Radbound University Nijmegen

Nijmegen, Netherlands

Radbound University Nijmegen

Nijmegen, Netherlands
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Jensen M.M.,Max Planck Institute for Marine Microbiology | Jensen M.M.,University of Southern Denmark | Lam P.,Max Planck Institute for Marine Microbiology | Revsbech N.P.,University of Aarhus | And 4 more authors.
ISME Journal | Year: 2011

A combination of stable isotopes (15 N) and molecular ecological approaches was used to investigate the vertical distribution and mechanisms of biological N 2 production along a transect from the Omani coast to the central-northeastern (NE) Arabian Sea. The Arabian Sea harbors the thickest oxygen minimum zone (OMZ) in the world's oceans, and is considered to be a major site of oceanic nitrogen (N) loss. Short (48 h) anoxic incubations with 15 N-labeled substrates and functional gene expression analyses showed that the anammox process was highly active, whereas denitrification was hardly detectable in the OMZ over the Omani shelf at least at the time of our sampling. Anammox was coupled with dissimilatory nitrite reduction to ammonium (DNRA), resulting in the production of double- 15 N-labeled N 2 from 15 NO 2 , a signal often taken as the lone evidence for denitrification in the past. Although the central-NE Arabian Sea has conventionally been regarded as the primary N-loss region, low potential N-loss rates at sporadic depths were detected at best. N-loss activities in this region likely experience high spatiotemporal variabilities as linked to the availability of organic matter. Our finding of greater N-loss associated with the more productive Omani upwelling region is consistent with results from other major OMZs. The close reliance of anammox on DNRA also highlights the need to take into account the effects of coupling N-transformations on oceanic N-loss and subsequent N-balance estimates. © 2011 International Society for Microbial Ecology. All rights reserved.


Wu R.R.,Wayne State University | Yang B.,Wayne State University | Berden G.,Radbound University Nijmegen | Oomens J.,Radbound University Nijmegen | And 2 more authors.
Journal of Physical Chemistry B | Year: 2014

The gas-phase structures of protonated 2′-deoxyguanosine, [dGuo+H]+, and its RNA analogue protonated guanosine, [Guo+H]+, are investigated by infrared multiple photon dissociation (IRMPD) action spectroscopy and theoretical electronic structure calculations. IRMPD action spectra are measured over the range extending from ∼550 to 1900 cm-1 using the FELIX free electron laser and from ∼2800 to 3800 cm-1 using an optical parametric oscillator/amplifier (OPO/OPA) laser system. The measured IRMPD spectra of [dGuo+ H]+ and [Guo+ H]+ are compared to each other and to B3LYP/6-311+G(d,p) linear IR spectra predicted for the stable low-energy conformations computed for these species to determine the most favorable site of protonation, identify the structures accessed in the experiments, and elucidate the influence of the 2′-hydroxyl substituent on the structures and the IRMPD spectral features. Theoretical energetics and the measured IRMPD spectra find that N7 protonation is preferred for both [dGuo+H]+ and [Guo+H]+, whereas O6 and N3 protonated conformers are found to be much less stable. The 2′-hydroxyl substituent does not exert