for the two accepted sections.

Taquet V.,NASA | Charnley S.B.,NASA | Sipila O.,University of Helsinki
Astrophysical Journal | Year: 2014

Extremely large deuteration of several molecules has been observed toward prestellar cores and low-mass protostars for a decade. New observations performed toward low-mass protostars suggest that water presents a lower deuteration in the warm inner gas than in the cold external envelope. We coupled a gas-grain astrochemical model with a one-dimensional model of a collapsing core to properly follow the formation and the deuteration of interstellar ices as well as their subsequent evaporation in the low-mass protostellar envelopes with the aim of interpreting the spatial and temporal evolutions of their deuteration. The astrochemical model follows the formation and the evaporation of ices with a multilayer approach and also includes a state-of-the-art deuterated chemical network by taking the spin states of H2 and light ions into account. Because of their slow formation, interstellar ices are chemically heterogeneous and show an increase of their deuterium fractionation toward the surface. The differentiation of the deuteration in ices induces an evolution of the deuteration within protostellar envelopes. The warm inner region is poorly deuterated because it includes the whole molecular content of ices, while the deuteration predicted in the cold external envelope scales with the highly deuterated surface of ices. We are able to reproduce the observed evolution of water deuteration within protostellar envelopes, but we are still unable to predict the super-high deuteration observed for formaldehyde and methanol. Finally, the extension of this study to the deuteration of complex organics, important for the prebiotic chemistry, shows good agreement with the observations, suggesting that we can use the deuteration to retrace their mechanisms and their moments of formation. © 2014. The American Astronomical Society. All rights reserved.

Bravin A.,European Synchrotron Radiation Facility | Coan P.,Ludwig Maximilians University of Munich | Suortti P.,University of Helsinki
Physics in Medicine and Biology | Year: 2013

Phase-contrast x-ray imaging (PCI) is an innovative method that is sensitive to the refraction of the x-rays in matter. PCI is particularly adapted to visualize weakly absorbing details like those often encountered in biology and medicine. In past years, PCI has become one of the most used imaging methods in laboratory and preclinical studies: its unique characteristics allow high contrast 3D visualization of thick and complex samples even at high spatial resolution. Applications have covered a wide range of pathologies and organs, and are more and more often performed in vivo. Several techniques are now available to exploit and visualize the phase-contrast: propagation- and analyzer-based, crystal and grating interferometry and non-interferometric methods like the coded aperture. In this review, covering the last five years, we will givean overview of the main theoretical and experimental developments and of the important steps performed towards the clinical implementation of PCI. © 2013 Institute of Physics and Engineering in Medicine.

Nygren A.,University of Helsinki
Environmental Values | Year: 2015

This article analyses the representational politics of global commodity networks, where certified forest products are produced and consumed, approaching them as complex forms of governance in which diverse actors, images, conventions and values interact. The study draws upon a case study of certified Honduran community forestry groups producing furniture and kitchenware for Danish design markets. Special focus is on the forms of negotiation and contestation through which the different actors mediate the representations and imagery circulating in the marketing of certified products and on their differential access to control and power. The research illustrates how leading retailers, in negotiation with environmental organisations, modify definitions of quality and guide consumers’ expectations of certified southern forest products, by building images of southern community forest producers as authentic and exotic ‘others’. The article concludes that certification as a market-based form of governance has had only limited impact on altering the unequal relationships characteristic of global networks of production and consumption. © 2015, The White Horse Press.

Jokela M.,University of Helsinki | Jokela M.,University of Cambridge
American Journal of Epidemiology | Year: 2014

People who live in disadvantaged neighborhoods tend to have poor physical and mental health, but this might be due to selective residential mobility rather than causal neighborhood effects. As a test of social causation, I examined whether persons were less healthy when they were living in disadvantaged neighborhoods than at other times when they were living in more advantaged neighborhoods. Data were taken from the 10-year Household, Income and Labour Dynamics in Australia (HILDA) prospective cohort study, which had annual follow-up waves between 2001 and 2010 (n = 112,503 person-observations from 20,012 persons). Neighborhood disadvantage was associated with poorer self-rated health, mental health, and physical functioning, higher probability of smoking, and less frequent physical activity. However, these associations were almost completely due to between-person differences; the associations were not replicated in within-person analyses that compared the same persons living in different neighborhoods over time. Results were similar when using neighborhood remoteness as the exposure and when focusing only on long-term residence. In contrast, poor health predicted selective residential mobility to less advantaged neighborhoods, which provided evidence of social selection. These findings provide little support for social causation in neighborhood health associations and suggest that correlations between neighborhoods and health may develop via selective residential mobility. © The Author 2014.

Hamalainen W.,University of Helsinki
Computational Statistics and Data Analysis | Year: 2016

In the dependency rule mining, the goal is to discover the most significant statistical dependencies among all possible collapsed 2×2 contingency tables. Fisher's exact test is a robust method to estimate the significance and it enables efficient pruning of the search space. The problem is that evaluating the required p-value can be very laborious and the worst case time complexity is O(n), where n is the data size. The traditional solution is to approximate the significance with the χ2-measure, which can be estimated in a constant time. However, the χ2-measure can produce unreliable results (discover spurious dependencies but miss the most significant dependencies). Furthermore, it does not support efficient pruning of the search space. As a solution, a family of tight upper bounds for Fisher's p is introduced. The new upper bounds are fast to calculate and approximate Fisher's p-value accurately. In addition, the new approximations are not sensitive to the data size, distribution, or smallest expected counts like the χ2-based approximation. In practice, the execution time depends on the desired accuracy level. According to experimental evaluation, the simplest upper bounds are already sufficiently accurate for dependency rule mining purposes and they can be estimated in 0.004-0.1% of the time needed for exact calculation. For other purposes (testing very weak dependencies), one may need more accurate approximations, but even they can be calculated in less than 1% of the exact calculation time. © 2015 Elsevier B.V. All rights reserved.

Raerinne J.,University of Helsinki
Biology and Philosophy | Year: 2013

There appear to be no biological regularities that have the properties traditionally associated with laws, such as an unlimited scope or holding in all or many possible background conditions. Mitchell, Lange, and others have therefore suggested redefining laws to redeem the lawlike status of biological regularities. These authors suggest that biological regularities are lawlike because they are pragmatically or paradigmatically similar to laws or stable regularities. I will review these re-definitions by arguing both that there are difficulties in applying their accounts to biology and difficulties in the accounts themselves, which suggests that the accounts are not adequate to redeem the lawlike status of biological regularities. Finally, I will suggest a new account of laws that also shows how non-laws might function in some of the roles of laws. © 2013 Springer Science+Business Media Dordrecht.

Hyvarinen A.,University of Helsinki
Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences | Year: 2013

Independent component analysis is a probabilistic method for learning a linear transform of a random vector. The goal is to find components that are maximally independent and non-Gaussian (nonnormal). Its fundamental difference to classical multivariate statistical methods is in the assumption of non-Gaussianity, which enables the identification of original, underlying components, in contrast to classical methods. The basic theory of independent component analysis was mainly developed in the 1990s and summarized, for example, in our monograph in 2001. Here, we provide an overview of some recent developments in the theory since the year 2000. The main topics are: analysis of causal relations, testing independent components, analysing multiple datasets (three-way data), modelling dependencies between the components and improved methods for estimating the basic model. © 2012 The Author(s) Published by the Royal Society. All rights reserved.

Brommer J.E.,University of Helsinki
Journal of Evolutionary Biology | Year: 2011

Local adaptation through natural selection can be inferred in case the additive genetic divergence in a quantitative trait across populations (Q st) exceeds the neutral expectation based on differentiation of neutral alleles across these populations (e.g. F st). As such, measuring Q st in relation to neutral differentiation presents a first-line investigation applicable in evolutionary biology (selection on functional genes) and conservation biology (identification of locally adapted coding genes). However, many species, especially those in need of conservation actions, are not amenable for the kind of breeding design required to estimate either narrow- or broad-sense Q st. In such cases, Q st has been approximated by the phenotypic divergence in a trait across populations (P st). I here argue that the critical aspect for how well P st approximates Q st depends on the extent that additive genetic effects determine variation between populations relative to within populations. I review how the sensitivity of conclusions regarding local adaptation based on P st have been evaluated in the literature and find that many studies make a anticonservative null assumption in estimating P st and/or use a nonconservative approach to explore sensitivity of their conclusions. Data from two studies that have provided a second, independent assessment of selection in their system suggest that P st-F st comparisons should be interpreted very conservatively. I conclude with recommendations for improving the robustness of the inferences drawn from comparing P st with neutral differentiation. © 2011 The Author. Journal of Evolutionary Biology © 2011 European Society For Evolutionary Biology.

Kuitunen M.,University of Helsinki
Current Opinion in Allergy and Clinical Immunology | Year: 2013

PURPOSE OF REVIEW: To describe the current literature on clinical trials of probiotics for eczema and food allergy prevention in view of recent new approaches and long-term follow-ups. RECENT FINDINGS: Attempting allergy prevention by probiotic administration has been most successful when assessing atopic eczema, the most prevalent allergic disease at an early age. More than half of the published studies demonstrate a decrease in eczema prevalence until 2 years, whereas the remaining studies fail to show an effect. Effects have been most consistent with combined prenatal and direct postnatal supplementation of the infant and appear strain-specific, with Lactobacillus rhamnosus most often showing an effect. Prenatal-only and postnatal-only studies often fail to show effects. Recent long-time follow-ups have shown promising but not consistent results. A very recent follow-up of a large well conducted cohort shows that long-term effects of eczema prevention persists until age 4 and prevention of respiratory allergies might also be possible. SUMMARY: Prevention of eczema with probiotics seem to work until age 2 years and extended effects until 4 years have been shown in high-risk for allergy cohorts. Effects are strain-specific, with L. rhamnosus showing the most consistent effects especially when combining pre and postnatal administration. © 2013 Wolters Kluwer Health | Lippincott Williams and Wilkins.

The taxonomy of Elachista (Aphelosetid) catalana Parenti, 1978 and its relatives is revised. Elachista modesta Parenti, 1978 is considered a valid species, stat. rev. and Elachista zuembaueri Traugott-Olsen, 1990 is considered a synonym of E. catalana, syn. n. Elachista liskai sp. n. is described from Slovakia, and Elachista vulcana sp. n. from Morocco and Spain. © Entomologica Fennica.

Paavilainen P.,University of Helsinki
International Journal of Psychophysiology | Year: 2013

The mismatch-negativity (MMN) component of the event-related potential (ERP) has been extensively used to study the preattentive processing and storage of regularities in basic physical stimulus features (e.g., frequency, intensity, spatial location). However, studies reviewed in the present article reveal that the auditory analysis reflected by MMN also includes the detection and use of more complex, "abstract", regularities based, for example, on relationships between various physical features of the stimuli or in patterns present in the auditory stream. When these regularities are violated, then MMN is elicited. Thus, the central auditory system performs even at the pre-attentive, auditory-cortex level surprisingly "cognitive" operations, such as generalization leading to simple concept formation, rule extraction and prediction of future stimuli. The information extracted often seems to be in an implicit form, not directly available to conscious processes and difficult to express verbally. It can nevertheless influence the behavior of the subject, for example, the regularity violations can temporarily impair performance in the primary task. Neural, behavioral and cognitive events associated with the development of the regularity representations are discussed. © 2013 Elsevier B.V.

Kluger N.,University of Helsinki
International Journal of Dermatology | Year: 2015

The tattoo removal market has boomed over the years following the increased prevalence of tattooed individuals around the world. Surgery and laser are currently the gold standards for tattoo removal. However, both of them have drawbacks. Surgery is better suited for small tattoos in areas of adequate skin laxity but leave a scar, while laser removal is a long and painful procedure, with no guarantee of a complete efficacy. Both are expensive procedures, and not all individuals are ready to fund them privately. Consequently, some individuals are in the search of faster, easier, and cheaper procedures that can be performed either by themselves or by laypeople. The unregulated market of internet provides a favorable ground for many websites to offer various tattoo removal methods. Besides, some tattooists and other non-medical laypeople have started to get interested by such a growing market, especially as some laser devices manufactured in Asia are now available at competitive prices, and due to weaknesses in the EU legislation regarding the use of lasers for cosmetic procedures by non-medical laypeople. We review here different do-it-yourself and over-the-counter tattoo removal methods. We discuss the potential risks for tattooed individuals and stress the importance of a better regulation of such a market. © 2014 The International Society of Dermatology.

Niitepold K.,University of Helsinki
Journal of Experimental Biology | Year: 2010

Metabolic rate is a highly plastic trait. Here I examine factors that influence the metabolic rate of the Glanville fritillary butterfly (Melitaea cinxia) in pupae and resting and flying adults. Body mass and temperature had consistent positive effects on metabolic rate in pupae and resting adults but not in flying adults. There was also a consistent nonlinear effect of the time of the day, which was strongest in pupae and weakest in flying adults. Flight metabolic rate was strongly affected by an interaction between the phosphoglucose isomerase (Pgi) genotype and temperature. Over a broad range of measurement temperatures, heterozygous individuals at a single nucleotide polymorphism (SNP) in Pgi had higher peak metabolic rate in flight, but at high temperatures homozygous individuals performed better. The two genotypes did not differ in resting metabolic rate, suggesting that the heterozygotes do not pay an additional energetic cost for their higher flight capacity. Mass-independent resting and flight metabolic rates were at best weakly correlated at the individual level, and therefore, unlike in many vertebrates, resting metabolic rate does not serve as a useful surrogate of the metabolic capacity of this butterfly. © 2010. Published by The Company of Biologists Ltd.

Krautkramer E.,University of Heidelberg | Zeier M.,University of Heidelberg | Plyusnin A.,University of Helsinki
Kidney International | Year: 2013

The function of the kidney with its highly differentiated and specialized cell types is affected by infection with several viruses. Viral infections of the kidney have a negative impact not only on patients undergoing renal transplantation and immunosuppression. Besides the increasing number of patients suffering from HIV-associated nephropathy, another group of viruses infects immunocompetent patients and induces renal failure. Hantaviruses belong nowadays to the emerging zoonoses that increase in number and geographic distribution. The viruses are distributed worldwide in endemic areas and distribution seems to expand. Together with the increase in the number of cases in the last few years, the understanding of epidemiology and pathology has deepened and some concepts had to be changed. Symptoms and mortality vary between species. The classification refers to geographical distribution: New World hantaviruses causing hantavirus cardiopulmonary syndrome (HCPS) and Old World hantaviruses causing hemorrhagic fever with renal syndrome (HFRS). Indeed, in most HFRS cases, the kidney is mainly affected and HCPS is characterized by cardiopulmonary involvement. But the picture of strict organ tropism is changing and reports of pulmonary findings and nonrenal manifestations in infections with Old World hantaviruses are increasing. However, the overall symptoms - vascular alterations and leakage - that are responsible for organ failure are characteristic for all diseases caused by hantaviruses. © 2012 International Society of Nephrology.

Hiilamo H.,University of Helsinki | Glantz S.A.,University of California at San Francisco
Social Science and Medicine | Year: 2015

We investigates the effects of ratifying the WHO Framework Convention of Tobacco Control (FTCT), state capacity, path-dependency and tobacco industry activity on the implementation of effective health warning labels (HWL) on cigarette packs among low and middle income countries (LMIC). Using logistic regression in separate analyses for FCTC Article 11 compliant HWLs and graphic HWLs (GHWL), we found that the odds of FCTC compliance increased by a factor of 1.31 for each year after FCTC entered into force in the country (. p<0.01). The odds of passing GHWLs increased by a factor of 1.46 (. p<0.05) per year after FCTC entered into force. The weaker the capacity of the states were, the less likely they were to have implemented FCTC compliant HWLs (. p<0.05). The countries with voluntary HWLs in 1992 were less likely (OR=0.19, p<0.01) to comply with FCTC 21 years later (in 2013). The FCTC has promoted HWL policies among LMICs. Public health regulations require investments in broader state capacity. As the theory of path-dependency predicts voluntary agreements have long lasting influence on the direction of tobacco control in a country. Adopting voluntary HWL policies reduced likelihood of having FCTC compliant HWLs decades later. The fact that voluntary agreements delayed effective tobacco regulations suggests that policymakers must be careful of accepting industry efforts for voluntary agreements in other areas of public health as well, such as alcohol and junk food. © 2014 Elsevier Ltd.

Stevanovic M.,University of Helsinki
Journal of Pragmatics | Year: 2015

Joint planning consists of people making proposals for future actions and events, and others accepting or rejecting these proposals. While proposals convey their speakers' judgments of some ideas as feasible, however, in anticipation of and in an attempt to pre-empt the recipients' rejection of their proposals, the speakers may begin to express doubt with the feasibility of their proposals. It is such "post-proposal displays of uncertainty," and their interactional corollaries, that this paper focuses on. Drawing on video-recorded planning meetings as data, and conversation analysis as a method, I describe three ways for the recipients to respond to post-proposal displays of uncertainty: the recipients may (1) overcome, (2) confirm, or (3) dispel their co-participants' doubts. Even if the outcome of the proposal, in each case, is its abandonment, the analysis points out to important differences in how these response options treat the first speakers' "proximal deontic claims" - that is, their implicit assertions of rights to control the participants' local interactional agenda. The paper concludes by discussing the idea of proximal deontics with reference to other related notions. © 2014 Elsevier B.V.

Palviainen M.,University of Helsinki | Finer L.,Finnish Forest Research Institute
European Journal of Forest Research | Year: 2012

Whole-tree harvesting (WTH), where logging residues are removed in addition to stems, is widely practised in Fennoscandian boreal forests. WTH increases the export of nutrients from forest ecosystems. The extent of nutrient removals may depend on tree species, harvesting method, and the intensity of harvesting. We developed generalized nutrient equations for Scots pine (Pinus sylvestris L.), Norway spruce (Picea abies Karsten), and birch (Betula pendula Roth and Betula pubescens Ehrh.) stands to be able to calculate the amounts of nitrogen, phosphorus, potassium, and calcium in stems and above-ground biomass (stem and crown) as a function of stand volume. The equations were based on Fennoscandian literature data from 34 pine, 26 spruce, and 5 birch stands, and they explained, depending on the tree species and nutrient, 61-99% and 56-87% of the variation in the nutrient amounts of stems and above-ground biomass, respectively. The calculations based on the equations showed that nutrient removals caused by stem-only harvesting (SOH) and WTH per harvested stem m 3 were smaller in pine than in spruce and birch stands. If the same volume of stem is harvested, nutrient removals are, in general, nearly equal at thinnings and final cuttings in SOH, but larger in thinnings than final cuttings in WTH. If the principal aim is to minimize the nutrient removals per harvested stem m 3, the harvesting should be done at mature pine stands. The effect of biomass removal on overall site nutrient status depends on site-specific factors such as atmospheric deposition, weathering of minerals, and the size of the nutrient pools in the soil. © 2011 Springer-Verlag.

Fyhrquist F.,Minerva Institute for Medical Research | Saijonmaa O.,Minerva Institute for Medical Research | Strandberg T.,University of Helsinki
Nature Reviews Cardiology | Year: 2013

Cellular senescence, defined as arrest during the cell cycle (G 0), is involved in the complex process of the biological ageing of tissues, organs, and organisms. Senescence is driven by many factors including oxidative stress, the DNA damage and repair response, inflammation, mitogenic signals, and telomere shortening. Telomeres are shortened by each cell division until a critical length is reached and dysfunction ensues. DNA-repair pathways are then recruited and cells enter senescence, losing their capacity to proliferate. In addition to cell division, factors causing telomere shortening include DNA damage, inflammation, and oxidative stress. Both cardiovascular risk factors and common cardiovascular diseases, such as atherosclerosis, heart failure, and hypertension, are associated with short leucocyte telomeres, but causality remains undetermined. Telomere length does not satisfy strict criteria for being a biomarker of ageing, but adds predictive power to that of chronological age, and can be considered a marker of cardiovascular ageing. The 'senescence-associated secretory phenotype' of senescent cells exerts a wide range of autocrine and paracrine activities aimed at tissue repair, but which also fuel degenerative and proliferative alterations that contribute to cardiovascular disease. In this Review, the relationship between telomere shortening, senescence, and cardiovascular disease is discussed. © 2013 Macmillan Publishers Limited.

Guled M.,University of Helsinki
Duodecim; lääketieteellinen aikakauskirja | Year: 2013

MicroRNAs (miRNAs) are group of noncoding RNAs that have been shown to regulate posttranscriptional gene expression. They have been under intense investigation since their association with cancer a decade ago. Genome wide detection methods have been developed to identify miRNA profiles in variety of biological systems and to confirm their involvement in different physiological and pathological processes. MiRNA implication in cancer pathology (tumor development, progression and response to therapy), perhaps the most widely studied miRNA topic, make them potential diagnostic, prognostic and predictive biomarkers. Currently, researchers are exploiting the possibilities of miRNA-based anti-cancer therapies and in the near future such therapies alone or in combination with other treatment modalities might be a reality.

Mikko S.,University of Helsinki
Journal of Gastroenterology and Hepatology (Australia) | Year: 2012

Cancer prevention is based on the identification of specific etiologic factors. Acetaldehyde derived from the alcoholic beverage itself and formed from ethanol endogenously has recently been classified by the International Agency for Research on Cancer/World Health Organization as a group 1 carcinogen to humans. This is based on the uniform epidemiological and biochemical evidence derived from individuals carrying alcohol and aldehyde dehydrogenase gene mutations. After drinking alcohol, these mutations are associated with increased exposure of the upper digestive tract to acetaldehyde and as well with a remarkably increased risk for upper gastrointestinal (GI) tract cancers. Acetaldehyde is the key intermediate in alcoholic fermentation and ethanol oxidation. Therefore, it is widely present in our environment. Furthermore, it is the most abundant carcinogenic compound of tobacco smoke. Most of the known risk factors for upper digestive tract cancer appear to be associated with an enhanced exposure of GI mucosa to locally formed acetaldehyde. In these process microbes, salivary glands and even mucosal cells appear to play an essential role. Consequently, in the presence of ethanol mutagenic acetaldehyde concentrations are found in the saliva, achlorhydric stomach and colon. Equal acetaldehyde concentrations are seen in saliva also during active smoking. ALDH2-deficiency and high active ADH1C result in two- to threefold salivary acetaldehyde concentrations after a dose of alcohol and this prevails for as long as ethanol is present in the blood and saliva. Regarding cancer prevention, the good news is that acetaldehyde exposure can be markedly reduced. This can be achieved by giving high priority for regulatory measures and consumer guidance. © 2012 Journal of Gastroenterology and Hepatology Foundation and Blackwell Publishing Asia Pty Ltd.

Meretoja A.,University of Helsinki
Neurology | Year: 2012

Efficacy of thrombolytic therapy for ischemic stroke decreases with time elapsed from symptom onset. We analyzed the effect of interventions aimed to reduce treatment delays in our single-center observational series. All consecutive ischemic stroke patients treated with IV alteplase (tissue plasminogen activator [tPA]) were prospectively registered in the Helsinki Stroke Thrombolysis Registry. A series of interventions to reduce treatment delays were implemented over the years 1998 to 2011. In-hospital delays were analyzed as annual median door-to-needle time (DNT) in minutes, with interquartile range. A total of 1,860 patients were treated between June 1995 and June 2011, which included 174 patients with basilar artery occlusion (BAO) treated mostly beyond 4.5 hours from symptom onset. In the non-BAO patients, the DNT was reduced annually, from median 105 minutes (65-120) in 1998, to 60 minutes (48-80) in 2003, further on to 20 minutes (14-32) in 2011. In 2011, we treated with tPA 31% of ischemic stroke patients admitted to our hospital. Of these, 94% were treated within 60 minutes from arrival. Performing angiography or perfusion imaging doubled the in-hospital delays. Patients with in-hospital stroke or arriving very soon from symptom onset had longer delays because there was no time to prepare for their arrival. With multiple concurrent strategies it is possible to cut the median in-hospital delay to 20 minutes. The key is to do as little as possible after the patient has arrived at the emergency room and as much as possible before that, while the patient is being transported.

Hyvarinen A.,University of Helsinki | Smith S.M.,University of Oxford
Journal of Machine Learning Research | Year: 2013

We present new measures of the causal direction, or direction of effect, between two non-Gaussian random variables. They are based on the likelihood ratio under the linear non-Gaussian acyclic model (LiNGAM). We also develop simple first-order approximations of the likelihood ratio and analyze them based on related cumulant-based measures, which can be shown to find the correct causal directions. We show how to apply these measures to estimate LiNGAM for more than two variables, and even in the case of more variables than observations. We further extend the method to cyclic and nonlinear models. The proposed framework is statistically at least as good as existing ones in the cases of few data points or noisy data, and it is computationally and conceptually very simple. Results on simulated fMRI data indicate that the method may be useful in neuroimaging where the number of time points is typically cuite small. © 2013 Aapo Hyvarinen and Stephen M. Smith.

Virta L.J.,The Social Insurance Institution of Finland KELA | Kolho K.-L.,University of Helsinki
Journal of Crohn's and Colitis | Year: 2013

Background and aims: The association of celiac disease with inflammatory bowel disease (IBD) in children is unclear. This study assesses the risk of IBD in children diagnosed with celiac disease and three other chronic diseases, namely epilepsy, juvenile idiopathic arthritis (JIA) and type 1 diabetes using nationwide, comprehensive registers. Methods: We identified Finnish children born between 1994 and 2008 and diagnosed with IBD (n= 596) by October 2010 (aged up to 16. years) in a national register of medical reimbursements, which all these patients are entitled to. The presence of other chronic diseases, such as celiac disease, epilepsy, JIA and type 1 diabetes, diagnosed before the diagnosis of IBD was accordingly identified in patients and their population-based, individually matched controls (n= 2380). The data on chronic diseases are based on certificates including the diagnostic criteria. The risk of contracting IBD in children with a diagnosis of a chronic disease was analyzed using conditional logistic regression analysis. Results: Chronic diseases were more common in children contracting IBD than in their matched controls (frequency of chronic diseases 5.9% and 1.0%, respectively, p< 0.001). Celiac disease associated with later development of ulcerative colitis (p< 0.01) but the association with Crohn's disease was less clear (p< 0.05). For the other chronic diseases, association was seen only between epilepsy and ulcerative colitis (p< 0.01). Conclusion: Pediatric patients with celiac disease or epilepsy have an increased risk of developing IBD during their childhood but the risk is not high. This finding warrants a thorough investigation of intestinal symptoms in these children. © 2012 European Crohn's and Colitis Organisation.

Bufalo R.,University of Helsinki | Bufalo R.,Sao Paulo State University
Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy Physics | Year: 2015

In this work we discuss the properties of a modified Born-Infeld electrodynamics in the framework of very special relativity (VSR). This proposal allows us to study VSR mass effects in a gauge-invariant context of nonlinear electrodynamics. It is analyzed in detail the electrostatic solutions for two different cases, as well as the VSR dispersion relations are found to be of a massive particle with nonlinear modifications. Afterwards, the field energy and static potential are computed, in the latter we find from the VSR contribution a novel long-range 1/L3 correction to the Coulomb potential, in contrast to the 1/L5 correction of the usual Born-Infeld theory. © 2015 The Authors.

Laaksonen T.,University of Turku | Lehikoinen A.,University of Helsinki
Biological Conservation | Year: 2013

When many environmental changes take place simultaneously, one of the first challenges for conservation efforts is to identify the species and environments that are in the most need of conservation measures. We studied whether there are differences in the population growth trends of 94 boreal bird species according to their migration strategies, breeding distributions (northern or southern), or breeding habitats. To this end, we examined recent trends in bird census data covering >1000. km along a north-south transect in Finland, from the deciduous forests on the southern coast through the boreal taiga forest to the alpine fell area in the north. Our results show that long-distance migrants (species wintering in western or eastern Africa or Asia), northern species, and species living in agricultural environments are in decline in north-eastern Europe. The results were the same for both the long-term (27. years; 1986-2012) and the short-term (12. years, the most recent reporting period of the EU bird directive; 2001-2012) data set. Additionally, species breeding mainly in urban/sub-urban environments, coniferous forests, or wetlands showed negative growth trends, especially over the short-term. These results provide updated information that can be used to determine the targets of conservation efforts focused on Northern Palaearctic birds. Several different conservation measures may be needed to help these populations, ranging from protecting habitat in the migration and wintering grounds to changing climate and agricultural policies at a national and/or international level. In addition, further research is needed to identify the particular mechanisms underlying the population trends. © 2013 Elsevier Ltd.

Kluger N.,University of Helsinki
American Journal of Emergency Medicine | Year: 2012

Permanent decorative tattooing involves the introduction of exogenous pigments and/or dyes into the dermis to produce the permanent design. Despite improved hygiene in the tattoo parlors of Western countries, this procedure still carries risk. Various complications may occur right after tattooing, from benign complications such as transient limb edema, palpable lymph nodes, and contact eczema, to more severe ones such as the inoculation of virulent microorganisms into the dermis, potentially life-threatening cellulitis, and necrotizing fasciitis or cutaneous vasculitis. This review focuses specifically on the complications that occur within the first month of tattooing that emergency physicians may have to manage. © 2012 Elsevier Inc. All rights reserved.

Bjorkman T.,Aalto University | Gulans A.,Aalto University | Krasheninnikov A.V.,Aalto University | Krasheninnikov A.V.,University of Helsinki | Nieminen R.M.,Aalto University
Physical Review Letters | Year: 2012

Although the precise microscopic knowledge of van der Waals interactions is crucial for understanding bonding in weakly bonded layered compounds, very little quantitative information on the strength of interlayer interaction in these materials is available, either from experiments or simulations. Here, using many-body perturbation and advanced density-functional theory techniques, we calculate the interlayer binding and exfoliation energies for a large number of layered compounds and show that, independent of the electronic structure of the material, the energies for most systems are around 20meV/2. This universality explains the successful exfoliation of a wide class of layered materials to produce two-dimensional systems, and furthers our understanding the properties of layered compounds in general. © 2012 American Physical Society.

Tahvonen O.,University of Helsinki
Canadian Journal of Forest Research | Year: 2011

Optimal harvesting of Norway spruce (Picea abies (L.) Karst.) forests is studied applying an individual-tree model for uneven-aged management. Optimization is carried out by gradient-based, large-scale interior point methods. Assuming volume maximization and natural regeneration, it is optimal to apply uneven-aged management. Under artificial regeneration, the result is the reverse. Economically optimal solutions with a 20-year harvesting interval produce an annual sawn timber output of 4.4-2.4 m 3·ha -1 depending on thermal zone and interest rate. Before harvest basal area varies between 18 and 12 m 2·ha -1 and the diameter of harvested trees between 15 and 33 cm. In contrast with the classic inverted J-structure, optimal steady-state size structure resembles a serrate form. Profitability of even- and uneven-aged management is compared assuming that the initial stand state represents an optimal uneven-aged steady state. A switch to even-aged management is optimal given the most favorable growth conditions and interest rate below 1%-2%. In other cases, it is economically optimal to continue uneven-aged management although volume output remains lower than under even-aged management.

Nathan R.,Hebrew University of Jerusalem | Horvitz N.,Hebrew University of Jerusalem | He Y.,University of Victoria | Kuparinen A.,University of Helsinki | And 2 more authors.
Ecology Letters | Year: 2011

Despite ample research, understanding plant spread and predicting their ability to track projected climate changes remain a formidable challenge to be confronted. We modelled the spread of North American wind-dispersed trees in current and future (c. 2060) conditions, accounting for variation in 10 key dispersal, demographic and environmental factors affecting population spread. Predicted spread rates vary substantially among 12 study species, primarily due to inter-specific variation in maturation age, fecundity and seed terminal velocity. Future spread is predicted to be faster if atmospheric CO2 enrichment would increase fecundity and advance maturation, irrespective of the projected changes in mean surface windspeed. Yet, for only a few species, predicted wind-driven spread will match future climate changes, conditioned on seed abscission occurring only in strong winds and environmental conditions favouring high survival of the farthest-dispersed seeds. Because such conditions are unlikely, North American wind-dispersed trees are expected to lag behind the projected climate range shift. © 2011 Blackwell Publishing Ltd/CNRS.

Louhiala P.,University of Helsinki
Journal of Medical Ethics | Year: 2012

The aim of the present study was to explore the use and understanding of the concepts 'placebo' and 'placebo effect' in 12 empirical studies that have addressed the prescription of placebos by doctors in clinical practice. There were great differences in the general methodology and in the definitions (or lack of any definition) of the basic concepts in these 12 studies. Therefore, the results reflect different things. They tell us a little about the use of 'pure placebos', more about the use of 'impure placebos', but most of all, they tell us about the conceptual confusion in this area.

Venta I.,University of Helsinki
Journal of Oral and Maxillofacial Surgery | Year: 2012

The preventive removal of third molars (M3s) should be based on evidence. To optimize the timing of removal of M3s, it is essential to predict the eruption of the tooth and, even more importantly, to recognize beforehand which teeth will become involved in pathologic conditions later in life. The first aim of this review was to determine how well physicians currently can predict the eruption of an M3. The second aim was to review how frequently impacted M3s are removed. The third aim was to summarize the indications for preventive removals as presented in the evidence-based Current Care Guideline for the management of M3s in Finland. The prediction of eruption can be made at accuracies from 80% to 97%. In addition, the decrease in the number of M3s is very rapid, with only 31% remaining at 38 years of age. According to the Current Care Guideline, preventive removals at a young age are justified for 3 groups of teeth in the mandible: partially impacted teeth in the horizontal position, partially erupted teeth in the vertical position, and incomplete roots growing close to the mandibular canal. In conclusion, one fourth of retained and disease-free M3s need to be removed preventively at a young age, whereas the rest should be treated according to signs and symptoms.

Heikkinen R.K.,Finnish Environment Institute | Marmion M.,University of Oulu | Luoto M.,University of Helsinki
Ecography | Year: 2012

Model transferability (extrapolative accuracy) is one important feature in species distribution models, required in several ecological and conservation biological applications. This study uses 10 modelling techniques and nationwide data on both (1) species distribution of birds, butterflies, and plants and (2) climate and land cover in Finland to investigate whether good interpolative prediction accuracy for models comes at the expense of transferability - i.e. markedly worse performance in new areas. Models' interpolation and extrapolation performance was primarily assessed using AUC (the area under the curve of a receiver characteristic plot) and Kappa statistics, with supplementary comparisons examining model sensitivity and specificity values. Our AUC and Kappa results show that extrapolation to new areas is a greater challenge for all included modelling techniques than simple filling of gaps in a well-sampled area, but there are also differences among the techniques in the degree of transferability. Among the machine-learning modelling techniques, MAXENT, generalized boosting methods (GBM), and artificial neural networks (ANN) showed good transferability while the performance of GARP and random forest (RF) decreased notably in extrapolation. Among the regression-based methods, generalized additive models (GAM) and generalized linear models (GLM) showed good transferability. A desirable combination of good prediction accuracy and good transferability was evident for three modelling techniques: MAXENT, GBM, and GAM. However, examination of model sensitivity and specificity revealed that model types may differ in their tendencies to either increased over-prediction of presences or absences in extrapolation, and some of the methods show contrasting changes in sensitivity vs specificity (e.g. ANN and GARP). Among the three species groups, the best transferability was seen with birds, followed closely by butterflies, whereas reliable extrapolation for plant species distribution models appears to be a major challenge at least at this scale. Overall, detailed knowledge of the behaviour of different techniques in various study settings and with different species groups is of utmost importance in predictive modelling. © 2011 The Authors. Ecography © 2012 Nordic Society Oikos.

Smits L.P.,University of Amsterdam | Bouter K.E.C.,University of Amsterdam | De Vos W.M.,Wageningen University | De Vos W.M.,University of Helsinki | And 2 more authors.
Gastroenterology | Year: 2013

There has been growing interest in the use of fecal microbiota for the treatment of patients with chronic gastrointestinal infections and inflammatory bowel diseases. Lately, there has also been interest in its therapeutic potential for cardiometabolic, autoimmune, and other extraintestinal conditions that were not previously considered to be associated with the intestinal microbiota. Although it is not clear if changes in the microbiota cause these conditions, we review the most current and best methods for performing fecal microbiota transplantation and summarize clinical observations that have implicated the intestinal microbiota in various diseases. We also discuss case reports of fecal microbiota transplantations for different disorders, including Clostridium difficile infection, irritable bowel syndrome, inflammatory bowel diseases, insulin resistance, multiple sclerosis, and idiopathic thrombocytopenic purpura. There has been increasing focus on the interaction between the intestinal microbiome, obesity, and cardiometabolic diseases, and we explore these relationships and the potential roles of different microbial strains. We might someday be able to mine for intestinal bacterial strains that can be used in the diagnosis or treatment of these diseases. © 2013 by the AGA Institute.

As a taxonomist Harald Lindberg mainly worked on North European and Mediterranean vascular plants. He published about 420 valid names of new taxa and in addition numerous invalid names or nomina nuda. In the present catalogue all the new names except those published under the apomictic genera Hieracium and Taraxacum, or names of mosses, are listed. Most of the North European new taxa are based on material collected by himself or others in Finland or adjacent Russia, rarely from Estonia or Sweden. The Mediterranean taxa are mostly based on the collections by his own hand from Croatia, Cyprus, Italy, Morocco, Spain or Tunisia, rarely from Bosnia and Herzegovina, Egypt, Hungary, Montenegro or Tunisia. Lindberg had no concept of type specimens and therefore all his taxa needed lectotypification. Most of the lectotypifications are performed in the present catalogue. Lindberg's main collections are preserved in the Botanical Museum, Finnish Museum of Natural History, University of Helsinki, Finland (H). Numerous types are represented in the exsiccata series Plantae Finlandiae Exsiccatae (nos. 1-2081) that Lindberg edited and distributed to other herbaria in 42 fascicules. His Mediterranean types specimens are frequently duplicated in the herbaria of Kew (K), Lund (LD) and/or Montpellier (MPU). Many of the names provided by Lindberg were validated by other authors, especially by I. Hiitonen in his Suomen Kasvio (1933). Many of the new taxa by Lindberg describe forms and varieties that are nowadays rarely recognized even though they are usually not based on obvious environmental modifications. In total, Lindberg described 321 vascular plant names Hieracium (34 taxa) and Taraxacum excluded (65). With these genera the total number is 420. © 2012 Magnolia Press.

In this article, the effect of spray solvent on the analysis of selected lipids including fatty acids, fat-soluble vitamins, triacylglycerols, steroids, phospholipids, and sphingolipids has been studied by two different ambient mass spectrometry (MS) methods, desorption electrospray ionization-MS (DESI-MS) and desorption atmospheric pressure photoionization-MS (DAPPI-MS). The ionization of the lipids with DESI and DAPPI was strongly dependent on the spray solvent. In most cases, the lipids were detected as protonated or deprotonated molecules; however, other ions were also formed, such as adduct ions (in DESI), [M-H](+) ions (in DESI and DAPPI), radical ions (in DAPPI), and abundant oxidation products (in DESI and DAPPI). DAPPI provided efficient desorption and ionization for neutral and less polar as well as for ionic lipids but caused extensive fragmentation for larger and more labile compounds because of a thermal desorption process. DESI was more suitable for the analysis of the large and labile lipids, but the ionization efficiency for less polar lipids was poor. Both methods were successfully applied to the direct analysis of lipids from pharmaceutical and food products. Although DESI and DAPPI provide efficient analysis of lipids, the multiple and largely unpredictable ionization reactions may set challenges for routine lipid analysis with these methods. Copyright © 2012 John Wiley & Sons, Ltd.

Hynninen N.,University of Helsinki
Journal of Pragmatics | Year: 2011

This paper investigates the mechanisms of mediation in an English-medium university seminar course. Mediation refers to a form of speaking for another where a co-participant starts rephrasing another participant's turn that was addressed to a third party. The paper sets out to investigate mediation in multiparty interaction. It adopts a situated approach and combines analysis of university seminar course interaction with interview data. The findings suggest that mediation occurs frequently in the university course analysed and that the institutional practices of the course influence the practice of mediation: the course teachers take on the role of an intermediary. Mediation seems to have three main functions: (1) It facilitates understanding between participants. By providing alternative ways of expressing the same thing, intermediaries help participants to take part in the discussion. (2) Mediation organises discourse, and it is a way for the teachers to manage interaction. (3) It also has a socialising function in that it can include evaluation of students' contributions. Mediation is a means to engage participants who otherwise may not be able to participate in the interaction, and thus serves as a useful co-operation strategy. © 2010 Elsevier B.V.

Aakala T.,University of Helsinki
Silva Fennica | Year: 2011

Reference deadwood volumes from natural forests for forest management and restoration are often derived from one-time measurements or from repeated measurements over short time-scales. Such an approach often assumes an equilibrium state between tree mortality and decomposition, which is questionable in many boreal forest ecosystems due to the occurrence of allogenic disturbances. Using a simulation model based on empirical estimates of tree mortality, disturbance chronologies and models of wood decay class dynamics, this study aimed at characterizing variability in the volume and quality of deadwood for the past 200 years. The variability of deadwood volumes in old-growth forests, arising from differences in disturbance regimes and differing decay rates, was exemplified in two areas of Picea abiesdominated forests in northern Europe. The results imply that with stable deadwood input and slow decay rates the deadwood volume may be in an equilibrium state. On the contrary, if moderate-severity disturbances occur such a state seems improbable. Both study areas displayed continuity in deadwood availability, although temporary paucity in the early decay classes with shortest residence times was also observed. The results stress the importance of understanding the dynamic nature of deadwood in old-growth forests, instead of the traditional view of deadwood as a static ecosystem component.

Mattsson T.,Helsinki Institute of Physics | Mattsson T.,University of Helsinki
General Relativity and Gravitation | Year: 2010

Motivated by the observed cosmic matter distribution, we present the following conjecture: due to the formation of voids and opaque structures, the average matter density on the path of the light from the well-observed objects changes from ΩM ≃ 1 in the homogeneous early universe to ΩM ≃ 0 in the clumpy late universe, so that the average expansion rate increases along our line of sight from EdS expansion Ht ≃ 2/3 at high redshifts to free expansion Ht ≃ 1 at low redshifts. To calculate the modified observable distance-redshift relations, we introduce a generalized Dyer-Roeder method that allows for two crucial physical properties of the universe: inhomogeneities in the expansion rate and the growth of the nonlinear structures. By treating the transition redshift to the void-dominated era as a free parameter, we find a phenomenological fit to the observations from the CMB anisotropy, the position of the baryon oscillation peak, the magnitude-redshift relations of type Ia supernovae, the local Hubble flow and the nucleosynthesis, resulting in a concordant model of the universe with 90% dark matter, 10% baryons, no dark energy, 15 Gyr as the age of the universe and a natural value for the transition redshift z0 = 0.35. Unlike a large local void, the model respects the cosmological principle, further offering an explanation for the late onset of the perceived acceleration as a consequence of the forming nonlinear structures. Additional tests, such as quantitative predictions for angular deviations due to an anisotropic void distribution and a theoretical derivation of the model, can vindicate or falsify the interpretation that light propagation in voids is responsible for the perceived acceleration. © 2009 Springer Science+Business Media, LLC.

Tarkoma S.,University of Helsinki | Ailisto H.,VTT Technical Research Center of Finland
IEEE Communications Magazine | Year: 2013

Recent advances in radio, network, mobile, and cloud technologies have supported the development of the first generation Internet of Things (IoT) services and products. IoT promises to connect various physical and digital objects to the Internet and thus enable a plethora of new innovative applications that enhance society and quality of life [1-3]. IoT and ubiquitous computing [4] extend the current mobile computing revolution by reaching beyond the current four billion mobile phones, connecting the phones, sensors, and other devices with the Internet. The resulting communications network is exponentially larger and more complex than the current Internet with potentially trillions of identifiers and communicating endpoints. This IoT revolution creates both technological and societal challenges that need to be addressed. © 1979-2012 IEEE.

Kauppi L.,University of Helsinki
Current Biology | Year: 2014

The distribution and number of reciprocal DNA exchange events (crossovers) along meiotic chromosomes is tightly controlled. A recent report shows that unperturbed meiotic chromosome structure is important for this control, and that crossovers in turn modify chromosome structure locally. © 2014 Elsevier Ltd.

Tammisola J.,University of Helsinki
GM crops | Year: 2010

A triple challenge will confront world plant production in a few forthcoming decades: population increase, worsening of growth conditions and changeover from fossil-based to renewable energy and raw materials. The challenge cannot be met without utilizing the best modern biological techniques, genetic modification included. In the current era of rapid environmental changes, plant breeding should take even greater responsibility for food, feed, fiber and fuels than in the past. There are good prospects for remarkable improvements in yield level and energy efficiency of plant production, as is exemplified with the cases of modern crop and especially sugarcane improvement in consideration. For example, sugar content, biomass yield, pest and disease resistance, environmental safety and resource use efficiency of biofuel crop production can be essentially improved on the basis of new genetic know-how and taking advantage of the richness of genetic resources available in the Plant Kingdom. In particular, the natural reservoir of 10,000 wild grass species should be exploited in the purest way possible, by means of modern and precise GM methods. Consequently, our vital needs in biofuel crop production can be fulfilled without increasing crop production areas untenably at the expense of the remaining wilderness or compromising food security in the world.

Zhou X.,University of Geneva | Sundholm D.,University of Helsinki | Wesolowski T.A.,University of Geneva | Kaila V.R.I.,TU Munich
Journal of the American Chemical Society | Year: 2014

Retinal is the light-absorbing biochromophore responsible for the activation of vision pigments and light-driven ion pumps. Nature has evolved molecular tuning mechanisms that significantly shift the optical properties of the retinal pigments to enable their absorption of visible light. Using large-scale quantum chemical calculations at the density functional theory level combined with frozen density embedding theory, we show here how the protein environment of vision pigments tunes the absorption of retinal by electrostatically dominated interactions between the chromophore and the surrounding protein residues. The calculations accurately reproduce the experimental absorption maxima of rhodopsin and the red, green, and blue color pigments. We further identify key interactions responsible for the color-shifting effects by mutating the rhodopsin structure in silico, and we find that deprotonation of the retinyl is likely to be responsible for the blue-shifted absorption in the blue cone vision pigment. © 2014 American Chemical Society.

Natural populations experience environmental conditions that vary across space and over time. This variation is often correlated between localities depending on the geographical separation between them, and different species can respond to local environmental fluctuations similarly or differently, depending on their adaptation. How this emerging structure in environmental correlation (between-patches and between-species) affects spatial community dynamics is an open question. This paper aims at a general understanding of the interactions between the environmental correlation structure and population dynamics in spatial networks of local communities (metacommunities), by studying simple two-patch, two-species systems. Three different pairs of interspecific interactions are considered: competition, consumer-resource interaction, and host-parasitoid interaction. While the results paint a relatively complex picture of the effect of environmental correlation, the interaction between environmental forcing, dispersal, and local interactions can be understood via two mechanisms. While increasing between-patch environmental correlation couples immigration and local densities (destabilising effect), the coupling between local populations under increased between-species environmental correlation can either amplify or dampen population fluctuations, depending on the patterns in density dependence. This work provides a unifying framework for modelling stochastic metacommunities, and forms a foundation for a better understanding of population responses to environmental fluctuations in natural systems. © 2013 Lasse Ruokolainen.

Lehikoinen A.,University of Helsinki | Virkkala R.,Finnish Environment Institute
Global Change Biology | Year: 2016

There is increasing evidence that climate change shifts species distributions towards poles and mountain tops. However, most studies are based on presence-absence data, and either abundance or the observation effort has rarely been measured. In addition, hardly any studies have investigated the direction of shifts and factors affecting them. Here, we show using count data on a 1000 km south-north gradient in Finland, that between 1970-1989 and 2000-2012, 128 bird species shifted their densities, on average, 37 km towards the north north-east. The species-specific directions of the shifts in density were significantly explained by migration behaviour and habitat type. Although the temperatures have also moved on average towards the north north-east (186 km), the species-specific directions of the shifts in density and temperature did not correlate due to high variation in density shifts. Findings highlight that climate change is unlikely the only driver of the direction of species density shifts, but species-specific characteristics and human land-use practices are also influencing the direction. Furthermore, the alarming results show that former climatic conditions in the north-west corner of Finland have already moved out of the country. This highlights the need for an international approach in research and conservation actions to mitigate the impacts of climate change. © 2016 John Wiley & Sons Ltd.

Physical inactivity and overweight are major threats to public health. However, it is not well understood to what extent physical activity might counteract the harmful effects of overweight on functioning. Thus, we examined the joint associations of leisure-time physical activity and body mass index (BMI) with subsequent physical and mental functioning over a follow-up of five to seven years. The data were derived from the Helsinki Health Study, which is a cohort study among employees of the City of Helsinki, Finland. The baseline postal survey data were collected among 40-60-year-old employees in 2000-02 (n = 8960, response rate 67%), and the follow-up data in 2007 among all baseline survey respondents (n = 7332, response rate 83%). We divided the participants into six groups according to their amount of physical activity (inactive, moderately active and highly active) and their relative weight (normal weight and overweight). Highly active normal-weight participants were used as a reference group in all the analyses. Poor functioning was defined as the lowest quartile of the Short Form 36 (SF-36) health survey's physical and mental component summaries, with the follow-up cut-off point also applied at baseline. We used logistic regression analysis adjusted for age, gender, baseline functioning, smoking, alcohol use, marital status, socioeconomic position and working conditions. At baseline 48% of the participants were overweight and 11% were inactive. After adjustments inactivity was associated with poor physical functioning at follow-up both among the normal-weight (OR 1.51, 95% CI 1.09-2.10) and overweight (OR 2.02, 95% CI 1.56-2.63) groups. Being overweight regardless of activity level was associated with poor physical functioning. Poor physical functioning was practically equally common among the highly active overweight group and the inactive normal-weight group. After adjustments, for mental functioning, only inactivity among the overweight was associated with poor mental functioning (OR 1.39, 95% CI 1.08-1.80). Physical activity is likely to be beneficial for physical and mental functioning among both those with overweight and normal weight. However, maintaining normal weight is also important for good physical functioning. Therefore, efforts should be made to recommend people to engage in physical activity regardless of weight.

Kujala E.,University of Helsinki
Journal of clinical oncology : official journal of the American Society of Clinical Oncology | Year: 2013

To refine the anatomic classification and staging of ciliary body and choroidal melanomas in the TNM classification. Tumor largest basal diameter and thickness of 7,369 patients were analyzed based on registry data from five ocular oncology centers. T categories were derived empirically by dividing data into blocks representing 3- × 3-mm fractions. Blocks with similar survival were grouped together so that no T category comprised a large majority of tumors, and each was uniform in survival, using randomly drawn 60% building and 40% validation data sets. Presence of ciliary body involvement (CBI) and extraocular extension (EXE) was analyzed among 5,403 patients to define T subcategories. Stages were generated by iteratively combining subcategories with similar survival. Of the 7,369 tumors analyzed, 24% were classified as T1, 33% as T2, 31% as T3, and 12% as T4. Ten-year Kaplan-Meier survival estimates for the T categories were 89%, 77%, 58%, and 39%, respectively (P < .001). Survival of patients in four subcategories based on presence or absence of CBI and EXE differed significantly within each T category (P = .018 for T1; P < .001 for T2 to T4). EXE exceeding 5 mm in largest diameter carried a worse prognosis than smaller extensions (P < .001) and was assigned a separate subcategory. Ten-year Kaplan-Meier survival estimates for stages I, IIA to IIB, and IIIA to IIIC were 88%, 80%, 67%, 45%, 27%, 10%, respectively (P < .001). This evidence-based anatomic classification provides a basis for staging ciliary body and choroidal melanomas in the seventh edition of the Cancer Staging Manual of the American Joint Committee on Cancer.

Pinto M.F.,University of Helsinki
Social Studies of Science | Year: 2015

As scientific research moves increasingly to the private sector, the social organization of science undergoes important transformations. Focusing on the production of ignorance, agnotology has been a fruitful approach to understanding the social and epistemic consequences of the recent commercialization of scientific research. Despite their important contributions, scholars working on agnotology seem to hold implicit normative commitments that are in tension with their descriptive accounts of ignorance-constructive practices. The main aim of this article is to uncover these commitments and to expose the emerging tensions. Thus, this article begins an exploration into normative aspects of the studies of ignorance. In particular, it shows that agnotology still needs the support of a well-articulated normative approach capable of identifying and evaluating the epistemic and social concerns raised by the private funding and performance of science. © The Author(s) 2015

Antibody class-switch recombination and somatic hypermutation critically depend on the function of activation-induced cytidine deaminase (AID). Rare variants in its gene AICDA have been reported to cause autosomal recessive AID deficiency (autosomal recessive hyper-IgM syndrome type 2 (HIGM2)). Exome sequencing of a multicase Finnish family with an HIGM2 phenotype identified a rare, homozygous, variant (c.416T>C, p.(Met139Thr)) in the AICDA gene, found to be significantly enriched in the Finnish population compared with other populations of European origin (38.56-fold, P<0.001). The population history of Finland, characterized by a restricted number of founders, isolation and several population bottlenecks, has caused enrichment of certain rare disease-causing variants and losses of others, as part of a phenomenon called the Finnish Disease Heritage. Accordingly, rare founder mutations cause the majority of observed Finnish cases in these mostly autosomal recessive disorders that consequently are more frequent in Finland than elsewhere. Screening of all currently known Finnish patients with an HIGM2 phenotype showed them to be homozygous for p.(Met139Thr). All the Finnish p.(Met139Thr) carriers with available data on their geographic descent originated from the eastern and northeastern parts of Finland. They were observed to share more of their genome identity by descent (IBD) than Finns in general (P<0.001), and they all carried a 207.5-kb ancestral haplotype containing the variant. In conclusion, the identified p.(Met139Thr) variant is significantly enriched in Finns and explains all thus far found AID deficiencies in Finland.European Journal of Human Genetics advance online publication, 4 May 2016; doi:10.1038/ejhg.2016.37. © 2016 Macmillan Publishers Limited

Soininen J.,University of Helsinki
Oikos | Year: 2016

The spatial structure of communities has recently gained much attention in ecology. Spatial structure comprises an important element in communities, but the literature lacks a thorough investigation about possible among-organism or among-ecosystem differences in the degree of spatial structure. Here, I conducted a quantitative review to determine if the degree of spatial structure varied predictably between the major organism types and ecosystems. Spatial structure was quantified as the relative fraction of community variation explained purely by spatial variables (fraction S/E). I integrated data from 322 variation partition analyses both in a generalized linear model (GLM) and using a boosted regression tree method, and showed that a mean of 11.0% of the variation in community composition was explained purely by spatial variables. Across all taxa, a body size-S/E relationship was positive. In GLM, fraction S/E increased highly significantly with study extent, it was highest among terrestrial taxa and higher in ectotherms than in homoiotherms. Spatial structure was also higher in omnivores than in autotrophs. These results suggest that the degree of spatial structure is jointly driven by extrinsic factors such as study extent and ecosystem type, and intrinsic factors such as body size, thermoregulation and interactions between body size and dispersal mode. These results should be important not only for basic research, but also conservation and bioassessment programs would benefit from the information about the magnitude of spatial variation in nature. Synthesis Spatial processes comprise an important element in most ecological communities, but the degree to which spatial structure varies across organisms or ecosystems is poorly known. Here, a quantitative review of 322 variation partition analyses indicated that spatial component varied predictably across ecological communities - it was driven by study extent and ecosystem type as well as by species traits such as body size and thermoregulation. These results give deep insights into the magnitude of spatial variation in nature and should be highly beneficial for conservation and bioassessment programs that are built on the information about how communities vary in space. © 2016 Nordic Society Oikos.

Kluger N.,University of Helsinki
Current Problems in Dermatology (Switzerland) | Year: 2015

In 1974, the first professional French tattooist C. Bruno wrote a book, entitled 'Tatoués, qui êtes-vous?', depicting his experience as a tattooist in the picturesque Pigalle tourist district of Paris. However, we have come a long way since then. Tattooing has gained tremendous visibility, notoriety and popularity in Western countries. In Germany, 8.5% of the population (aged between 14 and 90 years) has a tattoo. Similar trends have been found in France, Finland and Australia, where approximately 10% of the populations have at least one tattoo. However, the overall tattoo prevalences overseas and in Europe are even higher, especially among the youth, for whom it is up to 15-25% according to the country. Much has been written about the tattooed and tattooists. However, who are they currently? What motivates them to get tattooed and give tattoos? How do they see themselves? Why do some individuals remove their tattoos? Is there a 'profile' of the tattooed? Are they really 'risk takers'? And how do the nontattooed perceive them? Through a critical review of the literature, we will reconsider tattooing from an epidemiological aspect, challenge current beliefs and explore new insights into the motivations and fears of tattoo artists and their clients. © 2015 S. Karger AG, Basel.

Svedholm-Hakkinen A.M.,University of Helsinki
Acta Psychologica | Year: 2015

The processes underlying individual differences in reasoning performance are not entirely understood. What do people who do well on reasoning tasks where beliefs and logic conflict do differently from other people? Because abundant evidence shows that even poorer reasoners detect these conflicts, it has been suggested that individual differences in reasoning performance arise from inhibition failures later in the reasoning process. The present paper argues that a minority of highly skilled reasoners may deviate from this general reasoning process from an early stage. Two studies investigated signs of belief inhibition using a lexical access paradigm (Study 1) and a negative priming paradigm (Study 2). Study 1 showed that while other people exhibited signs of belief inhibition following a belief-logic conflict, people with the highest disposition for cognitive reflection did not. In Study 2, this finding was replicated and similar results were also obtained when comparing groups with higher and lower general cognitive ability. Two possible explanations are discussed.The reasoners with a highly reflective cognitive style or high general cognitive ability may have engaged and inhibited belief processing but if so, they may have been exceptionally efficient at recovering from it, wherefore no belief inhibition effects were found. An alternative account is that these reasoners started Type 2 processing directly, without first engaging in and then inhibiting belief-based processing. Under either explanation, the results indicate that individual differences in reasoning may partly arise from differences that occur early in the reasoning process. © 2014 Elsevier B.V.

Lappi O.,University of Helsinki
Journal of Vision | Year: 2014

Studying human behavior in the natural context of everyday visual tasks-including locomotor tasks such as driving-can reveal visual strategies or even suggest underlying visual mechanisms. This paper reviews empirical and theoretical work in the past 20 years (1994-2014) on the visual control of steering a vehicle along a winding path-one of the most comprehensively studied forms of visually guided locomotion in humans. The focus is on on-road studies of visual behavior and what they can reveal about the visual strategies in curve driving. Theoretical models and results from simulator studies are discussed where they have direct relevance to the interpretation of on-road data. For the past 20 years, the point of departure in studies of curve driving has been tangent point orientation, and tangent point models (models based on tracking the tangent point) have become established as the default account of how vision is used in curve negotiation. More recent studies have questioned the generality of the tangent point hypothesis, however, arguing that in addition to (or instead of) the tangent point, drivers target visual reference points on their future path. Ecological validity of real-world studies often comes at the cost of methodological challenges that make the data difficult to interpret in terms of underlying mechanisms, and the limitations of existing data and the complementary roles of real-world and laboratory studies are discussed. © 2014 ARVO.

Priklopil T.,University of Helsinki
Theoretical Population Biology | Year: 2012

I study the dynamics of allele frequencies in sexually reproducing populations where the choosy sex has a preference for condition-dependent displays of the opposite sex. The condition of an individual is assumed to be shaped by frequency-dependent selection. For sufficiently strong preferences the dynamics becomes increasingly complex, and periodic orbits and chaos are observed. Moreover, multiple attractors can exist simultaneously. The results hold also when the choosy sex is allowed to maintain a moderate level of assortative mating. Complex dynamics, a well studied phenomenon in a purely ecological setting, has been rarely observed in ecologically motivated population genetic models. © 2012 Elsevier Inc.

Priklopil T.,University of Helsinki
Journal of Mathematical Biology | Year: 2012

In this paper we present, in terms of invasion fitness functions, a sufficient condition for a coexistence of two strategies which are not protected from extinction when rare. In addition, we connect the result to the local characterization of singular strategies in the theory of adaptive dynamics. We conclude with some illustrative examples. © 2011 Springer-Verlag.

Mattila A.L.K.,University of Helsinki
Ecology and Evolution | Year: 2015

Knowledge of the effects of thermal conditions on animal movement and dispersal is necessary for a mechanistic understanding of the consequences of climate change and habitat fragmentation. In particular, the flight of ectothermic insects such as small butterflies is greatly influenced by ambient temperature. Here, variation in body temperature during flight is investigated in an ecological model species, the Glanville fritillary butterfly (Melitaea cinxia). Attention is paid on the effects of flight metabolism, genotypes at candidate loci, and environmental conditions. Measurements were made under a natural range of conditions using infrared thermal imaging. Heating of flight muscles by flight metabolism has been presumed to be negligible in small butterflies. However, the results demonstrate that Glanville fritillary males with high flight metabolic rate maintain elevated body temperature better during flight than males with a low rate of flight metabolism. This effect is likely to have a significant influence on the dispersal performance and fitness of butterflies and demonstrates the possible importance of intraspecific physiological variation on dispersal in other similar ectothermic insects. The results also suggest that individuals having an advantage in low ambient temperatures can be susceptible to overheating at high temperatures. Further, tolerance of high temperatures may be important for flight performance, as indicated by an association of heat-shock protein (Hsp70) genotype with flight metabolic rate and body temperature at takeoff. The dynamics of body temperature at flight and factors affecting it also differed significantly between female and male butterflies, indicating that thermal dynamics are governed by different mechanisms in the two sexes. This study contributes to knowledge about factors affecting intraspecific variation in dispersal-related thermal performance in butterflies and other insects. Such information is needed for predictive models of the evolution of dispersal in the face of habitat fragmentation and climate change. © 2015 Published by John Wiley & Sons Ltd.

Meurman J.H.,University of Helsinki
Oral Oncology | Year: 2010

In addition to the classic risk factors of oral cancer, namely alcohol and tobacco, other factors both infectious and environmental are thought to be associated with the development of oral malignancy. Infections in the oral cavity may be an important preventable cause of cancer. Poor oral hygiene, periodontal disease, chronic candidiasis, human papilloma virus (HPV) and herpesvirus infections link statistically with cancer but the mechanisms involved are largely unknown. Infections may trigger cell proliferation, inhibit apoptosis, interfere with cellular signaling mechanisms and up-regulate tumor promoters. In addition, several oral micro-organisms metabolize alcohol to carcinogenic acetaldehyde thus explaining the association between poor oral hygiene, alcohol consumption and carcinogenesis. With regards to dietary factors the Mediterranean-type fruit and vegetable rich diet has been shown to reduce the risk of oral cancer but the evidence is weak, the effect of individual food components and trace elements on carcinogenesis remains unclear at present. © 2010 Elsevier Ltd. All rights reserved.

Dashti R.,University of Helsinki
Acta neurochirurgica. Supplement | Year: 2011

Microscope integrated indocyanine green video-angiography (ICG-VA) is a new technique for intraoperative assessment of blood flow that has been recently applied to the field of Neurosurgery. ICG-VA is known as a simple and practical method of blood flow assessment with acceptable reliability. Real time information obtained under magnification of operating microscope has many potential applications in the microneurosurgical management of vascular lesions. This review is based on institutional experience with use of ICG-VA during surgery of intracranial aneurysms, AVMs and other vascular lesions at the Department of Neurosurgery at Helsinki University Central Hospital.

Hemila H.,University of Helsinki
Cochrane database of systematic reviews (Online) | Year: 2013

Vitamin C (ascorbic acid) for preventing and treating the common cold has been a subject of controversy for 70 years. To find out whether vitamin C reduces the incidence, the duration or severity of the common cold when used either as a continuous regular supplementation every day or as a therapy at the onset of cold symptoms. We searched CENTRAL 2012, Issue 11, MEDLINE (1966 to November week 3, 2012), EMBASE (1990 to November 2012), CINAHL (January 2010 to November 2012), LILACS (January 2010 to November 2012) and Web of Science (January 2010 to November 2012). We also searched the U.S. National Institutes of Health trials register and WHO ICTRP on 29 November 2012. We excluded trials which used less than 0.2 g per day of vitamin C and trials without a placebo comparison. We restricted our review to placebo-controlled trials. Two review authors independently extracted data. We assessed 'incidence' of colds during regular supplementation as the proportion of participants experiencing one or more colds during the study period. 'Duration' was the mean number of days of illness of cold episodes. Twenty-nine trial comparisons involving 11,306 participants contributed to the meta-analysis on the risk ratio (RR) of developing a cold whilst taking vitamin C regularly over the study period. In the general community trials involving 10,708 participants, the pooled RR was 0.97 (95% confidence interval (CI) 0.94 to 1.00). Five trials involving a total of 598 marathon runners, skiers and soldiers on subarctic exercises yielded a pooled RR of 0.48 (95% CI 0.35 to 0.64).Thirty-one comparisons examined the effect of regular vitamin C on common cold duration (9745 episodes). In adults the duration of colds was reduced by 8% (3% to 12%) and in children by 14% (7% to 21%). In children, 1 to 2 g/day vitamin C shortened colds by 18%. The severity of colds was also reduced by regular vitamin C administration.Seven comparisons examined the effect of therapeutic vitamin C (3249 episodes). No consistent effect of vitamin C was seen on the duration or severity of colds in the therapeutic trials.The majority of included trials were randomised, double-blind trials. The exclusion of trials that were either not randomised or not double-blind had no effect on the conclusions. The failure of vitamin C supplementation to reduce the incidence of colds in the general population indicates that routine vitamin C supplementation is not justified, yet vitamin C may be useful for people exposed to brief periods of severe physical exercise. Regular supplementation trials have shown that vitamin C reduces the duration of colds, but this was not replicated in the few therapeutic trials that have been carried out. Nevertheless, given the consistent effect of vitamin C on the duration and severity of colds in the regular supplementation studies, and the low cost and safety, it may be worthwhile for common cold patients to test on an individual basis whether therapeutic vitamin C is beneficial for them. Further therapeutic RCTs are warranted.

Pyykko P.,University of Helsinki
Physical Chemistry Chemical Physics | Year: 2011

Extended Average Level (EAL) Dirac-Fock calculations on atoms and ions agree with earlier work in that a rough shell-filling order for the elements 119-172 is 8s < 5g ≤ 8p1/2 < 6f < 7d < 9s < 9p 1/2 < 8p3/2. The present Periodic Table develops further that of Fricke, Greiner and Waber [Theor. Chim. Acta 1971, 21, 235] by formally assigning the elements 121-164 to (nlj) slots on the basis of the electron configurations of their ions. Simple estimates are made for likely maximum oxidation states, i, of these elements M in their MXi compounds, such as I = 6 for UF6. Particularly high I are predicted for the 6f elements. © the Owner Societies 2011.

Hamalainen R.H.,University of Helsinki
Methods in Enzymology | Year: 2014

Mitochondrial disease due to mutations in the mitochondrial DNA (mtDNA) is a common cause of human inherited disorders. Targeted modification of the mitochondrial genome has not succeeded with the current transgenic technologies. Furthermore, readily available cultured patient cells often do not manifest the disease phenotype. Therefore, pathogenic mechanisms underlying these disorders remain largely unknown, as the lack of model systems has hampered mechanistic studies. Stem cell technology has opened up new ways to use patient cells in research, through generation of induced pluripotent stem cells (iPSCs) and differentiation of these to disease-relevant cell types, including, for example, human neurons and cardiomyocytes. Here, we discuss the use of iPSC-derived models for disorders with mtDNA mutations. © 2014 Elsevier Inc.

Yki-Jarvinen H.,University of Helsinki
Current Opinion in Clinical Nutrition and Metabolic Care | Year: 2010

Purpose of review: Concomitant with the obesity epidemic, a fatty liver due to nonalcoholic causes has become the most common liver disorder. Nonalcoholic fatty liver disease (NAFLD) covers a range from benign steatosis to nonalcoholic steatohepatitis (NASH), which in turn may progress to cirrhosis. NAFLD predicts, independent of obesity, the metabolic syndrome and type 2 diabetes and can progress to cirrhosis. This review focuses on studies in humans addressing effects of dietary changes in NAFLD. Recent findings: Cross-sectionally, increased intake of fructose and simple sugars characterizes patients with NAFLD compared with weight-matched controls. Increased fructose intake is also associated with hepatic insulin resistance and fibrosis severity in NASH. Intake of saturated fat may also be increased in NAFLD. Dietary intervention studies have shown that liver volume and fat content changes significantly within a few days in response to caloric restriction or excess despite no or small changes in body weight. Weight loss by bariatric surgery decreases liver fat and inflammation but effects on fibrosis are uncertain. Hepatic insulin sensitivity generally changes in parallel with changes in liver fat content in NAFLD. Human data are limited regarding effects of isocaloric changes in diet composition on liver fat content. Summary: Maintenance of normal body weight and avoidance of intake of excess lipogenic simple sugars would seem beneficial for prevention of NAFLD and its metabolic consequences. © 2010 Wolters Kluwer Health. Lippincott Williams & Wilkins.

Rikkinen J.,University of Helsinki
Biodiversity and Conservation | Year: 2015

Cyanolichens are obligate symbioses between fungi and cyanobacteria. In these associations the cyanobacterial symbiont can either be the sole photosynthetic partner or a secondary symbiont in addition to a primary green algal photobiont. Lichen-symbiotic cyanobacteria can provide both photosynthate and fixed nitrogen to their symbiotic partners and the relative importance of these functions varies in different types of cyanolichens. Cyanolichens occur in many types of terrestrial environments ranging from arctic tundra and semi-deserts to tropical montane rainforests. As symbiotic cyanobacteria are able to fix atmospheric nitrogen, cyanolichens contribute significant amounts of nitrogen to some ecosystems. Many of them have been adversely affected by habitat loss and other human induced environmental changes and some species are used as biological indicators of air quality and/or habitat continuity. © 2015, Springer Science+Business Media Dordrecht.

Lamberg-Allardt C.,University of Helsinki
Scandinavian Journal of Clinical and Laboratory Investigation | Year: 2012

Vitamin D is essential for bone growth and development in children and adolescents. Vitamin D deficiency leads to rickets, characterized by defective bone formation, in infants and children. Vitamin D prophylaxis during the first years of life has empirically shown to be effective in combating rickets in infants in some countries. Vitamin D insufficiency can have negative effects on bone health in older children and in adolescents. Vitamin D supplementation has been shown to have an effect on bone mineral density at least in vitamin D deprived older children and adolescents but not in those with a normal vitamin D status. A good vitamin D status during pregnancy seems to be important for bone health in the off-spring later in life, but randomized controlled studies are needed to establish an effect of vitamin D during pregnancy on bone and other health outcomes in the offspring. Vitamin D supplementation during childhood may offer protection against diabetes type 1, but randomized controlled trials are needed to ascertain causality. © 2012 Informa Healthcare.

Rudels B.,University of Helsinki | Rudels B.,Finnish Meteorological Institute
Tellus, Series A: Dynamic Meteorology and Oceanography | Year: 2010

Extensive changes have been reported from the Arctic Mediterranean. The ice cover is retreating, the temperature in the Atlantic layer has been increasing, the salinity in the upper layers shows large variations and deep waters in the Greenland Sea have become warmer and more saline. These changes all appear externally forced; by the radiation balance, by the atmosphere, and by ocean advection. The question arises-are there processes inherent to the Arctic Ocean, which can constrain changes induced by external forcing? Three features are examined; the storage and export of liquid freshwater in the upper layers, the heat loss of the Atlantic water encountering sea ice and the possibility to define a salinity separating the two roles of the Arctic Mediterranean, as estuary and as concentration basin. If the freshwater outflow in the upper layer is rotationally controlled, the liquid freshwater storage and export only depend upon the freshwater input. The melting rate of sea ice is affected both by the heat transport and by the temperature of the inflowing Atlantic water. A salinity separating the estuarine and the deep-water circulation is proposed depending upon the salinity and the temperature of the Atlantic water as it encounters sea ice. © 2009 The Author Journal compilation © 2010 Blackwell Munksgaard.

Kulmala M.,University of Helsinki
Atmospheric Research | Year: 2010

Dynamical behavior of atmospheric molecular clusters was investigated. A model was developed to describe the evolution, concentration and sources of atmospheric clusters. The model includes sources of monomers, monomer - i-mer collisions and evaporation of i-mers. The developed model is agile and flexible. The evaporation rate is shown to be most important parameter describing the growth of clusters. The existence of dimers, trimers and bigger i-mers depends mainly on evaporation rate. In practice, the evaporation rate should be smaller than 1s -1 for atmospheric nucleation to occur. © 2010 Elsevier B.V.

Castren M.,University of Helsinki
Results and Problems in Cell Differentiation | Year: 2012

Neural stem/progenitor cell (NPC) cultures are a tool to study the differentiation of neuronal cells and can be used to model disease conditions in studies investigating the pathological mechanisms affecting the development and cellular plasticity of the central nervous system. There is evidence that abnormalities of NPCs and their differentiation contribute to the pathophysiology of fragile X syndrome. The results obtained with NPC cultures derived from human and mouse brain tissue with the fragile X mutation are in line with the abnormalities of Fmr1-knockout mouse brain in vivo indicating that NPC cultures can be useful as a model for fragile X syndrome. © 2012 Springer-Verlag Berlin Heidelberg.

A considerable body of literature exists on the use of subject pronouns in Spanish. However, the influence of semantic and pragmatic factors on subject pronoun usage has not been examined thoroughly enough. This paper deals with the frequency and patterns of usage of first and second person singular subject pronouns with 14 different verbs in a corpus of spoken Peninsular Spanish. It is argued that the differences attested in subject pronoun usage between the verbs can be explained by the focusing of attention on the clausal participants of the verbs involved (i.e., connected to the semantic role of the subject and the level of transitivity of the clause) and by the discourse functions of the verb forms in question. In addition, some frequently used first person singular verb forms can be analyzed as formulaic sequences which are used to express the speaker's subjective or epistemic stance. © 2010 Elsevier B.V.

Venalainen S.H.,University of Helsinki
Science of the Total Environment | Year: 2011

This study investigated the use of tailings from apatite ore beneficiation in the remediation of a heavily contaminated shooting range soil. The tailings originating in Siilinjärvi carbonatite complex, Finland, consist of apatite residues accompanied by phlogopite and calcite. In a pot experiment, organic top layer of a boreal forest soil predisposed to pellet-derived lead (Pb) was amended with tailings of various particle-sizes (Ø > 0.2 mm, Ø < 0.2 mm and unsieved material) differing in their mineralogical composition. After 9-, 10-, 14- and 21-month incubation, the samples were monitored for tailings-induced changes in the different Pb pools by means of sequential fractionation. Following the incubation, the samples were extracted with water and the extracts were analyzed for Pb species distribution by means of a cation exchange resin. The results revealed that Pb was continuously released from the shotgun pellet fragments due to weathering. However, the apatite and calcite compartments in the tailings counteracted the mobility of the released Pb through the formation of sparingly soluble fluorpyromorphite and cerussite. Furthermore, the tailings efficiently reduced the bioavailability of Pb by transferring it from the water-soluble and exchangeable pools into the organic one. The material also increased the proportion of the less toxic non-cationic Pb to the total dissolved Pb from the initial level of 5% to 9-12%. The results suggest that the tailings-induced stabilization of Pb may be an environmentally sound remediation technique at polluted sites. © 2011 Elsevier B.V.

Hukkinen J.I.,University of Helsinki
Environmental Values | Year: 2016

Nudging refers to the subtle design of the context of choice in a way that mobilises the unconscious mind and alters human behaviour predictably. Nudging has been criticised for entailing numerous practical and ethical problems, including manipulation, elitism and cultural insensitivity. To respond to the problems, participatory and deliberative procedures have been proposed that would enable the questioning of the power relations embedded in behavioural governance. Yet participation and deliberation are themselves characterised by unconscious behavioural influences. I argue that awareness of the prevalence of unconscious behavioural influences in environmental governance is a prerequisite for tackling the complex practical and ethical issues of nudging. I show that unconscious behavioural influences permeate environmental governance and outline analytical approaches for revealing them. © 2016 The White Horse Press.

Valentine H.T.,U.S. Department of Agriculture | Makela A.,University of Helsinki
New Phytologist | Year: 2012

• We formulate a dynamic evolutionary optimization problem to predict the optimal pattern by which carbon (C) and nitrogen (N) are co-allocated to fine-root, leaf, and wood production, with the objective of maximizing height growth rate, year by year, in an even-aged stand. • Height growth is maximized with respect to two adaptive traits, leaf N concentration and the ratio of fine-root mass to sapwood cross-sectional area. Constraints on the optimization include pipe-model structure, the C cost of N acquisition, and agreement between the C and N balances. The latter is determined by two models of height growth rate, one derived from the C balance and the other from the N balance; agreement is defined by identical growth rates. • Predicted time-courses of maximized height growth rate accord with general observations. Across an N gradient, higher N availability leads to greater N utilization and net primary productivity, larger trees, and greater stocks of leaf and live wood biomass, with declining gains as a result of saturation effects at high N availability. Fine-root biomass is greatest at intermediate N availability. • Predicted leaf and fine-root stocks agree with data from coniferous stands across Finland. Optimal C-allocation patterns agree with published observations and model analyses. © 2012 New Phytologist Trust.

Savijarvi H.,University of Helsinki
Icarus | Year: 2012

The daytime convective boundary layer (CBL) of Mars and the transition to it after the cold night is studied on a warm dusty sol at the rover Spirit using temperature profiles from the miniature thermal emission spectrometer (mini-TES) and a 1-D model. The model's net solar fluxes are linear in z in the CBL while the thermal fluxes decay logarithmically from about 8m upward, due mainly to the emissivity properties and density of CO 2. The induced strong radiative heating of the lower CBL is so well compensated by turbulent cooling (with an elevated maximum in the sensible heat flux H) that the growth of the CBL is uniform by the model, as observed by the mini-TES. Hence the net energy fluxes are linear and the shape of H in the lower CBL can be obtained as a residual. Moisture evolution is also considered although without validation. © 2012 Elsevier Inc.

Wheat C.W.,University of Helsinki | Wheat C.W.,University of Stockholm | Wahlberg N.,University of Turku
Systematic Biology | Year: 2013

The timing of the origin of arthropods in relation to the Cambrian explosion is still controversial, as are the timing of other arthropod macroevolutionary events such as the colonization of land and the evolution of flight. Here we assess the power of a phylogenomic approach to shed light on these major events in the evolutionary history of life on earth. Analyzing a large phylogenomic dataset (122 taxa, 62 genes) with a Bayesian-relaxed molecular clock, we simultaneously reconstructed the phylogenetic relationships and the absolute times of divergences among the arthropods. Simulations were used to test whether our analysis could distinguish between alternative Cambrian explosion scenarios with increasing levels of autocorrelated rate variation. Our analyses support previous phylogenomic hypotheses and simulations indicate a Precambrian origin of the arthropods. Our results provide insights into the 3 independent colonizations of land by arthropods and suggest that evolution of insect wings happened much earlier than the fossil record indicates, with flight evolving during a period of increasing oxygen levels and impressively large forests. These and other findings provide a foundation for macroevolutionary and comparative genomic study of Arthropoda. © 2012 The Author(s).

Perola M.,University of Helsinki
Hormone Research in Paediatrics | Year: 2011

Over the past 2 to 3 years, linkage disequilibrium mapping methods, or genome-wide association studies (GWAS), have made a seminal turn in the molecular genetic studies of complex human traits such as height, i.e., stature. Human stature is a highly heritable trait across populations and the phenotype for stature is easily measured and related to many other traits; therefore, it is available in most studies evaluating any phenotype. For this reason, it has become a beacon for large consortium genetic studies, during both the pre-GWAS and GWAS eras. Tens of thousands of genome-scanned individuals have been analysed together against their genome. Several loci have been implicated in association with stature (54 of these have been published), and most chromosomes have a locus linked to the trait in family studies. However, the prediction power of loci indentified by molecular genetic methods still remains inferior to clinical assessment of offspring stature using midparental height as a guide. Although the genomic methods provide important insights into heritability of stature, it will be a major challenge for molecular genetic studies to provide information that surpasses that of midparental height. Copyright © 2011 S. Karger AG, Basel.

Makitie O.,University of Helsinki
Endocrine Development | Year: 2011

Almost 400 different forms of skeletal dysplasias have been described, each with characteristic clinical and radiographic features. The underlying genetic and molecular pathology is known in several forms. Correct diagnosis is important for genetic counseling, treatment decisions, follow-up and for predicting long-term outcome. With advances in molecular genetics it has become evident that variable phenotypes can be caused by mutations in one gene, depending on the mutation type and location within the gene. On the other hand, mutations in different genes can result in similar phenotypes. Careful clinical assessment with thorough radiographic evaluation are of key importance. Copyright © 2011 S. Karger AG, Basel.

Kluger N.,University of Helsinki
Current Problems in Dermatology (Switzerland) | Year: 2015

Tattooing is getting increasingly popular among the young. However, not everyone is suited to getting tattooed. Indeed, it is not rare for patients with a chronic skin disease or another systemic condition to be eager to get a tattoo. They perceive tattooing as a harmless, risk-free procedure. Therefore, some patients may not seek medical advice before the procedure. Some also fear a judgmental approach by their physician, who may try to discourage them. Lastly, the tattooist does not have either the training or the education to properly advise a customer about his/her condition. Therefore, it is important that any physician be able to provide adequate counselling regarding the possibility of getting tattooed and under which conditions. Even though an exhaustive list is impossible to address, the main issues include chronic skin disorders, pigmented lesions of the skin, (congenital) heart disease, immunosuppressive diseases and treatments, blood clotting disorders, and pregnancy/breastfeeding. © 2015 S. Karger AG, Basel.

Zhao H.,University of Helsinki
Biophysical journal | Year: 2010

Actin-depolymerizing-factor (ADF)/cofilins have emerged as key regulators of cytoskeletal dynamics in cell motility, morphogenesis, endocytosis, and cytokinesis. The activities of ADF/cofilins are regulated by membrane phospholipid PI(4,5)P(2) in vitro and in cells, but the mechanism of the ADF/cofilin-PI(4,5)P(2) interaction has remained controversial. Recent studies suggested that ADF/cofilins interact with PI(4,5)P(2) through a specific binding pocket, and that this interaction is dependent on pH. Here, we combined systematic mutagenesis with biochemical and spectroscopic methods to elucidate the phosphoinositide-binding mechanism of ADF/cofilins. Our analysis revealed that cofilin does not harbor a specific PI(4,5)P(2)-binding pocket, but instead interacts with PI(4,5)P(2) through a large, positively charged surface of the molecule. Cofilin interacts simultaneously with multiple PI(4,5)P(2) headgroups in a cooperative manner. Consequently, interactions of cofilin with membranes and actin exhibit sharp sensitivity to PI(4,5)P(2) density. Finally, we show that cofilin binding to PI(4,5)P(2) is not sensitive to changes in the pH at physiological salt concentration, although the PI(4,5)P(2)-clustering activity of cofilin is moderately inhibited at elevated pH. Collectively, our data demonstrate that ADF/cofilins bind PI(4,5)P(2) headgroups through a multivalent, cooperative mechanism, and suggest that the actin filament disassembly activity of ADF/cofilin can be accurately regulated by small changes in the PI(4,5)P(2) density at cellular membranes. Copyright 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Peltomaki P.,University of Helsinki
Experimental Cell Research | Year: 2012

Cancer is traditionally viewed as a disease of abnormal cell proliferation controlled by a series of mutations. Mutations typically affect oncogenes or tumor suppressor genes thereby conferring growth advantage. Genomic instability facilitates mutation accumulation. Recent findings demonstrate that activation of oncogenes and inactivation of tumor suppressor genes, as well as genomic instability, can be achieved by epigenetic mechanisms as well. Unlike genetic mutations, epimutations do not change the base sequence of DNA and are potentially reversible. Similar to genetic mutations, epimutations are associated with specific patterns of gene expression that are heritable through cell divisions. Knudson's hypothesis postulates that inactivation of tumor suppressor genes requires two hits, with the first hit occurring either in somatic cells (sporadic cancer) or in the germline (hereditary cancer) and the second one always being somatic. Studies on hereditary and sporadic forms of colorectal carcinoma have made it evident that, apart from genetic mutations, epimutations may serve as either hit or both. Furthermore, recent next-generation sequencing studies show that epigenetic genes, such as those encoding histone modifying enzymes and subunits for chromatin remodeling systems, are themselves frequent targets of somatic mutations in cancer and can act like tumor suppressor genes or oncogenes. This review discusses genetic vs. epigenetic origin of cancer, including cancer susceptibility, in light of recent discoveries. Situations in which mutations and epimutations occur to serve analogous purposes are highlighted2copy; 2011 Elsevier Inc.

Blom T.,University of Helsinki
Cold Spring Harbor perspectives in biology | Year: 2011

Eukaryotic cells can synthesize thousands of different lipid molecules that are incorporated into their membranes. This involves the activity of hundreds of enzymes with the task of creating lipid diversity. In addition, there are several, typically redundant, mechanisms to transport lipids from their site of synthesis to other cellular membranes. Biosynthetic lipid transport helps to ensure that each cellular compartment will have its characteristic lipid composition that supports the functions of the associated proteins. In this article, we provide an overview of the biosynthesis of the major lipid constituents of cell membranes, that is, glycerophospholipids, sphingolipids, and sterols, and discuss the mechanisms by which these newly synthesized lipids are delivered to their target membranes.

Kiiski K.,University of Helsinki
European Journal of Human Genetics | Year: 2015

Recently, new large variants have been identified in the nebulin gene (NEB) causing nemaline myopathy (NM). NM constitutes a heterogeneous group of disorders among the congenital myopathies, and disease-causing variants in NEB are a main cause of the recessively inherited form of NM. NEB consists of 183 exons and it includes homologous sequences such as a 32-kb triplicate region (TRI), where eight exons are repeated three times (exons 82–89, 90–97, 98–105). In human, the normal copy number of NEB TRI is six (three copies in each allele). Recently, we described a custom NM-CGH microarray designed to detect copy number variations (CNVs) in the known NM genes. The array has now been updated to include all the currently known 10 NM genes. The NM-CGH array is superior in detecting CNVs, especially of the NEB TRI, that is not included in the exome capture kits. To date, we have studied 266 samples from 196 NM families using the NM-CGH microarray, and identified a novel recurrent NEB TRI variation in 13% (26/196) of the families and in 10% of the controls (6/60). An analysis of the breakpoints revealed adjacent repeat elements, which are known to predispose for rearrangements such as CNVs. The control CNV samples deviate only one copy from the normal six copies, whereas the NM samples include CNVs of up to four additional copies. Based on this study, NEB seems to tolerate deviations of one TRI copy, whereas addition of two or more copies might be pathogenic.European Journal of Human Genetics advance online publication, 22 July 2015; doi:10.1038/ejhg.2015.166. © 2015 Macmillan Publishers Limited

Arponen H.,University of Helsinki
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics | Year: 2010

The steady-state existence problem for Kraichnan advected passive vector models is considered for isotropic and anisotropic initial values in arbitrary dimension. The models include the magnetohydrodynamic (MHD) equations, linear pressure model, and linearized Navier-Stokes (LNS) equations. In addition to reproducing the previously known results for the MHD model, we obtain the values of the Kraichnan model roughness parameter ξ for which the LNS steady state exists. © 2010 The American Physical Society.

Pyykko P.,University of Helsinki
Chemical Reviews | Year: 2012

Quantum electrodynamics (QED) is the orders of magnitude below the Dirac-level relativistic effects and, being small, thus indirectly verifies the soundness of the latter. For neutral or nearly neutral systems, beyond Li, only one order-of-magnitude improvement of the computational accuracy, mainly the treatment of electron correlation with adequate basis sets, is estimated to separate the QED effects from being observed in head-on comparisons of theory and experiment. If the zero-point oscillations of the EM field are modified by objects ranging from molecules to macroscopic bodies, this leads to Casimir forces between them. The width of the chosen self-energy (SE) potential is arbitrary and could range from nuclear dimensions to much more diffuse values. Reviews on the finite nuclear charge distributions and their inclusion in quantum chemistry show that an explicit, quantum-mechanical description of both the nucleus and the electrons, is required.

Arponen A.,University of Helsinki
Biodiversity and Conservation | Year: 2012

The efforts to protect biological diversity must be prioritized because resources for nature conservation are limited. Conservation prioritization can be based on numerous criteria, from ecological integrity to species representation, but in this review I address only species-level prioritization. Criteria used for species prioritization range from aesthetical to evolutionary considerations, but I focus on the aspects that are biologically relevant. I distinguish between two main aspects of diversity that are used as objectives: Maintenance of biodiversity pattern, and maintenance of biodiversity process. I identify two additional criteria typically used in species prioritization that serve for achieving the objectives: The species' need of protection, and cost and effectiveness of conservation actions. I discuss how these criteria could be combined with either of the objectives in a complementarity-based benefit function framework for conservation prioritization. But preserving evolutionary process versus current diversity pattern may turn out to be conflicting objectives that have to be traded-off with each other, if pursued simultaneously. Although many reasonable criteria and methods exist, species prioritization is hampered by uncertainties, most of which stem from the poor quality of data on what species exist, where they occur, and what are the costs and benefits of protecting them. Surrogate measures would be extremely useful but their performance is still largely unknown. Future challenges in species prioritization lie in finding ways to compensate for missing information. © 2012 Springer Science+Business Media B.V.

Mikula K.M.,University of Helsinki
Frontiers in cellular and infection microbiology | Year: 2012

Among the seventeen species of the Gram-negative genus Yersinia, three have been shown to be virulent and pathogenic to humans and animals-Y. enterocolitica, Y. pseudotuberculosis, and Y. pestis. In order to be so, they are armoured with various factors that help them adhere to tissues and organelles, cross the cellular barrier and escape the immune system during host invasion. The group of proteins that mediate pathogen-host interactions constitute adhesins. Invasin, Ail, YadA, YadB, YadC, Pla, and pH 6 antigen belong to the most prominent and best-known Yersinia adhesins. They act at different times and stages of infection complementing each other by their ability to bind a variety of host molecules such as collagen, fibronectin, laminin, β1 integrins, and complement regulators. All the proteins are anchored in the bacterial outer membrane (OM), often forming rod-like or fimbrial-like structures that protrude to the extracellular milieu. Structural studies have shown that the anchor region forms a β-barrel composed of 8, 10, or 12 antiparallel β-strands. Depending on the protein, the extracellular part can be composed of several domains belonging to the immunoglobulin fold superfamily, or form a coiled-coil structure with globular head domain at the end, or just constitute several loops connecting individual β-strands in the β-barrel. Those extracellular regions define the activity of each adhesin. This review focuses on the structure and function of these important molecules, and their role in pathogenesis.

Jain S.M.,University of Helsinki
Emirates Journal of Food and Agriculture | Year: 2012

Genetic variability is needed for the improvement of crops, which can be either spontaneous or induced by mutagen treatments. The frequency rate of spontaneous mutations is very low and can't be used for plant breeding in developing new cultivars. Mutation breeding has been quite successful for producing new mutant cultivars with desirable traits in both seed and vegetative propagated crops (http://www-mvd.iaea.org). Somatic embryogenic cell cultures of date palm were irradiated with gamma radiation, and regenerated plants were transferred in the greenhouse and treated with Bayoud toxin, isolated from the causal fungus Fusarium oxysporum f. sp. albedinis. Several selected putative mutants tolerant to Bayoud disease were initially maintained in the greenhouse and finally transferred in the field for further evaluation. These plants have maintained tolerance to Bayoud disease under field conditions.

Mohan Jain S.,University of Helsinki
Emirates Journal of Food and Agriculture | Year: 2012

The date palm is one of the most ancient plants, grows in the regions of Middle East, North Africa, South Sahel, East and South Africa. Its sexually propagation hampers propagation of true-to-type genotypes due to heterozygosity. The vegetative propagation is carried out with the off shoots, produced from axillary buds situated at the base of the trunk during the juvenile life of palm tree. Offshoot production is slow; their numbers are limited, laborious and can't meet the rapidly growing demand of varieties. To speed up the date palm genetic improvement, in vitro culture techniques could be handy; however, genotype influence limits the effective use. Bioreactor is being used for large-scale production of somatic embryos. Somaclonal variation is common among in vitro-derived date palm plants. However, it could broaden genetic variability together with mutagenesis; molecular markers AFLP used to identify variability and to select useful variants. Dwarf date palm hybrid was developed by embryo rescue by interspecific hybridization of Phoenix dactylifera and P. pusilla. In vitro germplasm conservation is done by cryopreservation for long-term storage. Alternatively, in vitro shoot cultures and plantlets are stored at 4°C for short term-storage. Micro-calli is produced from date palm protoplasts; Agrobacterium-mediated transformation succeeded in GUS gene expression in callus. Date palm genomics can distinguish multiple varieties and a specific region of the genome linked to gender.

Vehkamaki H.,University of Helsinki | Riipinen I.,University of Stockholm
Chemical Society Reviews | Year: 2012

In this tutorial review we summarize the standard approaches to describe aerosol formation from atmospheric vapours and subsequent growth - with a particular emphasis on the interplay between equilibrium thermodynamics and non-equilibrium transport. We review the use of thermodynamics in describing phase equilibria and formation of aerosol particles from supersaturated vapour via nucleation. We also discuss the kinetics of cluster formation and transport phenomena, which are used to describe dynamic mass transport between the gaseous and condensed phases in a non-equilibrium system. Finally, we put these theories into the context of atmospheric observations of aerosol formation and growth. © 2012 The Royal Society of Chemistry.

Pyykko P.,University of Helsinki
Physical Chemistry Chemical Physics | Year: 2012

A combination of ab initio calculations with the isoelectronic principle and chemical intuition is a useful way to predict new species. Some experimentally verified examples are (1) the transition-metal hydrides, MH n (n = 4-12), (2) new members of the multiply-bonded 2nd- or 3rd-period species AB, ABC, ABCD or AB-CD, and ABCDE classes, the last-mentioned class including the cations N+5 and OCNCO +, (3) new members of the uranyl isoelectronic series, (4) actinyls where one of the oxygens is replaced by a 5d transition-metal (TM), (5) certain systems with noble-gas-noble-metal bonds, (6) the first argon compound HArF, (7) the cluster series of WAu 12, (8) TM-centred polyazide anions, (9) covalent molecules with a central -Zn-Zn- bond, (10) tetrahedral clusters of zinc and cadmium, (11) model systems for otherwise missing multiple bonds and (12) certain endohedral A@B systems. Further series of hypothetical species were used as a tool for developing recent sets of covalent radii, for studying the endohedral intermolecular interactions in A@B systems, or for finding examples of a 32-electron rule, corresponding to the well-known 8e- and 18e-rules. For obvious reasons, much of the molecular chemistry of the superheavy elements is based on studies of hypothetical model systems. This journal is © 2012 the Owner Societies.

Jain S.M.,University of Helsinki
Romanian Biotechnological Letters | Year: 2010

The purpose of mutation induction is to enhance mutation rate in a short duration in developing new plant varieties. The occurrence of spontaneous mutation frequency rate is very low and difficult to use in plant breeding. Traditionally mutations are induced by physical (e.g. gamma radiation) and chemical (e.g. ethylmethane sulfonate) mutagen treatment of both seed and vegetatively propagated crops. Recently high energy ion beams have been used for mutation induction. They induce largely deletion mutants. In International Atomic Energy Agency (IAEA) mutant database, over 3000 officially released mutant varieties have been released worldwide in cereals, ornamental plants, fruits, vegetables, and oil crops. As a result, sustainable food production has been maintained. By in vitro selection, desirable mutants with useful agronomical traits, e.g. abiotic and biotic stress tolerant can be isolated in a short period of time. The genetic fidelity of the regenerated plants is highly desirable for developing new improved plant varieties and a useful as a reliable tool for feeding the ever-growing human population, genomic function especially under climate change and limited arable land. © 2010 University of Bucharest.

Leppo A.,University of Helsinki
International Journal of Drug Policy | Year: 2012

Background: The dominant biomedical discourse stresses the physiological risks to the foetus or newborn posed by the prenatal use of illicit drugs. There is also a strong moral incentive for pregnant women to abstain from drugs. Yet few researchers have explored how pregnant, drug-using women themselves perceive the risks involved. The present paper investigates the reasoning by women about risks involved in prenatal drug use. Theoretically, a socio-cultural approach to risk is taken. Methods: The paper is based on fourteen ethnographic interviews with women who had used illicit drugs during pregnancy (mainly buprenorphine), had recently given birth and had regularly used prenatal services during pregnancy. The interviews were informal, semi-structured and focused on the women's experiences of pregnancy and service use. Each interview lasted about an hour. The interviews were transcribed and inductively analysed using thematic coding. Risk perceptions were identified in the interviewees' expressions and understanding of fears, dangers, threats and worries. Results: The women were not primarily concerned about health risks: their greatest fears in connection with the prenatal use of illicit drugs were giving birth to a child with withdrawal symptoms, child protection interventions and child removal, encountering negative attitudes in seeking professional help as well as terminating drug use. The interviewees did not see abstaining from drugs as a risk-free option. On the contrary, the prospect of a drug-free life was filled with fears linked to physical and mental pain and disruptions in significant social bonds. The women made use of biomedical and nonprofessional understandings of risks. The women's friends and acquaintances played a central role as providers of knowledge about risks. Conclusion: When providing health education to pregnant women with drug problems, professionals should take women's perceptions of risk seriously, treat the women respectfully and engage them in dialogue about the risks involved. Further studies on pregnant women's perceptions of risk in using illicit drugs would be highly valuable. © 2012 Elsevier B.V.

Pyykko P.,University of Helsinki
Annual Review of Physical Chemistry | Year: 2012

Relativistic effects can strongly influence the chemical and physical properties of heavy elements and their compounds. This influence has been noted in inorganic chemistry textbooks for a couple of decades. This review provides both traditional and new examples of these effects, including the special properties of gold, lead-acid and mercury batteries, the shapes of gold and thallium clusters, heavy-atom shifts in NMR, topological insulators, and certain specific heats. © Copyright ©2012 by Annual Reviews. All rights reserved.

Katila T.,University of Helsinki
Reproduction in Domestic Animals | Year: 2012

Contents: This review attempts to summarize the current knowledge on uterine inflammatory response after mating in horses, pigs and cattle. Post-mating endometritis has been extensively studied in horses as it has been considered to cause infertility. The inflammation is known to occur also in cattle, but it has not been investigated to a similar extent. There are a number of publications about mechanisms of post-mating uterine inflammation in pigs, which seem to resemble those in horses. The major focus of this review is the horse, but relevant literature is presented also on swine and cattle. Spermatozoa, seminal plasma and semen extenders play roles in the induction of inflammation. In addition, sperm numbers, concentration and viability, as well as the site of semen deposition may modulate the inflammatory response. Cytokines, polymorphonuclear leucocytes (PMN) and mononuclear cells represent the uterine inflammatory response to mating. Inflammation is the first line of defence against invasion and eliminates excess spermatozoa and bacteria. Semen deposition elicits a massive PMN invasion, followed by phagocytosis of sperm aided by the formation of neutrophil extracellular traps. Exposure of the female genital tract to semen is important also for endometrial receptivity and pre-implantation embryo development. Seminal plasma (SP) and inflammation elicit transient immune tolerance to antigens present in semen. SP contains immune-regulatory molecules that activate and control immune responses to antigens by stimulating expression of cytokines and growth factors and by initiating tissue remodelling. SP also regulates ovarian function. Effective elimination of excess sperm and inflammatory by-products and subsequent rapid return of the endometrium to the normal state is a prerequisite for pregnancy. Uterine backflow, driven by myometrial contractions and requiring a patent cervix, is an important physical tool in uterine drainage. © 2012 Blackwell Verlag GmbH.

Joensuu H.,University of Helsinki
Nature Reviews Clinical Oncology | Year: 2012

Tyrosine kinase inhibitors that target the key molecular drivers of gastrointestinal stromal tumour (GIST) are effective treatments of advanced-stage GIST. Yet, most of these patients succumb to the disease. Approximately 60% of patients with GIST are cured by surgery, and these individuals can be identified by risk stratification schemes based on tumour size, mitosis count and site, and assessment of rupture. Two large randomized trials have evaluated imatinib as adjuvant treatment for operable, KIT-positive GIST; adjuvant imatinib substantially improved time to recurrence. One of these trials reported that 3 years of adjuvant imatinib improves overall survival of patients who have a high estimated risk for recurrence of GIST compared with 1 year of imatinib. The optimal adjuvant strategy remains unknown and some patients might benefit from longer than 3 years of imatinib treatment. However, a strategy that involves GIST risk assessment following surgery using a validated scheme, administration of adjuvant imatinib for 3 years, patient monitoring during and after completion of imatinib to detect recurrence early, and reinstitution of imatinib if GIST recurs is a reasonable choice for care of patients with high-risk GIST. © 2012 Macmillan Publishers Limited. All rights reserved.

Wong B.B.M.,Monash University | Candolin U.,University of Helsinki
Behavioral Ecology | Year: 2015

Humans have brought about unprecedented changes to environments worldwide. For many species, behavioral adjustments represent the first response to altered conditions. In this review, we consider the pivotal role that behavior plays in determining the fate of species under human-induced environmental change and highlight key research priorities. In particular, we discuss the importance of behavioral plasticity and whether adaptive plastic responses are sufficient in keeping pace with changing conditions. We then examine the interplay between individual behavioral responses and population processes and consider the many ways in which changes in behavior can affect ecosystem function and stability. Lastly, we turn to the evolutionary consequences of anthropogenic change and consider the impact of altered behaviors on the evolutionary process and whether behavior can facilitate or hinder adaptation to environmental change. © The Author 2014. Published by Oxford University Press on behalf of the International Society for Behavioral Ecology.

Merila J.,University of Helsinki
Journal of Applied Ichthyology | Year: 2015

Different types of fishing gear are known to vary in catch per unit effort (CPUE), but little is known regarding this in respect to the three-spined stickleback Gasterosteus aculeatus (Linnaeus 1758). The influence of the three-spined stickleback CPUE by trap model, baiting and visual attractors was investigated. One trap type was found to out-perform the other; however, baiting or attractors did not influence the CPUE. Hence, the results suggest that while the choice of trap type may have an impact on the three-spined stickleback CPUE, baiting or attractors do not seem to improve the impact. © 2015 Blackwell Verlag GmbH.

Miettinen O.,University of Helsinki
Astronomy and Astrophysics | Year: 2014

Context. Infrared dark clouds (IRDCs) provide a useful testbed in which to investigate the genuine initial conditions and early stages of massive-star formation. Aims. We attempt to characterise the chemical properties of a sample of 35 massive clumps of IRDCs through multi-molecular line observations. We also search for possible evolutionary trends among the derived chemical parameters. Methods. The clumps are studied using the MALT90 (Millimetre Astronomy Legacy Team 90 GHz) line survey data obtained with the Mopra 22 m telescope. The survey covers 16 different transitions near 90 GHz. The spectral-line data are used in concert with our previous LABOCA (Large APEX BOlometer CAmera) 870 μm dust emission data. Results. Eleven MALT90 transitions are detected towards the clumps at least at the 3σ level. Most of the detected species (SiO, C 2H, HNCO, HCN, HCO+, HNC, HC3N, and N 2H+) show spatially extended emission towards many of the sources. Most of the fractional abundances of the molecules with respect to H2 are found to be comparable to those determined in other recent similar studies of IRDC clumps. We found that the abundances of SiO, HNCO, and HCO+ are higher in IR-bright clumps than in IR-dark sources, reflecting a possible evolutionary trend. A hint of this trend is also seen for HNC and HC3N. An opposite trend is seen for the C2H and N2H+ abundances. Moreover, a positive correlation is found between the abundances of HCO+ and HNC, and between those of HNC and HCN. The HCN and HNC abundances also appear to increase as a function of the N2H+ abundance. The HNC/HCN and N2H +/HNC abundance ratios are derived to be near unity on average, while that of HC3N/HCN is ∼10%. The N2H+/HNC ratio appears to increase as the clump evolves, while the HNC/HCO+ ratio shows the opposite behaviour. Conclusions. The detected SiO emission is probably caused by shocks driven by outflows in most cases, although shocks resulting from the cloud formation process could also play a role. Shock-origin for the HNCO, HC3N, and CH3CN emission is also plausible. The average HNC/HCN ratio is in good agreement with those seen in other IRDCs, but gas temperature measurements would be neeeded to study its temperature dependence. Our results support the finding that C2H can trace the cold gas, and not just the photodissociation regions. The HC3N/HCN ratio appears to be comparable to the values seen in other types of objects, such as T Tauri disks and comets. © ESO, 2014.

Haakana M.,University of Helsinki
Journal of Pragmatics | Year: 2010

This article analyses some functions of smiling in relation to laughter. Two kinds of cases are analysed. (i) Smiling can be used as a pre-laughing device: laughing together can be entered step-wise, and smiling is a common device for paving the way to the laughter. (ii) Smiling can be used as a response to laughter in the previous turn. The response can consist of just a smile or smiling can co-occur with some verbal utterance. The article shows that smiling as a response to laughter can have several interactional functions. It can be used to acknowledge the laughability of the previous turn, and sometimes even provides strong uptake of its laughability. However, smiling can also be an affiliative response to prior utterances that are constructed as delicate and troublesome (by laughter and other means). Laughter and smiling have different functions in different sequential and verbal contexts.The analysis concentrates on data from Finnish primary health care interactions and convenience store encounters. In addition, extracts of everyday telephone calls are analysed to show that smiling can also be an acoustic phenomenon and thus available also when the interactants do not have visual access to each other. © 2010 Elsevier B.V.

Hamalainen W.,University of Helsinki
Knowledge and Information Systems | Year: 2010

Searching statistically significant association rules is an important but neglected problem. Traditional association rules do not capture the idea of statistical dependence and the resulting rules can be spurious, while the most significant rules may be missing. This leads to erroneous models and predictions which often become expensive. The problem is computationally very difficult, because the significance is not a monotonic property. However, in this paper, we prove several other properties, which can be used for pruning the search space. The properties are implemented in the StatApriori algorithm, which searches statistically significant, non-redundant association rules. Empirical experiments have shown that StatApriori is very efficient, but in the same time it finds good quality rules. © 2009 Springer-Verlag London Limited.

Paavonen J.,University of Helsinki
Annals of Medicine | Year: 2012

Chlamydia trachomatis (CT) is the most common bacterial cause of sexually transmitted infections. CT infections are strongly associated with risk-taking behavior. Recommendations for testing have been implemented in many countries. The effectiveness of the screening programs has been questioned since chlamydia rates have increased. However, the complication rates including pelvic inflammatory disease, tubal factor infertility, and tubal pregnancy have been decreasing, which is good news. The complication rates associated with CT infection have clearly been over-estimated. Genetic predisposition and host immune response play important roles in the pathogenesis of long-term complications. CT plays a co-factor role in the development of cervical neoplasia caused by high-risk human papillomavirus (HPV) types. The evidence linking CT and other adverse pregnancy outcomes is weak. The current nucleic acid amplification tests perform well. A new genetic variant of CT was discovered in Sweden but has only rarely been detected elsewhere. Single-dose azithromycin remains effective against CT. Secondary prevention by screening is still the most important intervention to limit the adverse effects of CT on reproductive health. © 2012 Informa UK, Ltd.

Raivio K.,University of Helsinki
Journal of Cleaner Production | Year: 2011

The mounting evidence about human-induced environmental change, and about its expected detrimental effects on humans and their societies (IPCC, 2007; Reid et al., 2010; Rockström et al., 2009), has turned out to be exceedingly difficult to turn into political action to mitigate the change and adapt to its consequences. Economic self-interest creates friction between nation-states, within regional alliances like the EU, and across the divide between the developing and developed world. A significant factor is a vocal and well-funded group of climate skeptics, who question the credibility of mainstream earth system science, overemphasize the disagreements within the scientific community, argue for more research before any action is warranted, and in general create doubt to justify inaction or delay (Oreskes and Conway, 2010). A further problem is that both the decision-makers and the public have a very superficial understanding of the issues, cannot intellectually handle complex problems and uncertainty, and do not always know what and whom to believe. This constitutes a challenge to the education establishment. © 2011 Elsevier Ltd. All rights reserved.

Hyvarinen A.,University of Helsinki
Topics in Cognitive Science | Year: 2010

A fundamental question in visual neuroscience is: Why are the response properties of visual neurons as they are? A modern approach to this problem emphasizes the importance of adaptation to ecologically valid input, and it proceeds by modeling statistical regularities in ecologically valid visual input (natural images). A seminal model was linear sparse coding, which is equivalent to independent component analysis (ICA), and provided a very good description of the receptive fields of simple cells. Further models based on modeling residual dependencies of the ''independent" components have later been introduced. These models lead to emergence of further properties of visual neurons: the complex cell receptive fields, the spatial organization of the cells, and some surround suppression and Gestalt effects. So far, these models have concentrated on the response properties of neurons, but they hold great potential to model various forms of inference and learning. © 2009 Cognitive Science Society, Inc.

Salmela L.,University of Helsinki
Bioinformatics | Year: 2010

Motivation: High-throughput sequencing technologies produce large sets of short reads that may contain errors. These sequencing errors make de novo assembly challenging. Error correction aims to reduce the error rate prior assembly. Many de novo sequencing projects use reads from several sequencing technologies to get the benefits of all used technologies and to alleviate their shortcomings. However, combining such a mixed set of reads is problematic as many tools are specific to one sequencing platform. The SOLiD sequencing platform is especially problematic in this regard because of the two base color coding of the reads. Therefore, new tools for working with mixed read sets are needed. Results: We present an error correction tool for correcting substitutions, insertions and deletions in a mixed set of reads produced by various sequencing platforms. We first develop a method for correcting reads from any sequencing technology producing base space reads such as the SOLEXA/Illumina and Roche/454 Life Sciences sequencing platforms. We then further refine the algorithm to correct the color space reads from the Applied Biosystems SOLiD sequencing platform together with normal base space reads. Our new tool is based on the SHREC program that is aimed at correcting SOLEXA/Illumina reads. Our experiments show that we can detect errors with 99% sensitivity and >98% specificity if the combined sequencing coverage of the sets is at least 12. We also show that the error rate of the reads is greatly reduced. Availability: The JAVA source code is freely available at http://www.cs.helsinki.fi/u/lmsalmel/hybrid-shrec/. Contact: leena.salmela@cs.helsinki.fi. © The Author 2010. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org.

Shimmi O.,University of Helsinki | Newfeld S.J.,Arizona State University
Journal of Biochemistry | Year: 2013

Members of the transforming growth factor-β (TGF-b) family of secreted proteins are present in all multicellular animals. TGF-b proteins are versatile intercellular signalling molecules that orchestrate cell fate decisions during development and maintain homeostasis in adults. The Smad family of signal transducers implements TGF-β signals in responsive cells. Given the ability of TGF-β ligands to induce dramatic responses in target cells, numerous regulatory mechanisms exist to prevent unintended consequences. Here we review new reports of extracellular and post-translational regulation in Drosophila and vertebrates. Extracellular topics include the regulation of TGF-β signalling range and the coordination between tissue morphogenesis and TGF-β signalling. Post-translational topics include the regulation of TGF-β signal transduction by Gsk3-β phosphorylation of Smads and by cycles of Smad mono-and deubiquitylation. Extension of the ubiquitylation data to the Hippo pathway is also discussed.

Kujala H.,University of Helsinki | Vepsalainen V.,Finnish Museum of Natural History | Zuckerberg B.,University of Wisconsin - Madison | Brommer J.E.,University of Turku
Global Change Biology | Year: 2013

Global climate warming is predicted to lead to global and regional changes in the distribution of organisms. One influential approach to test this prediction using temporally repeated mapping surveys of organisms was suggested in a seminal paper by Thomas & Lennon (1999, Nature). The Thomas & Lennon approach corrects observed changes in the range margin for changes in the range size, and thus potentially controls for other broad-scale environmental changes between surveys, however the approach does not necessarily account for potential biases in sampling effort. To verify whether the issue of variation in sampling effort affects empirical estimates of shifts in range margin, we reanalyzed all three published studies exploring range margin changes of breeding birds in Great Britain (GB), Finland, and New York State (NY). Accounting for changes in survey effort on range margins lowered the estimated shift for breeding birds in New York, but the shift remained statistically significant. For Great Britain and Finland, for which no direct estimate of survey effort is available, we used species richness (a strong correlate of survey effort in New York) as a proxy and found that in both cases the estimated shift in range margin was significantly reduced and became nonsignificant. To understand how robust the approach is to sampling biases, we use a simulation model to show that the Thomas & Lennon approach is, under certain conditions, sensitive to changes in detection probability (probability to detect true occupancy) which in turn may be affected by changes in surveying effort between surveys. We thus found evidence that temporal changes in the distribution of breeding birds based on repeated mapping surveys may be inflated by changes in survey effort along range boundaries. We discuss possible approaches to deal with this issue in the analysis and design of national or regional surveys.copy; 2012 Blackwell Publishing Ltd.

Raerinne J.P.,University of Helsinki
BioScience | Year: 2013

Allometries and scaling relationships have become popular among biologists. One reason for this popularity is the generality of these relationships, which has provided authors hope that allometries and scaling relationships represent biological laws or explanatory generalizations. In this article, I discuss three roles of allometries and scaling relationships: the explanatory, the predictive, and the heuristic. I argue that allometries and scaling relationships often function successfully heuristically-that is, discovering or elucidating patterns from data rather than making accurate predictions or giving illuminating explanations. The heuristic role is not to be overlooked. A science or discipline without interesting objects of explanation lacks the potential to progress and mature. © 2013 by American Institute of Biological Sciences. All rights reserved. Request permission to photocopy or reproduce article content at the University of California Press's Rights and Permissions Web site at .

Mutanen M.,University of Oulu | Wahlberg N.,University of Turku | Kaila L.,University of Helsinki
Proceedings of the Royal Society B: Biological Sciences | Year: 2010

Lepidoptera (butterflies and moths) represent one of the most diverse animals groups. Yet, the phylogeny of advanced ditrysian Lepidoptera, accounting for about 99 per cent of lepidopteran species, has remained largely unresolved. We report a rigorous and comprehensive analysis of lepidopteran affinities. We performed phylogenetic analyses of 350 taxa representing nearly 90 per cent of lepidopteran families. We found Ditrysia to be a monophyletic taxon with the clade Tischerioidea \+ Palaephatoidea being the sister group of it. No support for the monophyly of the proposed major internested ditrysian clades, Apoditrysia, Obtectomera and Macrolepidoptera, was found as currently defined, but each of these is supported with some modification. The monophyly or near-monophyly of most previously identified lepidopteran superfamilies is reinforced, but several species-rich superfamilies were found to be para-or polyphyletic. Butterflies were found to be more closely related to 'microlepidopteran' groups of moths rather than the clade Macrolepidoptera, where they have traditionally been placed. There is support for the monophyly of Macrolepidoptera when butterflies and Calliduloidea are excluded. The data suggest that the generally short diverging nodes between major groupings in basal non-tineoid Ditrysia are owing to their rapid radiation, presumably in correlation with the radiation of flowering plants. © 2010 The Royal Society.

Savolainen O.,University of Oulu | Lascoux M.,Uppsala University | Merila J.,University of Helsinki
Nature Reviews Genetics | Year: 2013

It is increasingly important to improve our understanding of the genetic basis of local adaptation because of its relevance to climate change, crop and animal production, and conservation of genetic resources. Phenotypic patterns that are generated by spatially varying selection have long been observed, and both genetic mapping and field experiments provided initial insights into the genetic architecture of adaptive traits. Genomic tools are now allowing genome-wide studies, and recent theoretical advances can help to design research strategies that combine genomics and field experiments to examine the genetics of local adaptation. These advances are also allowing research in non-model species, the adaptation patterns of which may differ from those of traditional model species. © 2013 Macmillan Publishers Limited.

Berg B.,University of Helsinki
Soil Biology and Biochemistry | Year: 2014

For decomposing foliar litter in forest systems the pattern for accumulated mass loss vs time varies among litter species and environments. Thus, decomposition may be complete (100% accumulated mass loss) or the rate may cease and proceed at such a low rate that a limit value for decomposition may be estimated. Such limit values have been found to range from 42% accumulated mass loss to 100%, resulting in stable fractions of 58 and 0%, respectively.To support a discussion about pattern we need causal relationships and I have used a conceptual model with three decomposition stages as a reference and discuss that in relation to two nutrients that influence the degradation of lignin and lignified tissue. Whereas a high nitrogen (N) concentration may have a stimulating effect on degradation of holocellulose in the early stage the same high N concentration may retard the degradation of lignified tissue in the late stage and the higher the N concentration the stronger the retardation. Through the enzyme manganese peroxidase (MnP), manganese (Mn) stimulates lignin degradation and thus the lignified fraction of litter. A high level of Mn appears to support a further degradation of the lignified tissue and thus results in a high limit value, whereas a high N has been related to a low value.The aim behind this review is to: (i) identify specific factors that may influence the pattern of accumulated mass loss and thus the type of regression model that describes the data; and (ii) present a possible climate influence on decomposition pattern. To this purpose we need to discuss a possible variation in pattern following the variation in concentrations of the two nutrients N and Mn. Concentrations of N and Mn in newly shed litter are both influenced by site climate, with N increasing and Mn decreasing with increasing mean annual temperature (MAT) and increasing annual actual evapotranspiration (AET). Thus, climate becomes at least an indirect regulating factor for decomposition pattern.Two main regression models are used to describe the patterns, namely the single exponential and a function separating a readily decomposed and a stable fraction, by estimating a limit value (asymptotic function). For the discussion on decomposition pattern a model parameter was used, namely estimated limit values with a so far observed range in variation from 42 to 100%. The stabilized litter fraction defined by the limit value may be used for estimating the accumulation rate of stable carbon (C) in soil. © 2014 Elsevier Ltd.

Haapalainen M.,University of Helsinki
Annals of Applied Biology | Year: 2014

Candidatus Liberibacter species are Gram-negative bacteria that live as phloem-limited obligate parasites in plants, and are associated with several plant diseases. These bacteria are transmitted by insects called psyllids, or jumping plant lice, which feed on plant phloem sap. Citrus huanglongbing (yellow shoot) or citrus greening disease is associated with three different species of Ca. Liberibacter - Ca. L. asiaticus, Ca. L. africanus and Ca. L. americanus - all originally found on different continents. Ca. L. asiaticus is the most severe pathogen, spread by Asian citrus psyllid Diaphorina citri and causing devastating epidemics in several countries. Ca. L. africanus occurs in Africa where it is spread by the African citrus psyllid Trioza erytreae. Ca. Liberibacter solanacearum is associated with diseases in several solanaceous plants, and transmitted by potato psyllid Bactericera cockerelli. Zebra chip disease is causing large damage in potato crops in North America. In Europe Ca. Liberibacter solanacearum is associated with diseases of the Apiaceae family of plants, carrot and celery, and transmitted by psyllids Trioza apicalis and Bactericera trigonica. When Ca. Liberibacter is suspected as the disease agent, the diagnosis is confirmed by DNA-based detection methods. Ca. Liberibacter-associated plant diseases can be controlled by using healthy plant propagation material, eradicating symptomatic plants, and by controlling the psyllid populations spreading the disease. © 2014 Association of Applied Biologists.

Gucciardo E.,University of Helsinki
Cellular and molecular life sciences : CMLS | Year: 2014

The erythropoietin-producing hepatocellular (Eph) receptors comprise the largest family of receptor tyrosine kinases (RTKs). Initially regarded as axon-guidance and tissue-patterning molecules, Eph receptors have now been attributed with various functions during development, tissue homeostasis, and disease pathogenesis. Their ligands, ephrins, are synthesized as membrane-associated molecules. At least two properties make this signaling system unique: (1) the signal can be simultaneously transduced in the receptor- and the ligand-expressing cell, (2) the signaling outcome through the same molecules can be opposite depending on cellular context. Moreover, shedding of Eph and ephrin ectodomains as well as ligand-dependent and -independent receptor crosstalk with other RTKs, proteases, and adhesion molecules broadens the repertoire of Eph/ephrin functions. These integrated pathways provide plasticity to cell-microenvironment communication in varying tissue contexts. The complex molecular networks and dynamic cellular outcomes connected to the Eph/ephrin signaling in tumor-host communication and stem cell niche are the main focus of this review.

Niemela J.,University of Helsinki
Bioethics | Year: 2011

The advances in biotechnology have given rise to a discussion concerning the strong emotional reaction expressed by the public towards biotechnological innovations. This reaction has been named the 'Yuck-factor' by several theorists of bioethics. Leon Kass, the former chairman of the President's council on bioethics, has appraised this public reaction as 'an emotional expression of deep wisdom, beyond reason's power fully to articulate it'. Similar arguments have been forwarded by the Catholic Church, several Protestant denominations and the Pro-Life movement. Several bioethicists have, however, opposed the idea of a disgust-based morality. Recent findings in cognitive science support the view that the strong negative emotions people often experience when faced with biotechnological ideas are not expressions of inner wisdom. The negative emotions may rather be the result of a cognitive violation the biotechnological innovations easily cause. Due to their evolutionary background, people have certain automatic and quick cognitive tendencies routinely used for categorizing and reasoning about nature, usually termed 'folk biology'. Biotechnological processes like hybridisation and cloning clearly violate several of the cognitive rules people naturally apply for the explanation and categorization of their natural environment. As the cognitive tendencies routinely applied to the explanation of biological world are violated, an emotional response of fear, disgust and of something unnatural being underway is easily provoked. It is suggested in this paper that the reason behind the Yuck-factor is not a deep inner wisdom, but a violation of natural human cognitive tendencies concerning the biological world. © 2010 Blackwell Publishing Ltd.

Mahonen M.,University of Helsinki
European journal of preventive cardiology | Year: 2013

Population-based administrative registers could be used for identifying heart failure (HF) cases. However, the validity of the classification obtained from administrative registers is not known. The validity of HF diagnoses obtained by record linkage of administrative databases in Finland was assessed against classification by three independent physicians. Data from the nationwide registers in Finland - the Hospital Discharge Register, Causes of Death Register, Drug Reimbursement Register, and pharmacy prescription data - were linked with the FINRISK 1997 survey data. Cases with hospitalizations before the survey date with HF as one of the discharge diagnoses, cases with special reimbursement for HF drugs before the survey date and cases with the use of furosemide before the survey date were classified as HF in the registers. All these cases, cases with baseline brain natriuretic peptide > 100 pg/ml, and cases with use of digoxin were independently assessed by two physicians as HF/no HF. Discrepant cases were solved by a third physician. This classification was considered as the gold standard, against which the registers were assessed. The specificity of the registers was 99.7% (95% CI 99.5-99.8%), positive predictive value 85.9% (95% CI 79.7-90.5%), negative predictive value 97.9% (95% CI 97.6-98.2%), and sensitivity 48.5% (95% CI 42.9-54.2%). Classification obtained from administrative registers has high specificity and can be used in follow-up studies with HF as an end point. Sensitivity is modest and administrative data should be used with caution for surveillance.

Kellosalo J.,University of Helsinki
Molecular membrane biology | Year: 2013

Membrane-bound pyrophosphatases (M-PPases) are enzymes that enhance the survival of plants, protozoans and prokaryotes in energy constraining stress conditions. These proteins use pyrophosphate, a waste product of cellular metabolism, as an energy source for sodium or proton pumping. To study the structure and function of these enzymes we have crystallized two membrane-bound pyrophosphatases recombinantly produced in Saccharomyces cerevisae: the sodium pumping enzyme of Thermotoga maritima (TmPPase) and the proton pumping enzyme of Pyrobaculum aerophilum (PaPPase). Extensive crystal optimization has allowed us to grow crystals of TmPPase that diffract to a resolution of 2.6 Å. The decisive step in this optimization was in-column detergent exchange during the two-step purification procedure. Dodecyl maltoside was used for high temperature solubilization of TmPPase and then exchanged to a series of different detergents. After extensive screening, the new detergent, octyl glucose neopentyl glycol, was found to be the optimal for TmPPase but not PaPPase.

Loytynoja A.,European Bioinformatics Institute | Loytynoja A.,University of Helsinki | Vilella A.J.,European Bioinformatics Institute | Goldman N.,European Bioinformatics Institute
Bioinformatics | Year: 2012

Motivation: Accurate alignment of large numbers of sequences is demanding and the computational burden is further increased by downstream analyses depending on these alignments. With the abundance of sequence data, an integrative approach of adding new sequences to existing alignments without their full re-computation and maintaining the relative matching of existing sequences is an attractive option. Another current challenge is the extension of reference alignments with fragmented sequences, as those coming from next-generation metagenomics, that contain relatively little information. Widely used methods for alignment extension are based on profile representation of reference sequences. These do not incorporate and use phylogenetic information and are affected by the composition of the reference alignment and the phylogenetic positions of query sequences. Results: We have developed a method for phylogeny-aware alignment of partial-order sequence graphs and apply it here to the extension of alignments with new data. Our new method, called PAGAN, infers ancestral sequences for the reference alignment and adds new sequences in their phylogenetic context, either to predefined positions or by finding the best placement for sequences of unknown origin. Unlike profile-based alternatives, PAGAN considers the phylogenetic relatedness of the sequences and is not affected by inclusion of more diverged sequences in the reference set. Our analyses show that PAGAN outperforms alternative methods for alignment extension and provides superior accuracy for both DNA and protein data, the improvement being especially large for fragmented sequences. Moreover, PAGAN-generated alignments of noisy next-generation sequencing (NGS) sequences are accurate enough for the use of RNA-seq data in evolutionary analyses. © The Author(s) 2012. Published by Oxford University Press.

Hemila H.,University of Helsinki
Allergy, Asthma and Clinical Immunology | Year: 2013

Background: Asthma exacerbations are often induced by the common cold, which, in turn, can be alleviated by vitamin C.Objective: To investigate whether vitamin C administration influences common cold-induced asthma. Methods: Systematic review and statistical analysis of the identified trials. Medline, Scopus and Cochrane Central were searched for studies that give information on the effects of vitamin C on common cold-induced asthma. All clinically relevant outcomes related to asthma were included in this review. The estimates of vitamin C effect and their confidence intervals [CI] were calculated for the included studies. Results: Three studies that were relevant for examining the role of vitamin C on common cold-induced asthma were identified. The three studies had a total of 79 participants. Two studies were randomized double-blind placebo-controlled trials. A study in Nigeria on asthmatics whose asthma attacks were precipitated by respiratory infections found that 1 g/day vitamin C decreased the occurrence of asthma attacks by 78% (95% CI: 19% to 94%). A cross-over study in former East-Germany on patients who had infection-related asthma found that 5 g/day vitamin C decreased the proportion of participants who had bronchial hypersensitivity to histamine by 52 percentage points (95% CI: 25 to 71). The third study did not use a placebo. Administration of a single dose of 1 gram of vitamin C to Italian non-asthmatic common cold patients increased the provocative concentration of histamine (PC20) 3.2-fold (95% CI: 2.0 to 5.1), but the vitamin C effect was significantly less when the same participants did not suffer from the common cold.Conclusions: The three reviewed studies differed substantially in their methods, settings and outcomes. Each of them found benefits from the administration of vitamin C; either against asthma attacks or against bronchial hypersensitivity, the latter of which is a characteristic of asthma. Given the evidence suggesting that vitamin C alleviates common cold symptoms and the findings of this systematic review, it may be reasonable for asthmatic patients to test vitamin C on an individual basis, if they have exacerbations of asthma caused by respiratory infections. More research on the role of vitamin C on common cold-induced asthma is needed. © 2013 Hemilä; licensee BioMed Central Ltd.

Khriachtchev L.,University of Helsinki
Journal of Physical Chemistry A | Year: 2015

Noncovalent interactions are crucial for many physical, chemical, and biological phenomena. Matrix isolation is a powerful method to study noncovalent interactions, including hydrogen-bonded species, and it has been extensively used in this field. However, there are difficult situations, such as in the case of species that are impossible to prepare in the gas phase. In this article, we describe some advanced approaches allowing studies of complexes that are problematic for the traditional methods. Photolysis of a suitable precursor in a matrix can lead to a large concentration of 1:1 complexes, which are otherwise very difficult to prepare (e.g., the H2O···O complex). Photolysis of species combined with annealing can lead to complexes of molecules with mobile atoms (e.g., the same H2O···O complex). Simultaneous photolysis of two species combined with annealing can produce complexes of radicals via reactions of the photogenerated complexes with mobile atoms (e.g., the H2O···HCO complex). Interaction of noble-gas (Ng) hydrides with other species is another topic (e.g., the N2···HArF complex) and very large blue shifts of the H-Ng stretching modes are normally observed for these systems. Complexes and dimers of the higher-energy conformer of formic acid have been prepared by using selective vibrational excitation of the ground-state conformer. The higher-energy conformer of formic acid can be efficiently stabilized in the complexes with strong hydrogen bonding. We also consider some problematic cases when the changes in the vibrational frequencies of the 1:1 complexes are very small (e.g., the phenol···Xe complex) and when the complex formation is prevented by strong solvation in the matrix (e.g., species in solid xenon). © 2015 American Chemical Society.

Pyykko P.,University of Helsinki
Journal of Physical Chemistry A | Year: 2015

The recent fits of additive covalent radii RAB = rA + rB for the title systems are reviewed and compared with alternative systems of radii by other authors or with further experimental data. The agreement of the predicted R with experiment is good, provided that the A-B bond is not too ionic, or the coordination numbers of the two atoms too different from the original input data, used in the fit. Bonds between transition metals and halides are not included in the single-bond set, because of their partial multiple-bond character. © 2014 American Chemical Society.

Changes in snowfall in northern Europe (55–71°N, 5–35°E) are analysed from 12 regional model simulations of twenty-first century climate under the Special Report on Emissions Scenarios A1B scenario. As an ensemble mean, the models suggest a decrease in the winter total snowfall in nearly all of northern Europe. In the middle of the winter, however, snowfall generally increases in the coldest areas. The borderline between increasing and decreasing snowfall broadly coincides with the −11 °C isotherm in baseline (1980–2010) monthly mean temperature, although with variation between models and grid boxes. High extremes of daily snowfall remain nearly unchanged, except for decreases in the mildest areas, where snowfall as a whole becomes much less common. A smaller fraction of the snow in the simulated late twenty-first century climate falls on severely cold days and a larger fraction on days with near-zero temperatures. Not only do days with low temperatures become less common, but they also typically have more positive anomalies of sea level pressure and less snowfall for the same temperature than in the present-day climate. © 2015 Springer-Verlag Berlin Heidelberg

Katainen A.,University of Helsinki
Sociology of Health and Illness | Year: 2010

The dominant trend in smoking prevalence in most Western countries is its increasing association with lower socioeconomic positions, making it a major factor behind inequalities in health. This paper focuses on the reasoning behind smoking, as well as on its social significance among middle-class and working-class smokers. The data consist of 55 semi-structured interviews with daily smokers, ex-smokers and occasional smokers from different occupational backgrounds. The analysis revealed considerable differences in the ways of accounting for smoking, relating to the respondents' occupational backgrounds. Contrary to expectations, non-manual workers tended to consider their smoking functional, pleasurable and controlled, whereas the opposite was the case with the manual workers. Despite the high prevalence of smoking in that group, they were least willing to justify or rationalise their behaviour, whereas the agenda of middle-class smokers could be interpreted as the reconciliation of middle-class habitus with a risky, working-class habit. © 2010 The Author. Sociology of Health & Illness © 2010 Foundation for the Sociology of Health & Illness/Blackwell Publishing Ltd.

The taxonomy of Elachista (Aphelosetia) hedemanni Rebel, 1899, and its relatives is clarified. The following species are described as new: Elachista gilvula sp. n. from Russia: Tuva with additional record from Kazakhstan, Elachista galbina sp. n. from Kazakhstan and Elachista cirrhoplica sp. n. from Spain. The systematics of an assemblage of species related to Elachista (Aphelosetia) pollinariella Zeller is discussed, and characters possibly enabling the further division of the subgenus Aphelosetia to more manageable units are suggested. Copyright © 2012 · Magnolia Press.

Hanninen H.,University of Helsinki | Tanino K.,University of Saskatchewan
Trends in Plant Science | Year: 2011

Climate warming has increased researchers' interest in plant phenology and its modelling. Although the main focus is on projections of accelerated springtime phenological events, also a further extension of the growing season by delayed growth cessation is often projected. However, ecophysiological studies indicate that, for boreal and temperate trees, such generalisations are precluded owing to differential climatic conditions and inter- and intraspecific genetic differences. The annual cycle of these trees is an integrated system, where one phase affects subsequent phases, resulting in delayed impacts, which are only partially addressed in current ecophysiological models. Here, we outline an updated integrated conceptual model of the annual cycle by identifying ecophysiological phenomena that are particularly significant under climate warming. © 2011 Elsevier Ltd.

Gonsamo A.,University of Helsinki
International Journal of Applied Earth Observation and Geoinformation | Year: 2010

This study is aimed at demonstrating the feasibility of the large scale LAI inversion algorithms using red and near infrared reflectance obtained from high resolution satellite imagery. Radiances in digital counts were obtained in 10m resolution acquired on cloud free day of August 23, 2007, by the SPOT 5 high resolution geometric (HRG) instrument on mostly temperate hardwood forest located in the Great Lakes - St. Lawrence forest in Southern Quebec. Normalized difference vegetation index (NDVI), scaled difference vegetation index (SDVI) and modified soil-adjusted vegetation index (MSAVI) were applied to calculate gap fractions. LAI was inverted from the gap fraction using the common Beer-Lambert's law of light extinction under forest canopy. The robustness of the algorithm was evaluated using the ground-based LAI measurements and by applying the methods for the independently simulated reflectance data using PROSPECT + SAIL coupled radiative transfer models. Furthermore, the high resolution LAI was compared with MODIS LAI product. The effects of atmospheric corrections and scales were investigated for all of the LAI retrieval methods. NDVI was found to be not suitable index for large scale LAI inversion due to the sensitivity to scale and atmospheric effects. SDVI was virtually scale and atmospheric correction invariant. MSAVI was also scale invariant. Considering all sensitivity analysis, MSAVI performed best followed by SDVI for robust LAI inversion from high resolution imagery. © 2010 Elsevier B.V. All rights reserved.

Soininen J.,University of Helsinki
Ecology | Year: 2014

The estimation of the relative roles of environment, space, and their interactions in structuring community composition is one of the central topics of community ecology. I conducted a quantitative review to determine if the degree of species sorting (SS) by the abiotic environment varied predictably between organism types and ecosystems. SS was quantified as the relative fraction of community variation that is explained by environmental variables. I integrated data from 326 variation partition analyses in a generalized linear model, and found that a mean of 26.1% (minimum 0%, maximum 88%) of the variance in community composition was explained by environmental variables. I also found that organism body size and dispersal group were not related to the degree of SS. SS varied among trophic positions, being highest in autotrophs and omnivores and lowest in herbivores and decomposers. SS also varied among ecosystem types: it was lowest in lakes and highest in estuaries and marine environments. Studies using abundance data showed a higher degree of SS than studies based on presence-absence data. SS was lower when data sets were analyzed by spatial filters instead of by polynomials. These results suggest that although significant among-group differences emerged for trophic position and ecosystem type, variation in SS across body sizes or across different dispersal groups was relatively unpredictable. Nonetheless, these findings shed light on how the degree of SS varies across ecosystems or organism groups and may give important insights into the magnitude of environmental effects on biotic communities in a changing environment. © 2014 by the Ecological Society of America.

Background: Levosimendan has pharmacologic and hemodynamic advantages over conventional intravenous inotropic agents. It has been used mainly as a rescue drug in the pediatric intensive care unit or in the operating room. We present the largest single-center experience of levosimendan in children.Methods: Retrospective analysis of all children who received levosimendan infusions between July 5, 2001 and July 4, 2010 in a pediatric intensive care unit. The results of a questionnaire for physicians (anesthesiologist/intensivists, cardiologists and cardiac surgeons) concerning their clinical perceptions of levosimendan are evaluated. Results: During the study period a total of 484 infusions were delivered to 293 patients 53% of whom were male. The median age of the patients was 0.4 years (4 hours-21.1 years) at the time of levosimendan administration. A majority of levosimendan infusions were administered to children who were undergoing cardiac surgery (72%), 14% to children with cardiomyopathy and 14% to children with cardiac failure. Eighty-nine out of the 293 patients (30.4%) received repeated doses of levosimendan (up to 11 infusions). The most common indication for the use of levosimendan (94%) was when the other inotropic agents were insufficient to maintain stable hemodynamics. Levosimendan was especially used in children with cardiomyopathy (100%) or with low cardiac output syndrome (94%). A majority (89%) of the respondents believed that levosimendan administration postponed the need for mechanical assist devices in some children with cardiomyopathy. Moreover, 44% of respondents thought that the mechanical support was totally avoided in some patients undergoing cardiac surgery after receiving levosimendan.Conclusion: Levosimendan is widely used in our institution and many physicians believe that its use could decrease the need for mechanical support in children undergoing cardiac surgery or in children with decompensated heart failure. However, there is a lack of good empirical evidence in children to support this perception. © 2011 Suominen; licensee BioMed Central Ltd.

Thomas S.M.,University of Helsinki | Crowther T.W.,Yale University
Journal of Animal Ecology | Year: 2015

The stable isotopes of carbon (12C, 13C) and nitrogen (14N, 15N) represent powerful tools in food web ecology, providing a wide range of dietary information in animal consumers. However, identifying the temporal window over which a consumer's isotopic signature reflects its diet requires an understanding of elemental incorporation, a process that varies from days to years across species and tissue types. Though theory predicts body size and temperature are likely to control incorporation rates, this has not been tested empirically across a morphologically and phylogenetically diverse range of taxa. Readily available estimates of this relationship would, however, aid in the design of stable isotope food web investigations and improve the interpretation of isotopic data collected from natural systems. Using literature-derived turnover estimates from animal species ranging in size from 1 mg to 2000 kg, we develop a predictive tool for stable isotope ecologists, allowing for estimation of incorporation rates in the structural tissues of entirely novel taxa. In keeping with metabolic scaling theory, we show that isotopic turnover rates of carbon and nitrogen in whole organisms and muscle tissue scale allometrically with body mass raised approximately to the power -0·19, an effect modulated by body temperature. This relationship did not, however, apply to incorporation rates in splanchnic tissues, which were instead dependent on the thermoregulation tactic employed by an organism, being considerably faster in endotherms than ectotherms. We believe the predictive turnover equations we provide can improve the design of experiments and interpretation of results obtained in future stable isotopic food web studies. © 2014 British Ecological Society.

Lehtonen H.J.,University of Helsinki
Familial Cancer | Year: 2011

Hereditary leiomyomatosis and renal cell cancer (HLRCC, also known as multiple cutaneous and uterine leiomyomatosis, MCUL) is a highly penetrant autosomal dominant tumor predisposition syndrome characterized by benign leiomyomas of the skin and the uterus. Renal cell carcinomas, occurring in a subset of the HLRCC families, are exceptionally aggressive. Therefore careful, frequent surveillance strategies are recommended. Association of malignant smooth-muscle tumors, leiomyosarcomas, with HLRCC has been observed but the risk appears to be smaller than initially estimated. To date inactivating heterozygous mutations in the fumarate hydratase (FH, fumarase) gene, predisposing to HLRCC, have been found in approximately 180 families worldwide. The most extensively studied hypothesis on molecular mechanisms of HLRCC tumorigenesis is activation of the hypoxia pathway due to aberrant stabilization of the HIF1 transcription factor. HIF1 regulates transcription of genes relevant for vascularization, glucose transport and glycolysis, processes that facilitate tumor growth. However, additional mechanisms underlying tumor formation are likely to exist. © 2011 Springer Science+Business Media B.V.

Differentiated epithelial structure communicates with individual constituent epithelial cells to suppress their proliferation activity. However, the pathways linking epithelial structure to cessation of the cell proliferation machinery or to unscheduled proliferation in the context of tumorigenesis are not well defined. Here we demonstrate the strong impact of compromised epithelial integrity on normal and oncogenic Myc-driven proliferation in three-dimensional mammary epithelial organoid culture. Systematic silencing of 34 human homologs of Drosophila genes, with previously established functions in control of epithelial integrity, demonstrates a role for human genes of apico-basal polarity, Wnt and Hippo pathways and actin dynamics in regulation of the size, integrity and cell proliferation in organoids. Perturbation of these pathways leads to diverse functional interactions with Myc: manifested as a RhoA-dependent synthetic lethality and Par6-dependent effects on the cell cycle. Furthermore, we show a role for Par6G as a negative regulator of the phosphatidylinositol 3′-kinase/phosphoinositide-dependent protein kinase 1/Akt pathway and epithelial cell proliferation and evidence for frequent inactivation of Par6G gene in epithelial cancers. The findings demonstrate that determinants of epithelial structure regulate the cell proliferation activity via conserved and cancer-relevant regulatory circuitries, which are important for epithelial cell cycle restriction and may provide new targets for therapeutic intervention.Oncogene advance online publication, 15 June 2015; doi:10.1038/onc.2015.196. © 2015 Macmillan Publishers Limited

Jokela M.,University of Helsinki | Jokela M.,University of Cambridge
Journal of Epidemiology and Community Health | Year: 2015

Background Neighbourhood deprivation has been associated with poor health. The evidence for social causation, however, remains scarce because selective residential mobility may also create neighbourhood differences. The present study examined whether individuals had poorer health when they were living in a deprived neighbourhood compared to another time when the same individuals were living in a less deprived neighbourhood. Methods Participants were from the British Household Panel Survey prospective cohort study with 18 annual measurements of residential location and self-reported health outcomes between 1991 and 2009 (n=137 884 person-observations of 17 001 persons in England). Neighbourhood deprivation was assessed concurrently with health outcomes using the Index of Multiple Deprivation at the geographically detailed level of Lower Layer Super Output Areas. The main analyses were replicated in subsamples from Scotland (n=4897) and Wales (n=4442). Multilevel regression was used to separate within-individual and between-individuals associations. Results Neighbourhood deprivation was associated with poorer self-rated health, and with higher psychological distress, functional health limitations and number of health problems. These associations were almost exclusively due to differences between different individuals rather than within-individual variations related to different neighbourhoods. By contrast, poorer health was associated with lower odds of moving to less deprived neighbourhoods among movers. The analysis was limited by the restricted within-individual variation and measurement imprecision of neighbourhood deprivation. Conclusions Individuals living in deprived neighbourhoods have poorer health, but it appears that neighbourhood deprivation is not causing poorer health of adults. Instead, neighbourhood health differentials may reflect the more fundamental social inequalities that determine health and ability to move between deprived and non-deprived neighbourhoods.

Tastula E.-M.,University of Helsinki | Vihma T.,Finnish Meteorological Institute
Monthly Weather Review | Year: 2011

The standard and polar versions 3.1.1 of the Weather Research and Forecasting (WRF) model, both initialized by the 40-yr ECMWF Re-Analysis (ERA-40), were run in Antarctica for July 1998. Four different boundary layer-surface layer-radiation scheme combinations were used in the standard WRF. The model results were validated against observations of the 2-m temperature, surface pressure, and 10-m wind speed at 9 coastal and 2 inland stations. The best choice for boundary layer and radiation parameterizations of the standard WRF turned out to be the Yonsei University boundary layer scheme in conjunction with the fifthgeneration Pennsylvania State University-National Center for Atmospheric Research Mesoscale Model (MM5) surface layer scheme and the Rapid Radiative Transfer Model for longwave radiation. The respective temperature bias was on the order of 3°C less than the biases obtained with the other combinations. Increasing the minimum value for eddy diffusivity did, however, improve the performance of the asymmetric convective scheme by 0.8°C. Averaged over the 11 stations, the error growths in 24-h forecasts were almost identical for the standard and Polar WRF, but in 9-day forecasts Polar WRF gave a smaller 2-m temperature bias. For the Vostok station, however, the standardWRF gave a less positively biased 24-h temperature forecast. On average, the polar version gave the least biased surface pressure simulation. Thewind speed simulationwas characterized by low correlation values, especially under weak winds and for stations surrounded by complex topography. © 2011 American Meteorological Society.

Peranen J.,University of Helsinki
Cytoskeleton | Year: 2011

Endogenous Rab8 is found in dynamic cell structures like filopodia, lamellipodia, protrusions, ruffles, and primary cilia. Activation of Rab8 is linked to the formation of these actin containing structures, whereas inhibition of Rab8 affects negatively their appearance. The activity of Rab8 is controlled by specific guanine nucleotide exchange factors and GTPase activating proteins. Rab8 regulates a membrane recycling pathway that is linked to Arf6, EHD1, Myo5, and Rab11. A hypothesis is presented on the role of Rab8 in the formation of new cell surface domains. The review focuses on the function of Rab8 in cell migration, epithelial polarization, neuron differentiation, and ciliogenesis. © 2011 Wiley-Liss, Inc.

Lassila R.,University of Helsinki
Seminars in Thrombosis and Hemostasis | Year: 2016

Factor (F) XIII deficiency is a congenital rare bleeding disorder (RBD), with an estimated prevalence of 1 in 1 to 2 million individuals, and more than 1,200 patients have been diagnosed to date. In newborns, umbilical cord bleeding is typical, and later in life during trauma, surgery and even spontaneously prolonged bleeds, reproduction, and delivery complications occur frequently without appropriate replacement therapy. Also, an acquired form of FXIII deficiency may occur via massive bleeds or neutralizing antibodies. In the inherited form of FXIII deficiency, prophylaxis with FXIII concentrate is administered to prevent the very high risk of intracranial bleeds, the incidence being close to 30%. Laboratory diagnosis of FXIII deficiency is based on measuring plasma FXIII antigen and activity, and it is claimed that FXIII activity of around 5 IU/dL would suffice to protect from bleeds. However, at the low levels of detection, most FXIII methods are inaccurate, and quality controls and collaboration with reference laboratories are important to improve the accuracy of low-level FXIII measurements. The trough target for prophylaxis should be set to 10 to 20 IU/dL, which is achievable by administration of 25 to 35 IU/kg every 4 to 6 weeks. However, general risk factors influencing hemostasis should be carefully evaluated, including anemia and hypertension. Fibrin cross-linking by FXIII is of major importance and red cells bind to fibrin partially via platelets and FXIII to promote clot strength. Physiologically, platelets and macrophages contain FXIII providing cellular support; thus, the patients may benefit from platelet transfusion during problematic bleeds. Plasma-derived and recently a recombinant FXIII concentrate are available; however, the latter has mainly anecdotal data regarding management of bleeds and surgery, and its access is limited due to the high cost. The international registry RBD database, (RBDD) continues to gain cumulative knowledge, and registration of all FXIII deficient patients, both inherited and acquired, is highly recommended. © 2016 by Thieme Medical Publishers, Inc.

Paivaniemi O.E.,University of Helsinki
Respiratory research | Year: 2011

Bronchial epithelium is a target of the alloimmune response in lung transplantation, and intact epithelium may protect allografts from rejection and obliterative bronchiolitis (OB). Herein we study the influence of chimerism on bronchial epithelium and OB development in pigs. A total of 54 immunosuppressed and unimmunosuppressed bronchial allografts were serially obtained 2-90 days after transplantation. Histology (H&E) was assessed and the fluorescence in situ hybridization (FISH) method for Y chromosomes using pig-specific DNA-label was used to detect recipient derived cells in graft epithelium and bronchial wall, and donor cell migration to recipient organs. Ingraft chimerism was studied by using male recipients with female donors, whereas donor cell migration to recipient organs was studied using female recipients with male donors. Early appearance of recipient-derived cells in the airway epithelium appeared predictive of epithelial destruction (R=0.610-0.671 and p<0.05) and of obliteration of the bronchial lumen (R=0.698 and p<0.01). All allografts with preserved epithelium showed epithelial chimerism throughout the follow-up. Antirejection medication did not prevent, but delayed the appearance of Y chromosome positive cells in the epithelium (p<0.05), or bronchial wall (p<0.05). In this study we demonstrate that early appearance of Y chromosomes in the airway epithelium predicts features characteristic of OB. Chimerism occurred in all allografts, including those without features of OB. Therefore we suggest that ingraft chimerism may be a mechanism involved in the repair of alloimmune-mediated tissue injury after transplantation.

Kinnari T.J.,University of Helsinki
Current Opinion in Otolaryngology and Head and Neck Surgery | Year: 2015

Purpose of review The importance of bacterial biofilm in the human body, both when associated in chronic infections and as the default mode of microbial growth in the normal flora, has been understood during the last two decades. The word biofilm has recently entered into clinical vocabulary especially in dentistry, and oral hygienists have begun to talk of oral or dental biofilm instead of oral plaque. Biofilm presence has been demonstrated widely in otorhinolaryngology, related to chronic infections of middle ear, paranasal sinuses and lymphoid tissue of adenoids and tonsils and to implanted materials; however, less literature exists considering the implication of biofilm to laryngeal infections or head and neck cancer. The research until now has been mainly descriptive and the mechanisms that lead to biofilm formation are unclear and thus there are limited options for specific treatment of biofilm infection. The focus of this article is to review the recent literature considering the bacterial biofilm in larynx and in head and neck surgery. Recent findings Bacterial biofilm has now also been implicated in chronic laryngitis. Among head and neck cancer patients, biofilm is the main reason for the short life cycle of indwelling devices such as voice prostheses and tracheal tubes. Recently, bacterial biofilm has been related to dysplasia and malignancies both as an aetiological factor and as a source of complications. Summary It has been shown that microbial biofilm is implicated in the mechanisms leading to chronic recalcitrant infections, implant contamination and even to dysplasia. Biofilm has an important role in finding new preventive measures and treatment of these diseases. © 2015 Wolters Kluwer Health, Inc. All rights reserved.

Haanpaa M.,University of Helsinki | Treede R.-D.,University of Heidelberg
European Neurology | Year: 2012

Capsaicin has long been used as a traditional medicine to treat pain and, recently, its mechanism of analgesic action has been discovered. This review article documents the clinical development of capsaicin to demonstrate that pharmacognosy still has a profound influence on modern-day drug development programs. Capsaicin is a highly selective agonist for the transient receptor potential channel vanilloid-receptor type 1 (TRPV1), which is expressed on central and peripheral terminals of nociceptive primary sensory neurons. Knockout studies have revealed the importance of TRPV1 as a molecular pain integrator and target for novel analgesic agents. Topical application of capsaicin at the peripheral terminal of TRPV1-expressing neurons superficially denervates the epidermis in humans in a highly selective manner and results in hypoalgesia. In three recent randomized controlled trials, a patch containing high-concentration capsaicin demonstrated meaningful efficacy and tolerability relative to a low-concentration capsaicin control patch in patients with peripheral neuropathic pain. Data from clinical practice will determine if the high-concentration capsaicin patch is effective in real-world settings. Copyright © 2012 S. Karger AG, Basel.

Lassila R.,University of Helsinki
Seminars in Thrombosis and Hemostasis | Year: 2016

Functional disorders of platelets can involve any aspect of platelet physiology, with many different effects or outcomes. These include platelet numbers (thrombocytosis or thrombocytopenia); changes in platelet production or destruction, or capture to the liver (Ashwell receptor); altered adhesion to vascular injury sites and/or influence on hemostasis and wound healing; and altered activation or receptor functions, shape change, spreading and release reactions, procoagulant and antifibrinolytic activity. Procoagulant membrane alterations, and generation of thrombin and fibrin, also affect platelet aggregation. The above parameters can all be studied, but standardization and quality control of assay methods have been limited despite several efforts. Only after a comprehensive clinical bleeding assessment, including family history, information on drug use affecting platelets, and exclusion of coagulation factor, and tissue deficits, should platelet function testing be undertaken to confirm an abnormality. Current diagnostic tools include blood cell counts, platelet characteristics according to the cell counter parameters, peripheral blood smear, exclusion of pseudothrombocytopenia, whole blood aggregometry (WBA) or light transmission aggregometry (LTA) in platelet-rich plasma, luminescence, platelet function analysis (PFA-100) for platelet adhesion and deposition to collagen cartridges under blood flow, and finally transmission electron microscopy to exclude rare structural defects leading to functional deficits. The most validated test panels are included in WBA, LTA, and PFA. Because platelets are isolated from their natural environment, many simplifications occur, as circulating blood and interaction with vascular wall are omitted in these assays. The target to reach a highly specific platelet disorder diagnosis in routine clinical management can be exhaustive, unless needed for genetic counseling. The elective overall assessment of platelet function disorder primarily aims at better management of hemostasis in case of emergency surgery or other interventions and acute bleeding events. Copyright © 2016 by Thieme Medical Publishers, Inc.

de Vos W.M.,Wageningen University | de Vos W.M.,University of Helsinki | De Vos E.A.J.,University of Amsterdam
Nutrition Reviews | Year: 2012

Recorded observations indicating an association between intestinal microbes and health are long-standing in terms of specific diseases, but emerging high-throughput technologies that characterize microbial communities in the intestinal tract are suggesting new roles for the supposedly normal microbiome. This review considers the nature of the evidence supporting a relationship between the microbiota and the predisposition to disease as associative, correlative, or causal. Altogether, indirect or associative support currently dominates the evidence base, which now suggests that the intestinal microbiome can be linked to a growing number of over 25 diseases or syndromes. While only a handful of cause-and-effect studies have been performed, this form of evidence is increasing. The results of such studies are expected to be useful in monitoring disease development, in providing a basis for personalized treatments, and in indicating future therapeutic avenues. © 2012 International Life Sciences Institute.

Helve O.,University of Helsinki
Journal of Medical Internet Research | Year: 2014

Background: Social media is used increasingly by the general public to access health information. However, a lack of models for health information distribution limits the presence of publicly funded services on social media sites. Objective: The goal of the study was to present a model for delivering child health information to parents through a social media site. Methods: A Facebook site was launched for 11 months based on a question-and-answer service produced by a pediatrician and open to Facebook users over 18 years old. If the answer did not include a further referral to a health care service provider, the question was considered comprehensively answered. The site was funded by a pharmaceutical company, and it included an advertisement of a pharmaceutical product for children's fever and pain. Results: During the study, 768 questions were submitted: an average of 69.8 (SD 31.7) per month. There were 245,533 independent Facebook users on the site, with an average of 727.0 (SD 2280.6) per day. Infections were the most common theme in questions (355/768, 46.2%). Questions were more likely to be comprehensively answered if they were related to infections (279/355, 78.6%) than questions related to non-infectious symptoms (265/423, 64.2%, P=.003). Conclusions: On this site aimed at parents of small children, personalized answers were an effective way of delivering information. The service is likely to have reduced the need for further contacts with a health care service provider in more than half of the cases. The site could serve as a model for publicly funded health information distribution.

Here, I present the first comparison of the abundance of farmland birds in energy grass fields and in cereal-dominated conventionally cultivated fields (CCFs). I demonstrate that in boreal farmland, skylark (Alauda arvensis) densities were significantly lower in reed canary grass (RCG) (Phalaris arundinacea) fields than in CCFs. I found that during the early breeding season RCG fields and CCFs are equally good habitats, but over the ensuing couple of weeks RCG rapidly grows too tall and dense for field-nesting species. Consequently, RCG is an inferior habitat for skylark for laying replacement clutches (after failure of first nesting) or for a second clutch after one successful nesting. The results imply that if RCG cultivation is to be expanded, the establishment of large monocultures should be avoided in farmland landscapes; otherwise the novel habitat may affect detrimentally the seriously depleted skylark population, and probably also other field-nesting bird species with similar breeding habitats. © 2010 Elsevier Ltd.

Sundholm D.,University of Helsinki
Physical Chemistry Chemical Physics | Year: 2013

A new allotropic form of carbon is proposed. The molecular structure of a cavernous C72 molecule has been optimized at the density functional theory level. The structure belonging to the Oh point group was found to be a minimum on the potential energy surface. Current-density calculations show that the gaudiene molecule with formally 72 π electrons sustains strong diatropic currents when exposed to an external magnetic field. © 2013 the Owner Societies.

Partinen M.,Vitalmed Research Center | Partinen M.,University of Helsinki | Kornum B.R.,Molecular Sleep Laboratory | Plazzi G.,University of Bologna | And 5 more authors.
The Lancet Neurology | Year: 2014

Narcolepsy is a sleep disorder characterised by loss of hypothalamic hypocretin (orexin) neurons. The prevalence of narcolepsy is about 30 per 100 000 people, and typical age at onset is 12-16 years. Narcolepsy is strongly associated with the HLA-DQB1*06:02 genotype, and has been thought of as an immune-mediated disease. Other risk genes, such as T-cell-receptor α chain and purinergic receptor subtype 2Y11, are also implicated. Interest in narcolepsy has increased since the epidemiological observations that H1N1 infection and vaccination are potential triggering factors, and an increase in the incidence of narcolepsy after the pandemic AS03 adjuvanted H1N1 vaccination in 2010 from Sweden and Finland supports the immune-mediated pathogenesis. Epidemiological observations from studies in China also suggest a role for H1N1 virus infections as a trigger for narcolepsy. Although the pathological mechanisms are unknown, an H1N1 virus-derived antigen might be the trigger. © 2014 Elsevier Ltd.

Zhang Y.,University of Helsinki
Quality of life research : an international journal of quality of life aspects of treatment, care and rehabilitation | Year: 2014

To examine and compare health-related quality of life (HRQoL) in people with previously known diabetes, new screen-detected asymptomatic diabetes and people without diabetes. HRQoL of 4,613 individuals who participated in a population-based cross-sectional diabetes survey in Qingdao, China, in 2009, was assessed using the 15D instrument. A Tobit regression model to estimate the effects of diabetes on HRQoL separate from effects of other health determinants was constructed. Among the surveyed population, 220 (4.8%) individuals had previously known diabetes and 531 (11.5%) individuals had new screen-detected diabetes, defined by fasting plasma glucose ≥7.0 mmol/l and/or 2-h plasma glucose ≥11.1 mmol/l. The age-, gender-, and BMI-adjusted mean 15D score of people without diabetes, with new screen-detected diabetes, and previously known diabetes was 0.975, 0.975, and 0.964, respectively, for urban and 0.971, 0.972, and 0.960, respectively, for rural participants. HRQoL overall and on all the dimensions (p < 0.05) except for hearing, eating, and speech was worse in the people with previously known diabetes compared to those with new screen-detected diabetes and those without diabetes. Compared to people without diabetes, people with new screen-detected diabetes were worse off on the dimension of usual activities (p < 0.05). After adjusting for comorbid diseases and other confounders, the impact of diabetes on reduced HRQoL was diminished. Health-related quality of life was impaired in people with previously known diabetes who had co-morbid conditions, but was largely unaltered in people with newly detected asymptomatic diabetes as compared to people without diabetes.

Kukkonen J.P.,University of Helsinki
Cell Calcium | Year: 2011

Recent technical and conceptual advances in lipid analysis have given us a glimpse into the true versatility of the lipidome and the complexity of lipid signaling species. Progress alike in protein chemistry and genetics has presented us with new signal pathways and molecular mechanisms for the lipid actions. G-protein-coupled receptors (GPCR) appear to play a central role in the regulation of many lipid signals and are also themselves targets for some of these. TRP channels have recently been acknowledged as one of the most important GPCR effectors; in many cases the signals from GPCRs to TRPs are mediated via lipid signals. This review aims at presenting a view into the complex lipid signaling networks, their possible regulation by GPCRs and the signals transmitted to the TRP channels. Critical views and possible shortcomings in the composition of the studies are also presented. © 2011 Elsevier Ltd.

Michon F.,University of Helsinki
Birth Defects Research Part A - Clinical and Molecular Teratology | Year: 2011

Teeth, like all epithelial appendages, form via a sequential and reciprocal series of inductive signals between the epithelium and the underlying mesenchyme. The genes involved in this signaling network regulating ectodermal organ development have been highly conserved during evolution and are gaining more understanding in great detail. The specific functions of numerous genes during embryogenesis are known, and the involvement of their mutations in the pathogenesis of congenital defects is being extensively studied. Recently, the micro-RNA (miRNA) pathway has been associated with various aspects of embryogenesis including ectodermal organ formation and odontogenesis. In this review, I presented the genetic network involved during tooth formation and evolution, and several mutations that give rise to dental defects. The possible impact of fine-tuning and network regulation by miRNAs on development, evolution of teeth, and defects are, therefore, discussed. © 2011 Wiley-Liss, Inc.

Van Heurn L.W.E.,Maastricht University | Pakarinen M.P.,University of Helsinki | Wester T.,Karolinska University Hospital
British Journal of Surgery | Year: 2014

Background: Acute abdominal complaints in children are common presentations in the emergency department. The aetiology, presentation, diagnosis and management often differ from those in adults. Methods: This review was based on expert paediatric surgical experience confirmed by evidence from the literature obtained by searching PubMed and the Cochrane Library. Keywords used were the combinations of 'abdominal emergencies', 'acute abdomen' and the disorders 'acute appendicitis', 'intussusception', 'volvulus', 'Meckel's diverticulum', 'incarcerated inguinal hernia', 'testicular torsion' and 'ovarian torsion' with 'children'. Information was included from reviews, randomized clinical trials, meta-analyses, and prospective and retrospective cohort studies. Results: Presentation and symptoms of abdominal emergencies, especially in young children, vary widely, which renders recognition of the underlying disorder and treatment challenging. Critically targeted imaging techniques are becoming increasingly important in obtaining the correct diagnosis without unnecessary delay. Minimally invasive techniques have become the method of choice for the diagnosis and treatment of many abdominal emergencies in children. Conclusion: Knowledge of abdominal disorders in childhood, their specific presentation, diagnosis and treatment facilitates management of children with acute abdomen in emergency departments. Imaging and minimally invasive techniques are becoming increasingly important in the diagnosis of acute abdomen in children. Urgent operation remains the cornerstone of therapy for most acute abdominal disorders. © 2013 BJS Society Ltd.

Subject pronoun usage in Romance null-subject languages is often presented as a general, binary, language-wide phenomenon conditioned e.g. by sociolinguistic or information-structural factors. This paper argues that subject expression or omission should also be examined in specific local contexts where it may exhibit patterns of usage that diverge from the general tendencies. The study analyses the use of first person singular subject pronouns in high-frequency epistemic constructions containing the verbs creer 'think' in Peninsular Spanish and achar 'think' in European Portuguese spoken corpora. It is argued that the highly frequent expression of the first person singular subject pronoun in Spanish epistemic constructions is related to their higher degree of grammaticalization. In Portuguese the constructions appear to be less grammaticalized and do not exhibit a specific pattern of subject expression. The difference between the two languages is linked with the higher normalized frequency of the constructions in Spanish than in Portuguese which permits the entrenchment of a specific subject expression pattern. In addition, the fact that the original meaning of achar is 'find' and its use as a mental verb in Portuguese is a relatively recent development may explain that the verb does not exhibit subject expression patterns typical of other mental verbs in Spanish and Portuguese. © 2013 Elsevier B.V.

Stenman U.-H.,University of Helsinki
Critical Reviews in Clinical Laboratory Sciences | Year: 2016

This review describes studies performed by our group and other laboratories in the field aimed at development of biomarkers not only for cancer but also for other diseases. The markers covered include tumor-associated trypsin inhibitor (TATI), tumor-associated trypsin (TAT), human chorionic gonadotropin (hCG), prostate-specific antigen (PSA) and their various molecular forms, their biology and diagnostic use. The discovery of TATI was the result of a hypothesis-driven project aimed at finding new biomarkers for ovarian cancer among urinary peptides. TATI has since proved to be a useful prognostic marker for several cancers. Recently, it has been named Serine Peptidase Inhibitor Kazal Type 1 (SPINK1) after being rediscovered by several groups as a tumor-associated peptide by gene expression profiling and proteomic techniques and shown to promote tumor development by stimulating the EGF receptor. To explain why a trypsin inhibitor is strongly expressed in some cancers, research focused on the protease that it inhibited led to the finding of tumor-associated trypsin (TAT). Elevated serum concentrations of TAT-2 were found in some cancer types, but fairly high background levels of pancreatic trypsinogen-2 limited the use of TAT-2 for cancer diagnostics. However, trypsinogen-2 and its complex with α1-protease inhibitor proved to be very sensitive and specific markers for pancreatitis. Studies on hCG were initiated by the need to develop more rapid and sensitive pregnancy tests. These studies showed that serum from men and non-pregnant women contains measurable concentrations of hCG derived from the pituitary. Subsequent development of assays for the subunits of hCG showed that the β subunit of hCG (hCGβ) is expressed at low concentrations by most cancers and that it is a strong prognostic marker. These studies led to the formation of a working group for standardization of hCG determinations and the development of new reference reagents for several molecular forms of hCG. The preparation of intact hCG has been adopted as the fifth international standard by WHO. Availability of several well-defined forms of hCG made it possible to characterize the epitopes of nearly 100 monoclonal antibodies. This will facilitate design of immunoassays with pre-defined specificity. Finally, the discovery of different forms of immunoreactive PSA in serum from a prostate cancer patient led to identification of the complex between PSA and α1-antichymotrypsin, and the use of assays for free and total PSA in serum for improved diagnosis of prostate cancer. Epitope mapping of PSA antibodies and establishment of PSA standards has facilitated establishment well-standardized assays for the various forms of PSA. © 2015 Taylor and Francis.

Dittmann E.,University of Potsdam | Fewer D.P.,University of Helsinki | Neilan B.A.,University of New South Wales
FEMS Microbiology Reviews | Year: 2013

Cyanobacteria produce an unparalleled variety of toxins that can cause severe health problems or even death in humans, and wild or domestic animals. In the last decade, biosynthetic pathways have been assigned to the majority of the known toxin families. This review summarizes current knowledge about the enzymatic basis for the production of the hepatotoxins microcystin and nodularin, the cytotoxin cylindrospermopsin, the neurotoxins anatoxin and saxitoxin, and the dermatotoxin lyngbyatoxin. Elucidation of the biosynthetic pathways of the toxins has paved the way for the development of molecular techniques for the detection and quantification of the producing cyanobacteria in different environments. Phylogenetic analyses of related clusters from a large number of strains has also allowed for the reconstruction of the evolutionary scenarios that have led to the emergence, diversification, and loss of such gene clusters in different strains and genera of cyanobacteria. Advances in the understanding of toxin biosynthesis and evolution have provided new methods for drinking-water quality control and may inspire the development of techniques for the management of bloom formation in the future. We report the biosynthetic pathways of cyanobacterial toxins and describe the evolutionary scenarios that have led to the emergence, diversification and loss of such gene clusters. © 2012 Federation of European Microbiological Societies.

Shcherbakova D.M.,Yeshiva University | Verkhusha V.V.,Yeshiva University | Verkhusha V.V.,University of Helsinki
Current Opinion in Chemical Biology | Year: 2014

Recent progress in molecular engineering of genetically encoded probes whose spectral properties are controlled with light, such as photoactivatable, photoswitchable and reversibly switchable fluorescent proteins, has brought the new possibilities to bioimaging and super-resolution microscopy. The development of modern photoconvertible proteins is linked to the studies of light-induced chromophore transformations. Here, we summarize the current view on the chromophore chemistry in the photocontrollable fluorescent proteins. We describe both the fundamental principles and the specific molecular mechanisms underlying the irreversible and reversible chromophore photoconversions. We discuss advancements in super-resolution microscopy that became possible due to the engineering of new protein phenotypes and understanding of their chromophore transformations. © 2014 Elsevier Ltd.

Isopahkala-Bouret U.,University of Helsinki
Educational Gerontology | Year: 2013

The purpose of this study is to help understand the meaning of age as experienced by older university graduates. The participants of this study were Finnish healthcare and social work professionals who earned master's degrees in their late 40s and 50s. They were all female, and their main purpose of study was to upgrade credentials. The analysis was informed by the sociology of age. The research questions were the following: What kind of meaning did these older graduates give to their age? How did the social category of "old" influence their reflections on age? As a result, age was meaningful for the participants at least in three different ways. First, when age was seen as a resource, it referred to the prior life history, especially to all those earlier working experiences which have made the person who she was. Second, when age was seen as a difference, it referred to all those social and cultural differences that divided older and younger students. Third, when age was seen as a limiting option, it referred to the time that one had left to fulfill different life plans. © 2013 Copyright Taylor and Francis Group, LLC.

Taskinen S.,University of Helsinki
BJU international | Year: 2012

To evaluate sexual function and fertility in adult patients treated for posterior urethral valves (PUV) in childhood and to compare these patients with the normal population. To examine if patient characteristics such as chronic renal failure (CRF), history of cryptorchidism and bladder neck incision in childhood have an impact on sexual function. Information on sexual function was assessed using questions from the International Index of Erectile Function (IIEF). In addition, the patients were asked if they had had children or been treated for CRF. Out of 108 adult patients with PUV, 67 (62%) returned the questionnaires. Sexual function in these patients was compared with 201 controls and paternity rates were compared with a national database. The mean (sd) age of the patients and controls was 38 (9) and 38 (7) years, respectively. Six percent of the patients and 9% of the controls reported problems in achieving erection during sexual stimulation and 9% of the patients and 10% of the controls reported problems with the hardness of erection (P = nonsignificant). Ejaculation was absent in 1/61 sexually active patients (2%). The only significant risk factor in patients for erectile dysfunction (ED) was increasing age. Thirty-three (49%) of all 67 patients and four (57%) of the seven patients with kidney transplantation had had children. The paternity rates were similar to those in corresponding age groups of the general Finnish population. Eight patients (12%) had attempted to have children without success. Men treated for PUV have a similar prevalence of ED and similar paternity rates to men without PUV. Erectile function and paternity rates can be satisfactory in spite of CRF. © 2012 THE AUTHORS. BJU INTERNATIONAL © 2012 BJU INTERNATIONAL.

Hemila H.,University of Helsinki
BMJ Open | Year: 2013

Objective: To determine whether vitamin C administration influences exercise-induced bronchoconstriction (EIB). Design: Systematic review and meta-analysis. Methods: MEDLINE and Scopus were searched for placebo-controlled trials on vitamin C and EIB. The primary measures of vitamin C effect used in this study were: (1) the arithmetic difference and (2) the relative effect in the postexercise forced expiratory volume in 1 s (FEV1) decline between the vitamin C and placebo periods. The relative effect of vitamin C administration on FEV1 was analysed by using linear modelling for two studies that reported full or partial individual-level data. The arithmetic differences and the relative effects were pooled by the inverse variance method. A secondary measure of the vitamin C effect was the difference in the proportion of participants suffering from EIB on the vitamin C and placebo days. Results: 3 placebo-controlled trials that studied the effect of vitamin C on EIB were identified. In all, they had 40 participants. The pooled effect estimate indicated a reduction of 8.4 percentage points (95% CI 4.6 to 12) in the postexercise FEV1 decline when vitamin C was administered before exercise. The pooled relative effect estimate indicated a 48% reduction (95% CI 33% to 64%) in the postexercise FEV1 decline when vitamin C was administered before exercise. One study needed imputations to include it in the meta-analyses, but it also reported that vitamin C decreased the proportion of participants who suffered from EIB by 50 percentage points (95% CI 23 to 68); this comparison did not need data imputations. Conclusions: Given the safety and low cost of vitamin C, and the positive findings for vitamin C administration in the three EIB studies, it seems reasonable for physically active people to test vitamin C when they have respiratory symptoms such as cough associated with exercise. Further research on the effects of vitamin C on EIB is warranted.

Mutanen M.,University of Oulu | Kaila L.,University of Helsinki | Tabell J.,Laaksotie 28
Scientific Reports | Year: 2013

Rapid development of broad regional and international DNA barcode libraries have brought new insights into the species diversity of many areas and groups. Many new species, even within well-investigated species groups, have been discovered based initially on differences in DNA barcodes. We barcoded 437 collection specimens belonging to 40 pre-identified Palearctic species of the Elachista bifasciella group of moths (Lepidoptera, Elachistidae). Although the study group has been a subject of several careful morphological taxonomic examinations, an unexpectedly high number of previously undetected putative species is revealed, resulting in a 34% rise in species number in the study area. The validity of putative new species was subsequently supported with diagnostic morphological traits. We show that DNA barcodes provide a powerful method of detecting potential new species even in taxonomic groups and geographic areas that have previously been under considerable morphological taxonomic scrutiny.

Finnish differs from English and some other languages in that it has two 'yeah but' formats, joo mut ('yeah but') and nii mut ('yeah but'). Drawing on audio and videotaped talk-in-interaction between friends and relatives, and on conversation analysis as a method, I examine the extent to which these two formats share functions and to which extent they are used differently. This study argues that the basic difference between the two 'yeah but' formats in Finnish is that one disengages from the line of action that was projected by the prior speaker and one engages in it. The disengaging joo mut utterance implies that the participants' perspectives on the topic are divergent. The speaker of a joo mut utterance thus excludes at least some part of the opinion or the viewpoint of the prior speaker from the on-going discussion and, in addition, often suggests a closure of the sequence. By contrast, the engaging nii mut utterance is used when the speakers share some overall action line. Furthermore, the speaker of a nii mut utterance implies that the opinion or the prior speaker's viewpoint is included in her/his own position and projects to expand the on-going sequence. © 2013 Elsevier B.V.

Nadykto, Yu, Jakovleva, Herb and Xu have recently reported a DFT study on the structure and formation thermodynamics of sulfuric acid-base-water clusters, with ammonia and a handful of amines as bases [1]. This study partially overlaps with our previous work [2], and a significant part of the discussion in their manuscript concerns differences between their results and ours. This comment is intended to address some issues related to that discussion. Specifically, it is shown that the errors related to basis-set effects in our calculations are very likely much smaller than claimed by Nadykto et al. [1]. Composite calculations including e.g., higher-level electron correlation also agree better with our results. © 2011 by the author.

AIM - Culture is often used as a wildcard in cross-cultural studies. This article proposes a more diverse understanding of culture, as layered from "deep structures" towards institutional arrangements. It analyses which cultural levels are involved in Finnish and French social workers' understanding of problem drinking, gambling and eating. DESIGN - A stimulated focus group method (Reception Analytical Group Interview) RAGI was applied to eight groups of Finnish and five groups of French social workers not specialised in addiction. The interviews were analysed with a semiotic approach. RESULTS - Finnish social workers understand problem drinking, gambling and eating as rooted in society and harming the social environment. It is the individual's responsibility to solve the problem. French social workers conceptualise only problem eating similar to problem drinking as being caused by an individual defect. They identify problem gambling as a social issue. CONCLUSIONS - The results imply that both the institutional context and structures deeper in culture influence how we conceptualise excessive behaviours. This shows the usefulness of a layered concept of culture. The article recommends caution in using "addiction" as an umbrella concept for all kinds of excessive behaviours, as the perception of each problem depends not only on culture, but on the different cultural levels. Problem gambling in particular seems to evoke multiple understandings.

Alitalo K.,University of Helsinki
Cell Metabolism | Year: 2012

Striking results reported by Okuno et al. (2012) in the July issue of Nature Medicine show that the ataxia telangiectasia mutated (ATM) kinase counteracts excessive oxygen radical production in immature angiogenic blood vessels. Its deletion results in activation of the mitogen-activated protein kinase p38α and arrest of pathological angiogenesis. © 2012 Elsevier Inc.

Teeth develop as ectodermal appendages from epithelial and mesenchymal tissues. Tooth organogenesis is regulated by an intricate network of cell-cell signaling during all steps of development. The dental hard tissues, dentin, enamel, and cementum, are formed by unique cell types whose differentiation is intimately linked with morphogenesis. During evolution the capacity for tooth replacement has been reduced in mammals, whereas teeth have acquired more complex shapes. Mammalian teeth contain stem cells but they may not provide a source for bioengineering of human teeth. Therefore it is likely that nondental cells will have to be reprogrammed for the purpose of clinical tooth regeneration. Obviously this will require understanding of the mechanisms of normal development. The signaling networks mediating the epithelial-mesenchymal interactions during morphogenesis are well characterized but the molecular signatures of the odontogenic tissues remain to be uncovered.

Salazar-Ciudad I.,University of Helsinki | Salazar-Ciudad I.,Autonomous University of Barcelona
Current Opinion in Genetics and Development | Year: 2012

Teeth are a good system for studying development and evolution. Tooth development is largely independent of the rest of the body and teeth can be grown in culture to attain almost normal morphology. Their development is not affected by the patterns of movement or sensorial perception in the embryo. Teeth are hard and easily preserved. Thus, there is plenty of easily accessible information about the patterns of morphological variation occurring between and within species. This review summarises recent work and describes how tooth development can be understood as the coupling between a reaction-diffusion system and differential growth produced by diffusible growth factors: which growth factors are involved, how they affect each other's expression and how they affect the spatial patterns of proliferation that lead to final morphology. There are some aspects of tooth development, however, that do not conform to some common assumptions in many reaction-diffusion models. Those are discussed here since they provide clues about how reaction-diffusion systems may work in actual developmental systems. Mathematical models implementing what we know about tooth development are discussed. © 2012 Elsevier Ltd.

Context Impact avoidance and biodiversity offsetting are measures that can be used for alleviating environmental impacts of economic development projects. Offsetting is frequently implemented via habitat restoration. Biodiversity offsets should be designed in a cost-effective manner. Aims To investigate how spatial conservation prioritisation methods, most commonly used for reserve network design, could be used for informing impact avoidance and biodiversity offsetting. Methods Zonation is a publicly available framework and software for grid-based, large-scale, high-resolution spatial conservation prioritisation. Zonation produces a hierarchical, balanced, and complementarity-based priority ranking through the landscape, identifying areas of both highest and lowest conservation value in one analysis. It is shown how these capabilities can be utilised in the context of impact avoidance and offsetting. Key results Impact avoidance can be implemented by focusing environmentally harmful activity into low-priority areas of the spatial priority ranking. Offsets can be implemented via a more complicated analysis setup. First, identify development areas unavailable for conservation, which leads to a decrease in the quality of conservation value achievable in the landscape. Second, develop compensation layers that describe the difference made by allocation of extra conservation action. Running a spatial prioritisation, integrating information about where species are (representation), what areas and features are damaged (reduced condition and negative connectivity effects), and the difference made by remedial action, allows identification of areas where extra conservation effort maximally compensates for damage. Factors such as connectivity and costs can be included in this analysis. Impact avoidance and offsetting can also be combined in the procedure. Conclusions Spatial conservation-prioritisation methods can inform both impact avoidance and offsetting design. Implications Decision support tools that are commonly associated with reserve selection can be used for planning of impact avoidance and offsetting, conditional on the availability of high-quality data about the distributions of biodiversity features (e.g. species, habitat type, ecosystem services). © 2013 CSIRO.

Donato D.C.,U.S. Department of Agriculture | Kauffman J.B.,U.S. Department of Agriculture | Murdiyarso D.,Center for International Forestry Research | Kurnianto S.,Center for International Forestry Research | And 2 more authors.
Nature Geoscience | Year: 2011

Mangrove forests occur along ocean coastlines throughout the tropics, and support numerous ecosystem services, including fisheries production and nutrient cycling. However, the areal extent of mangrove forests has declined by 30-50% over the past half century as a result of coastal development, aquaculture expansion and over-harvesting 1-4. Carbon emissions resulting from mangrove loss are uncertain, owing in part to a lack of broad-scale data on the amount of carbon stored in these ecosystems, particularly below ground 5. Here, we quantified whole-ecosystem carbon storage by measuring tree and dead wood biomass, soil carbon content, and soil depth in 25 mangrove forests across a broad area of the Indo-Pacific region-spanning 30° of latitude and 73° of longitude-where mangrove area and diversity are greatest 4,6. These data indicate that mangroves are among the most carbon-rich forests in the tropics, containing on average 1,023 Mg carbon per hectare. Organic-rich soils ranged from 0.5 m to more than 3m in depth and accounted for 49-98% of carbon storage in these systems. Combining our data with other published information, we estimate that mangrove deforestation generates emissions of 0.02-0.12 Pg carbon per year-as much as around 10% of emissions from deforestation globally, despite accounting for just 0.7% of tropical forest area 6,7. © 2011 Macmillan Publishers Limited. All rights reserved.

Januzzi J.L.,Massachusetts General Hospital | Filippatos G.,National and Kapodistrian University of Athens | Nieminen M.,University of Helsinki | Gheorghiade M.,Northwestern University
European Heart Journal | Year: 2012

Cardiac troponin testing is commonly performed in patients with heart failure (HF). Despite being strongly linked to spontaneous (Type I) acute myocardial infarction (MI)a common cause of acute HF syndromesit is well recognized that concentrations of circulating troponins above the 99th percentile of a normal population in the context of both acute and chronic HF are highly prevalent, and frequently unrelated to Type I MI. Other mechanism(s) leading to troponin elevation in HF syndromes remain elusive in many cases but prominently includes supplydemand inequity (Type II MI), which may be associated with coronary artery obstruction and endothelial dysfunction, or may occur in the absence of coronary obstruction due to increased oxygen demand related to increased wall tension, anaemia, or other factors provoking subendocardial injury. Non-coronary triggers, such as cellular necrosis, apoptosis, or autophagy in the context of wall stress may explain the troponin release in HF, as can toxic effects of circulating neurohormones, toxins, inflammation, and infiltrative processes, among others. Nonetheless, across a wide spectrum of HF syndromes, when troponin elevation occurs, independent of mechanism, it is strongly predictive of an adverse outcome. Clinicians should be aware of the high frequency of troponin elevation when measuring the marker in patients with HF, should keep in mind the possible causes of this phenomenon, and, independent of a diagnosis of 'acute MI', should recognize the considerable ramifications of troponin elevation in this setting. © 2011 The Author.

Henriksson K.O.E.,University of Helsinki
Nuclear Instruments and Methods in Physics Research, Section B: Beam Interactions with Materials and Atoms | Year: 2015

Ferritic stainless steel can be modeled as an iron matrix containing precipitates of cementite (Fe3C) and Cr23C6. When used in nuclear power production the steels in the vicinity of the core start to accumulate damage due to neutrons. The role of the afore-mentioned carbides in this process is not well understood. In order to clarify the situation bulk cascades created by primary recoils in model steels have been carried out in the present work. Investigated configurations consisted of bulk ferrite containing spherical particles (diameter of 4 nm) of either (1) Fe3C or (2) Cr23C6. Primary recoils were initiated at different distances from the inclusions, with recoil energies varying between 100 eV and 1 keV. Results for the number of point defects such as vacancies and antisites are presented. These findings indicate that defects are also remaining when cascades are started outside the carbide inclusions. The work uses a recently developed Abell-Brenner-Tersoff potential for the Fe-Cr-C system. © 2014 Elsevier B.V. All rights reserved.

Klippi A.,University of Helsinki
Aphasiology | Year: 2015

Background: Relatively few qualitative studies have been published on the role of the embodied practices related to aphasic language problems during talk-in-interaction. It has been suggested that one way of adapting to aphasic language is by using different types of embodied practices. The use of embodied practices may reflect an effort to facilitate impaired verbal processing or their use may function as compensatory behavior to deal with troubles arising during conversation or to avoid these troubles arising in the first place. Pointing gestures may refer to the immediate physical environment, such as to a specific object or a specific place, to another participant, or even to speakers themselves. Occasionally, a pointing gesture may refer to more abstract entities, such as distant places or specific moments.Aims: The aim of this article is to explore conversational sequences with persons with aphasia (PWAs) that contain several pointing gestures. It is analysed how PWAs use pointing gestures in conversation when they are faced with complex comprehension problems as well as verbal output problems.Methods & Procedures: The method of conversation analysis is applied in this study.Outcomes & Results: The qualitative analysis in this study supports the assertion that pointing gestures are significant actions in conversation. Pointing is used in various places in talk where PWAs are experiencing difficulty, such as when problems occur in language comprehension as well as in language production, for example, in the absence of a specific word or the grammatical constructions that are needed. The results suggest that pointing gestures are used in a number of ways as an interactional resource. However, the identification of the referent may need extensive interactional work by the participants.Conclusions: These findings suggest that embodied interaction should be explored more extensively in aphasic talk-in-interaction. Conversation with PWAs is a joint and multimodal activity, which also needs to be taken into account in intervention targeted at aphasia. © 2014, © 2014 Taylor & Francis.

Jauhiainen J.,University of Helsinki | Hooijer A.,Deltares | Page S.E.,University of Leicester
Biogeosciences | Year: 2012

Peat surface CO2 emission, groundwater table depth and peat temperature were monitored for two years along transects in an Acacia plantation on thick tropical peat (>4 m) in Sumatra, Indonesia. A total of 2300 emission measurements were taken at 144 locations, over a 2 year period. The autotrophic root respiration component of CO2 emission was separated from heterotrophic emission caused by peat oxidation in three ways: (i) by comparing CO2 emissions within and beyond the tree rooting zone, (ii) by comparing CO2 emissions with and without peat trenching (i.e. cutting any roots remaining in the peat beyond the tree rooting zone), and (iii) by comparing CO2 emissions before and after Acacia tree harvesting. On average, the contribution of autotrophic respiration to daytime CO 2 emission was 21% along transects in mature tree stands. At locations 0.5 m from trees this was up to 80% of the total emissions, but it was negligible at locations more than 1.3m away. This means that CO2 emission measurements well away from trees were free of any autotrophic respiration contribution and thus represent only heterotrophic emissions. We found daytime mean annual CO2 emission from peat oxidation alone of 94 t ha-1 y-1 at a mean water table depth of 0.8 m, and a minimum emission value of 80 t ha-1 y-1 after correction for the effect of diurnal temperature fluctuations, which may result in a 14.5% reduction of the daytime emission. There is a positive correlation between mean long-term water table depth and peat oxidation CO2 emission. However, no such relation is found for instantaneous emission/water table depth within transects and it is clear that factors other than water table depth also affect peat oxidation and total CO2 emissions. The increase in the temperature of the surface peat due to plantation establishment may explain over 50% of peat oxidation emissions. Our study sets a standard for greenhouse gas flux studies from tropical peatlands under different forms of agricultural land management. It is the first to purposefully quantify heterotrophic CO 2 emissions resulting from tropical peat decomposition by separating these from autotrophic emissions. It also provides the most scientifically- and statistically-rigorous study to date of CO2 emissions resulting from anthropogenic modification of this globally significant carbon rich ecosystem. Our findings indicate that past studies have underestimated emissions from peatland plantations, with important implications for the scale of greenhouse gas emissions arising from land use change, particularly in the light of current, rapid agricultural conversion of peatlands in the Southeast Asian region. © Author(s) 2012.

Background: Searching for words is a common phenomenon in conversations of people with aphasia. When searching for a word the speaker interrupts the emerging conversational turn with a pause, vocalisation (e.g., uh), and/or a question (e.g., what is it). Previous studies suggest that gazing and pointing can be used to invite conversational partners to join the search.Aims: This study compares the collaborative actions of different conversational partners of people with aphasia (significant others vs. speech and language therapists) during aphasic word searching. The aphasic speakers’ actions inviting assistance from the partners in the search are also examined.Methods & Procedures: The data for the study comprised 20 conversations, half videotaped at the participants’ homes and half in aphasia therapy sessions. The conversations were transcribed and analysed sequentially with a special emphasis on taking non-verbal actions into account. In the analysis, word search sequences were identified and the collaborative participation of the significant others, as well as the speech and language therapists, compared.Outcomes & Results: The analysis showed that institutional and non-institutional conversational partners collaborate in different ways during word searching. When invited to join the search, often non-verbally, the significant others quickly offer words for the aphasic speakers to complete the search. When successful, these immediate completions solve the search and the core conversation can continue. On the other hand, even if invited non-verbally, speech and language therapists do not join in searching by offering words. Instead, they ask questions or offer their candidate understandings that are more elaborate than one word. Furthermore, they regularly shift the speaking turn back to the aphasic speaker encouraging the aphasic speaker to continue the search by him or herself.Conclusions: The institutional and everyday practices of sequential resolutions of word searching differ to a great extent. Everyday conversational practices of collaborative completion appear more effective in solving the search and allow the aphasic speaker to experience smoothly flowing conversational interaction. Everyday practices could also be systematically used within aphasia therapy. Furthermore, if necessary, speech and language therapists should promote the use of these practices within daily interactions of the aphasic clients and their significant others. © 2014, © 2014 Taylor & Francis.

Ahonen J.,University of Helsinki
Current Opinion in Anaesthesiology | Year: 2012

Purpose of review: To review the literature regarding the use of recombinant activated factor FVII (rFVIIa) in the treatment of postpartum hemorrhage (PPH). Recent findings: The previous and recent case reports and case series suggest a potential benefit of rFVIIa in the management of severe PPH refractory to standard treatment. However, the lack of randomized controlled studies limits the value of the available data. rFVIIa cannot work optimally if there is a shortage of the basic components of the coagulation cascade such as fibrinogen. New experimental data suggest that rFVIIa can relocate into the extravascular space and remain functionally active which may prolong its hemostatic effect longer than the short circulatory half-life indicates. Summary: Although some preliminary guidelines have been published, the case reports and case series illustrate that the practice of using rFVIIa in PPH is far from uniform. rFVIIa should usually not be used to compensate for an inadequate transfusion therapy. Therefore, early and effective administration of red blood cells, fresh frozen plasma, fibrinogen concentrate (or cryoprecipitate), and platelets as well as the control of uterine atony are essential before considering administration of rFVIIa in the treatment of PPH. © 2012 Wolters Kluwer Health | Lippincott Williams & Wilkins.

Neuvonen P.J.,University of Helsinki
Current Opinion in Investigational Drugs | Year: 2010

HMG-CoA reductase inhibitors (statins) can cause skeletal muscle toxicity; the risk of toxicity is elevated by drug interactions and pharmacogenetic factors that increase the concentration of statins in the plasma. Statins are substrates for several membrane transporters that may mediate drug interactions. Inhibitors of the organic anion transporting polypeptide 1B1 can decrease the hepatic uptake of many statins, as well as the therapeutic index of these agents. Potent inhibitors of cytochrome P450 (CYP)3A4 can significantly increase the plasma concentrations of the active forms of simvastatin, lovastatin and atorvastatin. Fluvastatin, which is metabolized by CYP2C9, is less prone to pharmacokinetic interactions, while pravastatin, rosuvastatin and pitavastatin are not susceptible to any CYP inhibition. An understanding of the mechanisms of statin interactions will help to minimize drug interactions and to develop statins that are less prone to adverse interactions. © Thomson Reuters (Scientific) Ltd.

Merila J.,University of Helsinki
Annals of the New York Academy of Sciences | Year: 2013

The nine-spined stickleback (Pungitius pungitius) is emerging as a model for evolutionary biology, genetic, and behavioral research in the wake of its better-known relative, the three-spined stickleback (Gasterosteus aculeatus). This interest has been fed by its fascinating biological features, such as the repeated evolution of similar phenotypes in isolated pond populations. A large body of recent research has uncovered the finding that pond nine-spined sticklebacks have evolved numerous morphological, life history, neuroanatomical, and behavioral adaptations-possibly in response to reduced threat of fish predation-which differentiate them from their marine conspecifics. These features, together with insights from recent population genetic studies, suggest that this species provides an interesting model for studies aiming to understand-and differentiate between-genetic convergence and parallelism as underlying mechanism(s) of evolution of similar phenotypes in multiple independent sites. This review provides a synopsis of and reflections on the insights borne out of recent studies of nine-spined sticklebacks-the little sister of ecology's "new supermodel". © 2013 New York Academy of Sciences.

Sihvola N.,University of Helsinki
The British journal of nutrition | Year: 2013

Dietary components may affect brain function and influence behaviour by inducing the synthesis of neurotransmitters. The aim of the present study was to examine the influence of consumption of a whey protein-containing breakfast drink v. a carbohydrate drink v. control on subjective and physiological responses to mental workload in simulated work. In a randomised cross-over design, ten healthy subjects (seven women, median age 26 years, median BMI 23 kg/m(2)) participated in a single-blinded, placebo-controlled study. The subjects performed demanding work-like tasks after having a breakfast drink high in protein (HP) or high in carbohydrate (HC) or a control drink on separate sessions. Subjective states were assessed using the NASA Task Load Index (NASA-TLX), the Karolinska sleepiness scale (KSS) and the modified Profile of Mood States. Heart rate was recorded during task performance. The ratio of plasma tryptophan (Trp) to the sum of the other large neutral amino acids (LNAA) and salivary cortisol were also analysed. The plasma Trp:LNAA ratio was 30 % higher after the test drinks HP (median 0·13 (μmol/l)/(μmol/l)) and HC (median 0·13 (μmol/l)/(μmol/l)) than after the control drink (median 0·10 (μmol/l)/(μmol/l)). The increase in heart rate was smaller after the HP (median 2·7 beats/min) and HC (median 1·9 beats/min) drinks when compared with the control drink (median 7·2 beats/min) during task performance. Subjective sleepiness was reduced more after the HC drink (median KSS - 1·5) than after the control drink (median KSS - 0·5). There were no significant differences between the breakfast types in the NASA-TLX index, cortisol levels or task performance. We conclude that a breakfast drink high in whey protein or carbohydrates may improve coping with mental tasks in healthy subjects.

Asmi A.,University of Helsinki
Atmospheric Environment | Year: 2012

Weekday related anthropogenic aerosol emissions have been suggested to affect regional climate via indirect aerosol effects. I studied the variability of potential cloud condensation nuclei using measurements of number size distributions of Cloud Condensation Nuclei (CCN)-sized aerosol particles and CCNs measured at several European regional background stations, located at a wide variety of environments. With notably rare exceptions, there were no statistically significant difference between concentrations on different weekdays. I further analysed the concentration time-series of four long-period datasets in Germany and Finland with wavelet analysis. Outside of urban areas, very little weekday-connected variability was found. The lack of 7-day variability outside of cities is in contrast of earlier studies in this field, which used mostly particle mass as the representative measure of aerosol concentration. A time-scale and variability analysis showed that PM 10 and PM 2.5 are more sensitive for the weekly variation than CCN-sized particles. Using mass-based variations as a proxy for short-term variations of CCN particle numbers can thus overestimate the weekend effect for these particles. The results of this study do not support aerosol indirect effects from 50 to 500 nm diameter particles as a major contributor on potential weekday connected variations in European meteorology. © 2012 Elsevier Ltd.

Alitalo K.,University of Helsinki
Nature Medicine | Year: 2011

Blood vessels form a closed circulatory system, whereas lymphatic vessels form a one-way conduit for tissue fluid and leukocytes. In most vertebrates, the main function of lymphatic vessels is to collect excess protein-rich fluid that has extravasated from blood vessels and transport it back into the blood circulation. Lymphatic vessels have an important immune surveillance function, as they import various antigens and activated antigen-presenting cells into the lymph nodes and export immune effector cells and humoral response factors into the blood circulation. Defects in lymphatic function can lead to lymph accumulation in tissues, dampened immune responses, connective tissue and fat accumulation, and tissue swelling known as lymphedema. This review highlights the most recent developments in lymphatic biology and how the lymphatic system contributes to the pathogenesis of various diseases involving immune and inflammatory responses and its role in disseminating tumor cells. © 2011 Nature America, Inc. All rights reserved.

Koskela H.,University of Helsinki
Theoretical Criminology | Year: 2011

This article examines the relationships between the authorities of surveillance and the public. Four 'modalities of surveillance' are used as a contextual framework to describe different relationships and to demonstrate that they can be bidirectional as well as unidirectional. In contemporary surveillance there is a dialogue between traditional surveillance and counter-surveillance which is targeted against the authorities. Yet, surveillance also contains performative practices and incidental witnessing in which the authorities play no role. The latest development involves responsibilizing the public, as citizens are encouraged to participate in gathering evidence for crime control. The article shows how the mutual correlations between surveillance, crime and evidence are constantly transforming. © The Author(s) 2011.

Palta P.,University of Helsinki
Nature Genetics | Year: 2016

Migraine is a debilitating neurological disorder affecting around one in seven people worldwide, but its molecular mechanisms remain poorly understood. There is some debate about whether migraine is a disease of vascular dysfunction or a result of neuronal dysfunction with secondary vascular changes. Genome-wide association (GWA) studies have thus far identified 13 independent loci associated with migraine. To identify new susceptibility loci, we carried out a genetic study of migraine on 59,674 affected subjects and 316,078 controls from 22 GWA studies. We identified 44 independent single-nucleotide polymorphisms (SNPs) significantly associated with migraine risk (P < 5 × 10-8) that mapped to 38 distinct genomic loci, including 28 loci not previously reported and a locus that to our knowledge is the first to be identified on chromosome X. In subsequent computational analyses, the identified loci showed enrichment for genes expressed in vascular and smooth muscle tissues, consistent with a predominant theory of migraine that highlights vascular etiologies. © 2016 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.

Hydrophobins are small, secreted proteins playing important roles at different stages of fungal life cycles. Their characteristic feature is the presence of eight highly conserved cysteine residues. Here we present an inventory and evolutionary analysis of hydrophobin genes from three wood-degrading basidiomycetes, Phlebia brevispora, Ganoderma sp. and Bjerkandera adusta. The genomes of the three analyzed species are characterized by the presence of high copy numbers of hydrophobin genes. Results of the phylogenetic analysis of the identified proteins revealed that many of them share a high degree of sequence similarity and probably originated from a series of duplication events. The presence of several clusters of adjacent copies of the hydrophobin gene in a particular location in the genome further supports the interpretation that gene duplication has played a role in the evolution of hydrophobins in the analyzed species.

Biancari F.,University of Oulu | Venermo M.,University of Helsinki
British Journal of Surgery | Year: 2011

Background: Open repair of ruptured abdominal aortic aneurysm (RAAA) in patients aged 80 years and older may be questioned owing to the patients' high operative risk and short life expectancy. Methods: Data on patients aged at least 80 years, admitted for RAAA at four Finnish university hospitals, were collected and analysed retrospectively. Results: Three hundred and ten consecutive patients aged 80 years and older with RAAA reached hospital alive; 200 (64̇5 per cent) underwent open repair. The number of open repairs increased during the last 5 years (49̇0 per cent of the whole series), with no significant increase in the number of patients treated conservatively. The overall in-hospital mortality rate was 72̇9 per cent. The operative mortality rate was 59̇0 per cent and decreased from 66 to 52 per cent during the last 5 years (P = 0̇050). On multivariable analysis, shock was the only independent predictor of immediate postoperative death (odds ratio 4̇97, 95 per cent confidence interval 2̇09 to7̇94; P < 0̇001). Classification and regression tree analysis showed that preoperative haemoglobin level and presence of shock were predictive of immediate postoperative death; 19 (95 per cent) of 20 patients with shock and a haemoglobin level below 68 g/l died immediately after surgery. Among the 82 survivors of surgery, survival rates at 1, 3 and 5 years were 90, 68 and 45 per cent respectively. These values were not significantly different from those of the age-, sex- and year-matched general population (P = 0̇885). Conclusion: Survival after open repair of RAAA among patients aged 80 years and older is sufficient to justify the procedure, particularly in patients in a stable haemodynamic condition. © 2011 British Journal of Surgery Society Ltd.

Nakao M.,Asahikawa University | Lavikainen A.,University of Helsinki | Yanagida T.,Asahikawa University | Ito A.,Asahikawa University
International Journal for Parasitology | Year: 2013

Echinococcosis is a serious helminthic zoonosis in humans, livestock and wildlife. The pathogenic organisms are members of the genus Echinococcus (Cestoda: Taeniidae). Life cycles of Echinococcus spp. are consistently dependent on predator-prey association between two obligate mammalian hosts. Carnivores (canids and felids) serve as definitive hosts for adult tapeworms and their herbivore prey (ungulates, rodents and lagomorphs) as intermediate hosts for metacestode larvae. Humans are involved as an accidental host for metacestode infections. The metacestodes develop in various internal organs, particularly in liver and lungs. Each metacestode of Echinococcus spp. has an organotropism and a characteristic form known as an unilocular (cystic), alveolar or polycystic hydatid. Recent molecular phylogenetic studies have demonstrated that the type species, Echinococcus granulosus, causing cystic echinococcosis is a cryptic species complex. Therefore, the orthodox taxonomy of Echinococcus established from morphological criteria has been revised from the standpoint of phylogenetic systematics. Nine valid species including newly resurrected taxa are recognised as a result of the revision. This review summarises the recent advances in the phylogenetic systematics of Echinococcus, together with the historical backgrounds and molecular epidemiological aspects of each species. A new phylogenetic tree inferred from the mitochondrial genomes of all valid Echinococcus spp. is also presented. The taxonomic nomenclature for Echinococcus oligarthrus is shown to be incorrect and this name should be replaced with Echinococcus oligarthra. © 2013 Australian Society for Parasitology Inc.

Multiple factors including unhealthy living habits influence the life-maintaining functions of the endoplasmic reticulum (ER) and induce ER stress and metabolic abnormalities. The ER responds to the disturbances by activating mechanisms that increase the capacity to eliminate ER stress. This article elucidates the effects of ER activation that eliminates both ER stress and associated cardiovascular, type 2 diabetic (DM2), and other metabolic diseases. ER-activating compounds eliminate ER stress by lowering elevated cholesterol, regress atherosclerosis, decrease cardiovascular mortality, reduce blood glucose and insulin, and, together with the normalization of glucose-insulin homeostasis, remove insulin resistance, pancreatic β-cell failure, and DM2. A deficient cytochrome P450 activity in hepatic ER leads to cholesterol accumulation that induces stress and xanthoma formation, whereas P450-activating therapy up-regulates apolipoprotein AI and LDLR genes, down-regulates apolipoprotein B gene, and produces an antiatherogenic plasma lipoprotein profile. The ER activation reduces the stress also by eliminating hepatic fat and converting saturated fatty acids (FAs) to unsaturated FAs. Cognitive processes require gene expression modification, and preclinical studies indicate that ER-activating therapy improves cognition. Promotion of healthy lifestyle choices and indicated therapies are key factors in the prevention and elimination of ER stress and associated global health problems. © 2013 Informa UK, Ltd.

Hellman M.,University of Helsinki
Substance Use and Misuse | Year: 2012

This article discusses the failure to succeed in the treatment of the heterogeneous population of substance users, in terms of too little, or a total absence of, necessary available knowledge from an ethnographic perspective of the user's mental geographies. I suggest three dimensions that are critical to be knowledgeable about at the beginning planning stages of any intervention and on any level of policy, namely, insights into time, space, and bodily perceptions of drug users. In these scopes, barriers are drawn and upheld between caregiver and intervention planners, on the one hand, and the client, on the other. In cases when treatment has proven successful, however success is defined, the gap between the addict's mental geography and the surrounding world has been overcome to some degree. Previous research in the area of substance users' perspective of time, space, and body, and estimates of its value for success in and posttreatment, support, and care of people with severe drug-use-related problems, are discussed. © 2012 Informa Healthcare USA, Inc.

Lahdenne P.,University of Helsinki
Arthritis care & research | Year: 2010

OBJECTIVE: To study whether premedication with an oral antifebrile agent (acetaminophen) and antihistamine (cetirizine) could decrease the frequency of acute infusion reactions in pediatric patients. METHODS: All pediatric patients scheduled for infliximab infusions at the Helsinki University Central Hospital, a tertiary care center, were prospectively introduced to a standard oral premedication of acetaminophen (20 mg/kg) and cetirizine (10 mg) prior to infliximab infusions for a period of 1 year. All acute adverse events related to infliximab infusions given according to the guidelines of pediatric rheumatologists or gastroenterologists were registered for this time period and retrospectively during the preceding year. RESULTS: During the study period, infliximab infusions with premedication were given to 64 pediatric patients (48 with rheumatic disease and l6 with inflammatory bowel disease, mean age 13 years, n = 34 boys, and n = 30 girls). Infliximab was introduced to 14 children; the rest were on maintenance therapy. Twelve infusion reactions, 4 mild and 8 severe, were observed in 8 (12.5%) of the 64 subjects, and in 1 subject 4 times. During the preceding year, 60 pediatric patients had received infliximab infusions without premedication. In this latter group, infusion reactions occurred in 5 children (8.3%; P > 0.05). The presentation of an acute infusion reaction was not related to the sex or diagnosis of the patient. CONCLUSION: In pediatric patients, acute infusion reactions related to infliximab could not be prevented with premedication with oral acetaminophen and cetirizine.

Kukkonen J.P.,University of Helsinki
Cellular Signalling | Year: 2016

There are two subtypes of orexin receptors, OX1 and OX2. Signalling pathways have been mapped in much higher detail for OX1 receptors than OX2 receptors. Almost all the detailed studies have been performed in Chinese hamster ovary cells, and we thus chose the same cell background for the studies on human OX2 receptors to allow comparison to human OX1 receptors. Adenylyl cyclase, phospholipase A2, C and D and diacylglycerol lipase activities were assessed by precursor radiolabelling and chromatographic separation (ion exchange, affinity or thin layer), calcium by a fluorescent method, and receptor binding with [125I]-orexin-A. Upon activation with orexin-A, OX2 receptors stimulated phospholipase A2, C and D, diacylglycerol lipase and calcium elevation, and both inhibited and stimulated adenylyl cyclase; i.e., the responses to OX2 activation by orexin-A were principally like those of OX1, in contrast to some previous suggestions. The responses occurred mostly in the same concentration range as those for OX1 activation and via the same signal cascades. However, some responses were weaker, suggesting a partially differential coupling to some cascades. In summary, OX2 receptor signalling is principally similar to OX1 receptor signalling suggesting also a physiologically similar coupling, though this needs to be verified in physiological contexts. Some (relatively weak) differences between the receptors may be investigated in further studies. © 2015 Elsevier Inc..

Yki-Jarvinen H.,University of Helsinki | Yki-Jarvinen H.,Minerva Foundation Institute for Medical Research
Diabetologia | Year: 2016

Non-alcoholic fatty liver disease (NAFLD) increases risk of mortality from liver and cardiovascular disease (CVD) and is the major cause of hepatocellular carcinoma (HCC), which may develop without cirrhosis. NAFLD predicts type 2 diabetes, even independently of obesity. Globally, the prevalence of NAFLD averages 25% and is as common as the metabolic syndrome. The majority of patients with type 2 diabetes have NAFLD. The challenge for the diabetologist is to identify patients at risk of advanced liver disease and HCC. At a minimum, liver function tests (LFTs), despite being neither specific nor sensitive, should be performed in all patients with the metabolic syndrome or type 2 diabetes. Increases in LFTs, for which the updated reference values are lower (serum ALT ≈30 U/l in men and ≈20 U/l in women) than those hitherto used in many laboratories, should prompt assessment of fibrosis biomarkers and referral of individuals at risk to a NAFLD/hepatology clinic. Preferably, evaluation of NAFLD should be based on measurement of steatosis biomarkers or ultrasound if easily available. A large number of individuals carry the patatin-like phospholipase domain containing 3 (PNPLA3) I148M variant (30–50%) or the transmembrane 6 superfamily member 2 (TM6SF2) E167K variant (11–15%). These variants increase the risk of advanced liver disease and HCC but not of diabetes or CVD. Genotyping of selected patients for these variants is recommended. Many patients have ‘double trouble’, i.e. carry both a genetic risk factor and have the metabolic syndrome. Excess use of alcohol could be a cause of ‘triple trouble’, but such patients would be classified as having alcoholic fatty liver disease. This review summarises a presentation given at the symposium ‘The liver in focus’ at the 2015 annual meeting of the EASD. It is accompanied by two other reviews on topics from this symposium (by Kenneth Cusi, DOI: 10.1007/s00125-016-3952-1, and by John Jones, DOI: 10.1007/s00125-016-3940-5) and a commentary by the Session Chair, Michael Roden (DOI: 10.1007/s00125-016-3911-x). © 2016, Springer-Verlag Berlin Heidelberg.

Sulonen A.M.,University of Helsinki
Genome biology | Year: 2011

Techniques enabling targeted re-sequencing of the protein coding sequences of the human genome on next generation sequencing instruments are of great interest. We conducted a systematic comparison of the solution-based exome capture kits provided by Agilent and Roche NimbleGen. A control DNA sample was captured with all four capture methods and prepared for Illumina GAII sequencing. Sequence data from additional samples prepared with the same protocols were also used in the comparison. We developed a bioinformatics pipeline for quality control, short read alignment, variant identification and annotation of the sequence data. In our analysis, a larger percentage of the high quality reads from the NimbleGen captures than from the Agilent captures aligned to the capture target regions. High GC content of the target sequence was associated with poor capture success in all exome enrichment methods. Comparison of mean allele balances for heterozygous variants indicated a tendency to have more reference bases than variant bases in the heterozygous variant positions within the target regions in all methods. There was virtually no difference in the genotype concordance compared to genotypes derived from SNP arrays. A minimum of 11× coverage was required to make a heterozygote genotype call with 99% accuracy when compared to common SNPs on genome-wide association arrays. Libraries captured with NimbleGen kits aligned more accurately to the target regions. The updated NimbleGen kit most efficiently covered the exome with a minimum coverage of 20×, yet none of the kits captured all the Consensus Coding Sequence annotated exons.

Vaara M.,Northern Antibiotics Ltd. | Vaara M.,University of Helsinki
Current Opinion in Microbiology | Year: 2010

The emerging very multiresistant Gram-negative bacteria cause remarkable therapeutic challenges. There are no novel classes of agents in clinical development for the treatment of Gram-negative infections. Polymyxins (polymyxin B and colistin) were abandoned in the seventies but are now back in the therapy as the last resort. Their nephrotoxicity may complicate the therapy or even necessitate its discontinuation. Less toxic polymyxin derivatives would be highly welcome. Novel derivatives lack in strategic positions two of the five cationic charges of polymyxins, differ from polymyxins in their renal handling and affinity to kidney brush-border membrane, and are in preclinical studies. Less characterized other recent derivatives, also reviewed here, have increased the collective knowledge on the structure-function relationships in polymyxins. Acquired resistance to polymyxins has been encountered. However, the resistance mechanism compromises the function of the bacterial outer membrane as a permeability barrier to other noxious agents. © 2010 Elsevier Ltd.

Gaily E.,University of Helsinki
Expert Review of Neurotherapeutics | Year: 2012

Infantile spasms syndrome (IS) (also known as West syndrome) is an epileptic encephalopathy with a heterogeneous etiology. One of the most common specific causes is tuberous sclerosis, diagnosed in almost 10% of the affected infants. Adrenocorticotropic hormone or steroids have been the preferred treatments for IS for several decades. Clinical studies have shown that vigabatrin is superior to placebo in decreasing the frequency of infantile spasms. In tuberous sclerosis, vigabatrin may be considered the first-line treatment for IS. The mode of action is increasing concentrations of the inhibitory neurotransmitter GABA in the brain. The use of vigabatrin is limited by a serious adverse effect, permanent visual field constriction, which may affect 6-7% of exposed infants. Treatment choices are based on balancing the potential adverse effects against the risk of catastrophic cognitive and behavioral outcomes caused by uncontrolled spasms. © 2012 Expert Reviews Ltd.

Bos N.,University of Helsinki
Communicative and Integrative Biology | Year: 2014

Animals constantly face the challenge of extracting important information out of their environment, and for many animals much of this information is chemical in nature. The ability to discriminate and generalize between chemical stimuli is extremely important and is commonly thought to depend mostly on the structural similarity between the different stimuli. However, we previously provided evidence that in the carpenter ant Camponotus aethiops, generalization not only depends on structural similarity, but also on the animal's previous training experience. When individual ants were conditioned to substance A, they generalized toward a mixture of A and B. However, when trained to substance B, they did not generalize toward this mixture, resulting in asymmetrical generalization. This asymmetry followed an inclusion criterion, where the ants consistently generalized from a molecule with a long carbon chain to molecules with a shorter chain, but not the other way around. Here I will review the evidence for the inclusion criterion, describe possible proximate mechanisms underlying this phenomenon as well as discuss its potential adaptive significance. © 2014 Landes Bioscience.

Silvetti S.,San Raffaele Scientific Institute | Nieminen M.S.,University of Helsinki
International Journal of Cardiology | Year: 2016

Introduction: Advanced heart failure is a malignant disease characterized by a debilitating late course, with increasingly frequent hospitalisations and high rate of mortality. Levosimendan, an inodilator developed for the treatment of acutely decompensated chronic heart failure, has been recently proposed also as a repetitive treatment of advanced heart failure. Several studies on the use of levosimendan in this settings report mortality data. Independent meta-analyses on the effect on mortality of repetitive or intermittent levosimendan administration in advanced heart failure has been published but were criticized in regard to the selection of the studies. Meanwhile new data became available. We therefore updated the selection of studies and re-analyzed all the available data. Methods & results: Data from seven randomized trial and a total of 438 adult patients using intermittent levosimendan in a cardiological setting were included in the present analysis. The average follow-up period was 8 ± 3.8 months. The use of levosimendan was associated with a significant reduction in mortality at the longest follow-up available [41 of 257 (16%) in the levosimendan group vs. 39 of 181 (21.5%) in the control arm, OR = 0.54 (95% CI 0.32-0.91), p for effect = 0.02, p for heterogeneity = 0.64, I2 = 0%]. Conclusions: The updated results suggest that repetitive or intermittent levosimendan administration in advanced heart failure is associated with a significant reduction in mortality at the longest follow-up available. There is therefore a strong rationale for a randomized clinical trial with adequate power on mortality. © 2015 The Authors.

Puig O.,Merck And Co. | Mattila J.,University of Helsinki
Antioxidants and Redox Signaling | Year: 2011

Drosophila melanogaster is one of the most widely used model organisms. About 77% of known human disease genes have an ortholog in Drosophila, and many of the cellular signaling pathways are common between fruit flies and mammals. For example, a key signaling pathway in the regulation of growth and metabolism, the insulin/insulin-like growth factor 1 signaling pathway, is well conserved between flies and humans. Downstream effectors of this pathway are the Forkhead box class O (FOXO) family of transcription factors, with four members in mammals and a single FOXO protein in Drosophila, dFOXO. Research in Drosophila has been critical to elucidate the molecular mechanisms by which FOXO transcription factors regulate insulin signaling. In this review, we summarize the studies leading to dFOXO identification and its characterization as a central regulator of metabolism, life span, cell cycle, growth, and stress resistance. © 2011 Mary Ann Liebert, Inc.

Hepsin belongs to a family of cell-surface serine proteases, which have sparked interest as therapeutic targets because of the accessibility of extracellular protease domain for inhibitors. Hepsin is frequently amplified and/or overexpressed in epithelial cancers, but it is not clear how enhanced hepsin expression confers a potential for oncogenicity. We show that hepsin is consistently overexpressed in more than 40% of examined breast cancers, including all major biological subtypes. The effects of doxycycline-induced hepsin overexpression were examined in mammary epithelial organoids, and we found that induced hepsin acutely downmodulates its cognate inhibitor, hepatocyte growth factor (HGF) activator inhibitor type 1 (HAI-1). Hepsin-induced depletion of cellular HAI-1 led to a sharp increase in pericellular serine protease activity. The derepressed hepsin proteolytically activated downstream serine proteases, augmented HGF/MET signalling and caused deterioration of desmosomes and hemidesmosomes; structures important for cell cohesion and cell-basement membrane interaction. Moreover, chronic induction of hepsin considerably shortened the latency of Myc-dependent tumourigenesis in the mouse mammary gland. The serine protease and uPA system inhibitor WX-UK1, identified as a micromolar range hepsin inhibitor, prevented hepsin from augmenting HGF/MET signalling and disrupting desmosomes and hemidesmosomes. The findings suggest that the oncogenic activity of hepsin arises not only from elevated expression level but also from depletion of HAI-1, events which together trigger gain-of-function activity impacting HGF/MET signalling and epithelial cohesion. Thus, hepsin overexpression is a major oncogenic conferrer to a serine protease activity involved in breast cancer dissemination.Oncogene advance online publication, 13 July 2015; doi:10.1038/onc.2015.248. © 2015 Macmillan Publishers Limited

Linden A.,University of Oslo | Mantyniemi S.,University of Helsinki
Ecology | Year: 2011

A Poisson process is a commonly used starting point for modeling stochastic variation of ecological count data around a theoretical expectation. However, data typically show more variation than implied by the Poisson distribution. Such overdispersion is often accounted for by using models with different assumptions about how the variance changes with the expectation. The choice of these assumptions can naturally have apparent consequences for statistical inference. We propose a parameterization of the negative binomial distribution, where two overdispersion parameters are introduced to allow for various quadratic mean-variance relationships, including the ones assumed in the most commonly used approaches. Using bird migration as an example, we present hypothetical scenarios on how overdispersion can arise due to sampling, flocking behavior or aggregation, environmental variability, or combinations of these factors. For all considered scenarios, mean-variance relationships can be appropriately described bthe negative binomial distribution with two overdispersion parameters. To illustrate, we apply the model to empirical migration data with a high level of overdispersion, gaining clearly different model fits with different assumptions about mean-variance relationships. The proposed framework can be a useful approximation for modeling marginal distributions of independent count data in likelihood-based analyses. © 2011 by the Ecological Society of America..

Holmberg V.,University of Helsinki
Malaria journal | Year: 2012

Innate immunity plays a crucial role in the host defense against malaria including Plasmodium falciparum malaria in pregnancy, but the roles of the various underlying genes and mechanisms predisposing to the disease are poorly understood. 98 single-nucletoide polymorphisms were genotyped in a set of 17 functionally related genes of the complement system in 145 primiparous Ghanaian women with placental malaria, defined by placental parasitaemia or malaria pigment, and as a control, in 124 non-affected primiparae. Placental malaria was significantly associated with SNPs in the lectin pathway genes MBL2, MASP2, FCN2 and in properdin. In particular, the main African mannose-binding lectin deficiency variant (MBL2*G57E, rs1800451) increased the odds of placental malaria (OR 1.6; permuted p-value 0.014). In contrast, a common MASP2 mutation (R439H, rs12085877), which reduces the activity of MBL-MASP2 complexes occurred in 33% of non-affected women and in 22% primiparae with placental malaria (OR 0.55, permuted p-value 0.020). Excessive complement activation is of importance in the pathogenesis of placental malaria by mediating inflammation, coagulation, and endothelial dysfunction. Mutated MBL and MASP2 proteins could have direct intrinsic effects on the susceptibility to placental malaria, in addition to their roles in regulation of downstream complement activation.

Mutshinda C.M.,University of Helsinki | O'Hara R.B.,Biodiversity and Climate Research Center
Oecologia | Year: 2011

Elucidating the mechanisms underlying the assembly and dynamics of ecological communities is a fundamental goal of ecology. Two conceptual approaches have emerged in this respect: the niche-assembly view and the neutral perspective. The debate as to which approach best explains the biodiversity patterns observed in nature is becoming outdated, as ecologists increasingly agree on the existence of a niche-neutral continuum of community dynamical behaviors. However, attempts to make the continuum idea operational and measurable remain sparse. Here, we propose a model-based approach to achieving this. The proposed methodology consists of separating out fluctuations in species abundances into niche-mediated and stochastic factors, linking the niche configuration to community dynamics through competition, and adding demographic stochasticity. This results in a comprehensive framework including neutrality and strict niche segregation as extreme cases. We develop an index of departure from neutral drift as a surrogate for community position on the niche-neutral continuum. We evaluate the performance of our modeling approach with simulated data, and subsequently use the model to analyze rodent web-trapping data from a real-world system. The model fitting is carried out with a Bayesian approach using Markov chain Monte Carlo simulation methods. © 2010 Springer-Verlag.

Siren H.,University of Helsinki
Data in Brief | Year: 2015

Organic acids are used for starting compounds in material sciences and in biorefinery, food, fuel, pharmaceutical, and medical industry. Here, we provide the data from a biochemical approach made to investigate production of organic acids and isolation of metals from wood, which is the most abundant biomass. Spruce and bark, phloem, and heartwood from pine were fermented with either microbes of oyster mushroom (Pleurotus ostreatus), baker's yeast, or lactic acid bacteria to improve selective fermentation.Using capillary electrophoresis and liquid chromatography techniques, we identified 14 different organic acids and phenolic acids with good yields. With inductively coupled plasma atomic emission spectroscopy 11 metals were quantified and further detailed analysis/results from these data are available in Sirén et al. (2015) [1]. © 2015.

Larjavaara M.,Smithsonian Tropical Research Institute | Larjavaara M.,University of Helsinki | Muller-Landau H.C.,Smithsonian Tropical Research Institute
Global Ecology and Biogeography | Year: 2012

Aim To develop and test a simple climate-based ecophysiological model of above-ground biomass - an approach that can be applied directly to predicting the effects of climate change on forest carbon stores. Location Humid lowland forests world-wide. Methods We developed a new approach to modelling the aboveground biomass of old-growth forest (AGB max) based on the influences of temperature on gross primary productivity (GPP) and what we call total maintenance cost (TMC), which includes autotrophic respiration as well as leaf, stem and other plant construction required to maintain biomass. We parameterized the models with measured carbon fluxes and tested them by comparing predicted AGB max with measured AGB for another 109 old-growth sites. Results Our models explained 57% of the variation in GPP across 95 sites and 79% of the variation in TMC across 17 sites. According to the best-fit models, the ratio of GPP to maintenance cost per unit biomass (MCB) peaks at 16.5°C, indicating that this is the air temperature leading to the highest possible AGB max when temperatures are constant. Seasonal temperature variation generally reduces predicted AGB max, and thus maritime temperate climates are predicted to have the highest AGB max. The shift in temperatures from temperate maritime to tropical climates increases MCB more than GPP, and thus decreases AGB max. Overall, our model explains exactly 50% of the variation in AGB among humid lowland old-growth forests. Main conclusions Temperature plays an important role in explaining global variation in biomass among humid lowland old-growth forests, a role that can be understood in terms of the dual effects of temperature on GPP and TMC. Our simple model captures these influences, and could be an important tool for predicting the effects of climate change on forest carbon stores. © 2011 Blackwell Publishing Ltd. Published 2011. This article is a US Government work and is in the public domain in the USA.

Seppala E.H.,University of Helsinki
PLoS genetics | Year: 2011

One quadrillion synapses are laid in the first two years of postnatal construction of the human brain, which are then pruned until age 10 to 500 trillion synapses composing the final network. Genetic epilepsies are the most common neurological diseases with onset during pruning, affecting 0.5% of 2-10-year-old children, and these epilepsies are often characterized by spontaneous remission. We previously described a remitting epilepsy in the Lagotto romagnolo canine breed. Here, we identify the gene defect and affected neurochemical pathway. We reconstructed a large Lagotto pedigree of around 34 affected animals. Using genome-wide association in 11 discordant sib-pairs from this pedigree, we mapped the disease locus to a 1.7 Mb region of homozygosity in chromosome 3 where we identified a protein-truncating mutation in the Lgi2 gene, a homologue of the human epilepsy gene LGI1. We show that LGI2, like LGI1, is neuronally secreted and acts on metalloproteinase-lacking members of the ADAM family of neuronal receptors, which function in synapse remodeling, and that LGI2 truncation, like LGI1 truncations, prevents secretion and ADAM interaction. The resulting epilepsy onsets at around seven weeks (equivalent to human two years), and remits by four months (human eight years), versus onset after age eight in the majority of human patients with LGI1 mutations. Finally, we show that Lgi2 is expressed highly in the immediate post-natal period until halfway through pruning, unlike Lgi1, which is expressed in the latter part of pruning and beyond. LGI2 acts at least in part through the same ADAM receptors as LGI1, but earlier, ensuring electrical stability (absence of epilepsy) during pruning years, preceding this same function performed by LGI1 in later years. LGI2 should be considered a candidate gene for common remitting childhood epilepsies, and LGI2-to-LGI1 transition for mechanisms of childhood epilepsy remission.

Taube R.,Ben - Gurion University of the Negev | Peterlin B.M.,University of California at San Francisco | Peterlin B.M.,University of Helsinki
Viruses | Year: 2013

Highly active antiretroviral therapy (HAART) has limited the replication and spread of the human immunodeficiency virus (HIV). However, despite treatment, HIV infection persists in latently infected reservoirs, and once therapy is interrupted, viral replication rebounds quickly. Extensive efforts are being directed at eliminating these cell reservoirs. This feat can be achieved by reactivating latent HIV while administering drugs that prevent new rounds of infection and allow the immune system to clear the virus. However, current approaches to HIV eradication have not been effective. Moreover, as HIV latency is multifactorial, the significance of each of its molecular mechanisms is still under debate. Among these, transcriptional repression as a result of reduced levels and activity of the positive transcription elongation factor b (P-TEFb: CDK9/cyclin T) plays a significant role. Therefore, increasing levels of P-TEFb expression and activity is an excellent strategy to stimulate viral gene expression. This review summarizes the multiple steps that cause HIV to enter into latency. It positions the interplay between transcriptionally active and inactive host transcriptional activators and their viral partner Tat as valid targets for the development of new strategies to reactivate latent viral gene expression and eradicate HIV. © 2013 by the authors; licensee MDPI, Basel, Switzerland.

Rajilic-Stojanovic M.,University of Belgrade | Rajilic-Stojanovic M.,Wageningen University | de Vos W.M.,Wageningen University | de Vos W.M.,University of Helsinki
FEMS Microbiology Reviews | Year: 2014

The microorganisms that inhabit the human gastrointestinal tract comprise a complex ecosystem with functions that significantly contribute to our systemic metabolism and have an impact on health and disease. In line with its importance, the human gastrointestinal microbiota has been extensively studied. Despite the fact that a significant part of the intestinal microorganisms has not yet been cultured, presently over 1000 different microbial species that can reside in the human gastrointestinal tract have been identified. This review provides a systematic overview and detailed references of the total of 1057 intestinal species of Eukarya (92), Archaea (8) and Bacteria (957), based on the phylogenetic framework of their small subunit ribosomal RNA gene sequences. Moreover, it unifies knowledge about the prevalence, abundance, stability, physiology, genetics and the association with human health of these gastrointestinal microorganisms, which is currently scattered over a vast amount of literature published in the last 150 years. This detailed physiological and genetic information is expected to be instrumental in advancing our knowledge of the gastrointestinal microbiota. Moreover, it opens avenues for future comparative and functional metagenomic and other high-throughput approaches that need a systematic and physiological basis to have an impact. This historical review summarizes the over 1000 species associated with the human gastrointestinal tract - it provides a systematic presentation of all currently recognized gastrointestinal tract Bacteria, Archaea and Eukarya coupled with the reports of their prevalence, abundance, their stability in the ecosystem, physiology, genetics, and association with human health. © 2014 The Authors. FEMS Microbiology Reviews published by John Wiley & Sons Ltd on behalf of Federation of European Microbiological Societies.

Joensuu H.,University of Helsinki | Dematteo R.P.,Sloan Kettering Cancer Center
Annual Review of Medicine | Year: 2012

Gastrointestinal stromal tumor (GIST) has become a model for targeted therapy in cancer. The vast majority of GISTs contain an activating mutation in either the KIT or platelet-derived growth factor A (PDGFRA) gene. GIST is highly responsive to several selective tyrosine kinase inhibitors. In fact, this cancer has been converted to a chronic disease in some patients. Considerable progress has been made recently in our understanding of the natural history and molecular biology of GIST, risk stratification, and drug resistance. Despite the efficacy of targeted therapy, though, surgery remains the only curative primary treatment and cures >50% of GIST patients who present with localized disease. Adjuvant therapy with imatinib prolongs recurrence-free survival and may improve overall survival. Combined or sequential use of tyrosine kinase inhibitors with other agents following tumor molecular subtyping is an attractive next step in the management of GIST. © 2012 by Annual Reviews. All rights reserved.

Muratore-Ginanneschi P.,University of Helsinki
Physica D: Nonlinear Phenomena | Year: 2012

The paper revisits the compressible Kraichnan model of turbulent advection in order to derive explicit quantitative relations between scaling exponents and Lagrangian particle configuration geometry. © 2010 Elsevier B.V. All rights reserved.

Clemmensen K.E.,Swedish University of Agricultural Sciences | Bahr A.,Lund University | Ovaskainen O.,University of Helsinki | Dahlberg A.,Swedish University of Agricultural Sciences | And 6 more authors.
Science | Year: 2013

Boreal forest soils function as a terrestrial net sink in the global carbon cycle. The prevailing dogma has focused on aboveground plant litter as a principal source of soil organic matter. Using 14C bomb-carbon modeling, we show that 50 to 70% of stored carbon in a chronosequence of boreal forested islands derives from roots and root-associated microorganisms. Fungal biomarkers indicate impaired degradation and preservation of fungal residues in late successional forests. Furthermore, 454 pyrosequencing of molecular barcodes, in conjunction with stable isotope analyses, highlights root-associated fungi as important regulators of ecosystem carbon dynamics. Our results suggest an alternative mechanism for the accumulation of organic matter in boreal forests during succession in the long-term absence of disturbance.

Vaara M.,University of Helsinki | Vaara M.,Northern Antibiotics Ltd.
Journal of Antimicrobial Chemotherapy | Year: 2013

BPolymyxin B and colistin (polymyxin E) are bactericidal pentacationic lipopeptides that act specifically on Gramnegative bacteria, first by disrupting their outermost permeability barrier, the outer membrane (OM), and then damaging the cytoplasmic membrane. Both were discovered in the mid-1950s and subsequently used in intravenous therapy, but soon largely abandoned because of nephrotoxicity. The emergence of extremely multiresistant strains has now forced clinicians to reinstate them in the therapy of severe infections caused by such strains. This article reviews recent attempts to develop novel derivatives of polymyxins that exhibit less toxicity and greater potency than the existing drugs. In addition, studies of novel des-fatty acyl-polymyxin derivatives that display activity against Pseudomonas aeruginosa are included. The review also covers recent studies of derivatives that lack potent bactericidal action, but which disrupt the OM, which increases bacterial permeability to other antibiotics, facilitating their entry into the cell © The Author 2013.

Gylling H.,University of Helsinki
Current Opinion in Lipidology | Year: 2014

PURPOSE OF REVIEW: The serum noncholesterol sterols are widely used today in clinical lipid research as surrogate markers of cholesterol absorption and synthesis. Their applicability and some aspects related to their analysis, use, and interpretations are discussed. RECENT FINDINGS: The serum markers of cholesterol metabolism have been carefully validated in several populations and during different interventions. If the homeostasis between cholesterol absorption and synthesis is lost, the markers cannot be used as surrogates. The markers have been applied in large population and cohort studies to find out how cholesterol metabolism is related to coronary artery disease. Most of the large studies suggested that increased levels of the markers of cholesterol absorption may conceivably be a risk factor for coronary artery disease. SUMMARY: Results even from large population studies vary from population to population. The large number of factors, which interfere with cholesterol metabolism, such as age, sex, BMI, diet, health status, medication, and genetic background, and differences in the analysis methods of the serum markers should be taken into consideration when interpreting the data. © 2014 Wolters Kluwer Health | Lippincott Williams & Wilkins.

Rivinoja A.,University of Helsinki
Methods in molecular biology (Clifton, N.J.) | Year: 2011

Each normal organ and pathological condition expresses a distinct set of molecules on their vasculature. These molecular signatures have been efficiently profiled using in vivo phage display technology. Using this technology, several peptides homing specifically to tumour blood vessels, lymphatic vessels, and/or tumour cells as well as to various normal organs have been isolated. Peptides homing to specific vascular addresses have revealed novel tissue-specific biomarkers of the normal and diseased vasculature. Tumour homing peptides have been successfully used to target therapies and imaging agents to tumours. In this review, we describe experimental setup for a combined ex vivo and in vivo screening procedure to select peptides homing to tumours.

Abrescia N.G.A.,CIC Biomagune | Abrescia N.G.A.,Ikerbasque | Bamford D.H.,University of Helsinki | Grimes J.M.,University of Oxford | And 3 more authors.
Annual Review of Biochemistry | Year: 2012

Is it possible to meaningfully comprehend the diversity of the viral world? We propose that it is. This is based on the observation that, although there is immense genomic variation, every infective virion is restricted by strict constraints in structure space (i.e., there are a limited number of ways to fold a protein chain, and only a small subset of these have the potential to construct a virion, the hallmark of a virus). We have previously suggested the use of structure for the higher-order classification of viruses, where genomic similarities are no longer observable. Here, we summarize the arguments behind this proposal, describe the current status of structural work, highlighting its power to infer common ancestry, and discuss the limitations and obstacles ahead of us. We also reflect on the future opportunities for a more concerted effort to provide high-throughput methods to facilitate the large-scale sampling of the virosphere. © 2012 by Annual Reviews. All rights reserved.

The moral problem of heavy drinking has become medicalised. However, when taking into account the different levels of medicalisation, French alcohol policy and treatment organisation has traditionally gone further than Finnish policy, although physicians in both countries are now becoming more important in the treatment of alcoholism. General practitioners (GPs) are often the first to diagnose alcoholism and they are expected to apply brief interventions, which have been proven effective in reducing heavy alcohol consumption. Focus-group interviews were conducted in Finland and France using three film clips as a stimulus for discussion. The short vignettes show incidences of alcohol problems from scenes in international fictional movies, with themes of loss of control, harm of loved ones and cue dependency. Interviews were analysed for GPs' narratives about alcohol problems and alcoholism, using the semiotic concept of focalisation. The influence of historical approaches to alcohol problems was evident in the French GPs' focus on the suffering of the alcoholic in comparison with the Finnish GPs' emphasis on the alcoholic's family misery and their obligation only in caring for the physical problems of the alcoholic. The organisation of primary health care is identified as one important factor for these differences in conceptualising heavy drinking. Implications are that the compatibility of brief interventions with institutional and cultural contexts of health care should be considered before implementation. © 2012 Copyright Taylor and Francis Group, LLC.

Koskela H.,University of Helsinki
Journal of Chromatography B: Analytical Technologies in the Biomedical and Life Sciences | Year: 2010

This review presents with selected examples the versatility of nuclear magnetic resonance (NMR) spectroscopy in the analysis of toxic organophosphorus (OP) compounds, i.e. OP pesticides and chemical warfare agents (CWAs). Several NMR applications of biological importance, like studies on inhibition mechanism, metabolism, and exposure determination, are presented. The review also concerns with the environmental analysis of OP compounds by NMR spectroscopy. Residue analysis of environment and food samples as well as characterization of degradation in environment is discussed. Some of the NMR studies that have been done to support the Chemical Weapons Convention, i.e. the development of suitable CWA detoxification means and the method development of verification analysis for CWAs and their degradation products, are outlined. © 2009 Elsevier B.V.

Alaluusua S.,University of Helsinki
European archives of paediatric dentistry : official journal of the European Academy of Paediatric Dentistry | Year: 2010

AIM: This was to review and assess the studies on aetiology of Molar-Incisor Hypomineralisation (MIH) or, as a proxy, of demarcated opacities in permanent first molars and to consider the potential factors involved with findings obtained in animal experiments. METHODS: A systematic search by Medline online database was performed. Abstracts behind appropriate titles were studied and finally the full articles were evaluated for their strength of evidence in the aetiology of MIH. RESULTS: From a total of 1,142 articles 28 were identified and selected for review. The selected papers covered medical problems in prenatal, perinatal and postnatal period, medication of the child during the first years of life, and exposure to fluoride or environmental toxicants (dioxins and PCBs) in the early childhood. Based on the assessment of the articles it was still not possible to specifically name those factors causing MIH although correlations between several potential factors and MIH were presented. Among the factors suggested and found to cause enamel defects in animal experiments were: high fever, hypoxia, hypocalcaemia, exposure to antibiotics (amoxicillin, a macrolide), and dioxins. CONCLUSION: Despite increased knowledge on the aetiology of MIH insufficient evidence to verify the causative factors exists. Further studies, especially prospective ones, are needed to improve the level and strength of evidence of the role of the present putative factors and to reveal new factors that may be involved. Any combined effect of several factors should be taken into account. Experimental dose/response studies and research on the molecular mechanisms causing the abnormal function of the ameloblasts are also necessary to deepen our knowledge of MIH.

Korhonen T.K.,University of Helsinki
Journal of Thrombosis and Haemostasis | Year: 2015

Pla of the plague bacterium Yersinia pestis and PgtE of the enteropathogen Salmonella enterica are surface-exposed, transmembrane β-barrel proteases of the omptin family that exhibit a complex array of interactions with the hemostatic systems in vitro, and both proteases are established virulence factors. Pla favors fibrinolysis by direct activation of plasminogen, inactivation of the serpins plasminogen activator inhibitor-1 and α2-antiplasmin, inactivation of the thrombin-activable fibrinolysis inhibitor, and activation of single-chain urokinase. PgtE is structurally very similar but exhibits partially different functions and differ in expression control. PgtE proteolysis targets control aspects of fibrinolysis, and mimicry of matrix metalloproteinases enhances cell migration that should favor the intracellular spread of the bacterium. Enzymatic activity of both proteases is strongly influenced by the environment-induced variations in lipopolysaccharide that binds to the β-barrel. Both proteases cleave the tissue factor pathway inhibitor and thus also express procoagulant activity. © 2015 International Society on Thrombosis and Haemostasis.

Korpela K.,University of Helsinki | Korpela K.,University of Aberdeen | Korpela K.,University of Eastern Finland
PloS one | Year: 2014

BACKGROUND: Interactions between the diet and intestinal microbiota play a role in health and disease, including obesity and related metabolic complications. There is great interest to use dietary means to manipulate the microbiota to promote health. Currently, the impact of dietary change on the microbiota and the host metabolism is poorly predictable and highly individual. We propose that the responsiveness of the gut microbiota may depend on its composition, and associate with metabolic changes in the host.METHODOLOGY: Our study involved three independent cohorts of obese adults (n = 78) from Belgium, Finland, and Britain, participating in different dietary interventions aiming to improve metabolic health. We used a phylogenetic microarray for comprehensive fecal microbiota analysis at baseline and after the intervention. Blood cholesterol, insulin and inflammation markers were analyzed as indicators of host response. The data were divided into four training set - test set pairs; each intervention acted both as a part of a training set and as an independent test set. We used linear models to predict the responsiveness of the microbiota and the host, and logistic regression to predict responder vs. non-responder status, or increase vs. decrease of the health parameters.PRINCIPAL FINDINGS: Our models, based on the abundance of several, mainly Firmicute species at baseline, predicted the responsiveness of the microbiota (AUC  =  0.77-1; predicted vs. observed correlation  =  0.67-0.88). Many of the predictive taxa showed a non-linear relationship with the responsiveness. The microbiota response associated with the change in serum cholesterol levels with an AUC of 0.96, highlighting the involvement of the intestinal microbiota in metabolic health.CONCLUSION: This proof-of-principle study introduces the first potential microbial biomarkers for dietary responsiveness in obese individuals with impaired metabolic health, and reveals the potential of microbiota signatures for personalized nutrition.

Predation affects life history traits of nearly all organisms and the population consequences of predator avoidance are often larger than predation itself. Climate change has been shown to cause phenological changes. These changes are not necessarily similar between species and may cause mismatches between prey and predator. Eurasian sparrowhawk Accipiter nisus, the main predator of passerines, has advanced its autumn phenology by about ten days in 30 years due to climate change. However, we do not know if sparrowhawk migrate earlier in response to earlier migration by its prey or if earlier sparrowhawk migration results in changes to predation risk on its prey. By using the median departure date of 41 passerine species I was able to show that early migrating passerines tend to advance, and late migrating species delay their departure, but none of the species have advanced their departure times as much as the sparrowhawk. This has lead to a situation of increased predation risk on early migrating long-distance migrants (LDM) and decreased the overlap of migration season with later departing short-distance migrants (SDM). Findings highlight the growing list of problems of declining LDM populations caused by climate change. On the other hand it seems that the autumn migration may become safer for SDM whose populations are growing. Results demonstrate that passerines show very conservative response in autumn phenology to climate change, and thus phenological mismatches caused by global warming are not necessarily increasing towards the higher trophic levels. © 2011 Aleksi Lehikoinen.

Ristola M.,University of Helsinki
Clinical science (London, England : 1979) | Year: 2014

Nephrin and Neph-family proteins [Neph1-3 (nephrin-like 1-3)] belong to the immunoglobulin superfamily of cell-adhesion receptors and are expressed in the glomerular podocytes. Both nephrin and Neph-family members function in cell adhesion and signalling, and thus regulate the structure and function of podocytes and maintain normal glomerular ultrafiltration. The expression of nephrin and Neph3 is altered in human proteinuric diseases emphasizing the importance of studying the transcriptional regulation of the nephrin and Neph3 genes NPHS1 (nephrosis 1, congenital, Finnish type) and KIRREL2 (kin of IRRE-like 2) respectively. The nephrin and Neph3 genes form a bidirectional gene pair, and they share transcriptional regulatory mechanisms. In the present review, we summarize the current knowledge of the functions of nephrin and Neph-family proteins and transcription factors and agents that control nephrin and Neph3 gene expression.

Lunden J.,University of Helsinki
Food Control | Year: 2013

The reasons for the use of enforcement measures (coercive measures) in food premises were analysed. Decisions made by local food control authorities on enforcement measures in food premises are not collected by any authority in Finland. Therefore, the type and seriousness of non-compliance leading to the use of these measures in different types of food premises are generally unknown, which may increase uncertainty in their application. Decisions on enforcement measures were requested from 29 (34%) local food control units in Finland, resulting in a total of 166 decisions from 19 control units. The non-compliance underlying these decisions was categorized into 27 categories, which were further identified as contributing factors or risk factors for outbreaks based on knowledge from previous studies.The most frequent non-compliances leading to the use of enforcement measures were incorrect labelling (34.3%), unapproved premises or activities (25.9%), poor condition of surfaces (25.9%), and inadequate cleaning (24.7%). Premises with poor condition of surfaces correlated significantly with premises showing inadequate cleaning (Fisher's exact test, p < 0.01), which is of concern because worn and dirty surfaces may cause food contamination. Temperature abuse in addition to incorrect labelling was the most frequent non-compliance being the main sole reason for enforcement measures. Several non-compliances were recorded in 64.5% of the decisions, which demonstrates that some food premises have multiple problems in complying with food legislation. Restaurants, fish processing plants, meat processing plants, and bakeries, in particular, had multiple problems in complying with food safety regulations. Restaurants and fish processing plants had the highest number of non-compliances reported as risk factors for outbreaks, the non-compliances being serious, e.g. cross-contamination and temperature abuse. The frequency of non-compliance was usually low in retail stores, warehouses, and milk processing plants. Market square premises and mobile premises had significantly higher frequency of incorrect labelling than fixed restaurants (Fisher's exact test, p < 0.05), and market place and mobile premises also showed higher frequency of temperature abuse.Several of the non-compliances (33.3%) recorded in the decisions had been recorded as contributing or risk factors for outbreaks, and 65.1% of the decisions included at least one of these non-compliances. Authorities appear therefore to use enforcement measures in cases where the occurrence of a health hazard is obvious or possible. © 2012 Elsevier Ltd.

Farkkila N.,University of Helsinki
Quality of life research : an international journal of quality of life aspects of treatment, care and rehabilitation | Year: 2014

To explore end-stage breast, prostate, and colorectal cancer patients' health-related quality of life (HRQoL); to compare results obtained by different HRQoL instruments; and to explore factors related to impaired HRQoL. A cross-sectional observational study utilized two generic HRQoL instruments, the 15D and the EQ-5D, and a cancer-specific instrument, the EORTC QLQ-C30. Patients were recruited from the Helsinki University Hospital's Department of Oncology and from a local hospice. Of the 114 palliative care patients included in the analysis, 27 had breast cancer, 30 had prostate cancer, and 57 had colorectal cancer. Of these, 28 % died within 3 months after their response, while 32 % died within three to 6 months, and 39 % died more than 6 months after. Utility values varied widely by instrument: the 15D gave the highest utility values and VAS the lowest (15D: 0.74, EQ-5D: 0.59 and VAS: 55). Patients close to death had lower HRQoL scores independently from the instrument used. The EQ-5D showed a pronounced ceiling effect, with 13 % of patients reporting full health, whereas the corresponding figures for the 15D and VAS were 1 and 0 %, respectively. Fatigue was the most common symptom and also predicted impaired HRQoL most significantly. All instruments were applicable for the evaluation of HRQoL among end-stage cancer patients. Fatigue seemed to be the most significant deteriorating factor, whereas clinical and demographic factors had less of an effect on HRQoL.

Johansson P.H.,University of Helsinki | Johansson P.H.,University of Turku | Naab T.,Max Planck Insitut fur Astrophysik | Ostriker J.P.,Peyton Hall
Astrophysical Journal | Year: 2012

We present a sample of nine high-resolution cosmological simulations in the mass range of M vir = 7 × 1011-4 × 10 12 M starting from ΛCDM initial conditions. Our simulations include primordial radiative cooling, photoionization, star formation, supernova II feedback, but exclude supernova-driven winds and active galactic nucleus feedback. The simulated galaxies assemble in two phases, with the initial growth dominated by compact (r < r eff) in situ star formation fueled by cold, low-entropy gas streams resulting in a very similar mean assembly redshift of z f, ins 2.5 for the in situ stellar component in all galaxies. The late growth is dominated by accretion of old stars formed in subunits outside the main galaxy (r > r eff) resulting in an assembly redshift of z f, acc 0.5-1.5 with much larger scatter. We find a positive correlation between the fraction of accreted stars and the final mass of our galaxies. We show that gravitational feedback strongly suppresses late star formation in massive galaxies contributing to the observed galaxy color bimodality. The accretion of stellar material is also responsible for the observed size growth of early-type galaxies. In addition, we find that the dark matter fractions within the stellar half-mass radii continuously increase toward lower redshift from about f DM 0.05 at z 3 to f DM 0.1-0.3 at z = 0. Furthermore, the logarithmic slope of the total density profile is nearly isothermal at the present day (γ′ 1.9-2.2). Finally, the input of gravitational heating lowers the central dark matter densities in the galaxies, with the effect being smaller compared to simulations without supernova feedback. © 2012. The American Astronomical Society. All rights reserved.

Legume plants can obtain combined nitrogen for their growth in an efficient way through symbiosis with specific bacteria. The symbiosis between Rhizobium galegae and its host plant Galega is an interesting case where the plant species G. orientalis and G. officinalis form effective, nitrogen-fixing, symbioses only with the appropriate rhizobial counterpart, R. galegae bv. orientalis and R. galegae bv. officinalis, respectively. The symbiotic properties of nitrogen-fixing rhizobia are well studied, but more information is needed on the properties of the host plants. The Caucasus region in Eurasia has been identified as the gene centre (centre of origin) of G. orientalis, although both G. orientalis and G. officinalis can be found in this region. In this study, the diversity of these two Galega species in Caucasus was investigated to test the hypothesis that in this region G. orientalis is more diverse than G. officinalis. The amplified fragment length polymorphism fingerprinting performed here showed that the populations of G. orientalis and R. galegae bv. orientalis are more diverse than those of G. officinalis and R. galegae bv. officinalis, respectively. These results support the centre of origin status of Caucasus for G. orientalis at a genetic level. Analysis of the symbiosis-related plant genes NORK and Nfr5 reveals remarkable diversity within the Nfr5 sequence, although no evidence of adaptive evolution could be found. © 2011 Blackwell Publishing Ltd.

Luoto T.P.,Austrian Academy of Sciences | Luoto T.P.,University of Helsinki
Journal of Paleolimnology | Year: 2012

Surface sediment samples from Lake Moaralmsee in the Austrian Alps were examined for fossil remains of aquatic insects and mites. This study investigated the influence of water depth on the fauna, to explore the possibility of using such fossil remains in sediment cores to reconstruct past water level changes. In addition, instar-specific patterns of chironomid (Diptera: Chironomidae) head capsule accumulation were examined to evaluate whether the smaller, lighter-weight early instars are more easily transported within the lake basin, creating a potential source of error for paleolimnological inferences. Results showed that intra-lake distribution of these zoological remains is closely related to water depth and suggested that the fossils accumulate near each species' habitat. In addition, the ratio between exoskeletons of oribatid mites (Acari: Oribatida) and chironomid head capsules was strongly related to water depth. Examination of instar-specific accumulation patterns of all chironomid remains showed no significant relationship between specific instars and water depth, though littoral samples consisted only of the 3rd and 4th instars. A taxon-specific examination revealed that the early instars of Paracladius are significantly focused to the deeper parts of the basin. Because most taxa displayed significant relations with water depth, a transfer function was developed, relating fossil chironomids to water depth. This model has a high coefficient of determination and a low estimate of prediction error. In this study, Paracladius was found to prefer shallow and intermediate water depths, hence enhanced offshore transport of early instar head capsules may weaken model performance statistics. Results indicate that intra-lake calibration sets of invertebrate remains have great potential in paleolimnological research, though there is a possible risk of spatial autocorrelation. Such datasets also contribute to the understanding of the modern ecology of the fauna because fossil assemblages in surface deposits provide habitat-specific autecological information. More effort should be directed at evaluating how remains of different instars are transported within other lake basins, because selective offshore transport of head capsules of different larval stages can potentially cause bias in environmental reconstructions. © 2011 Springer Science+Business Media B.V.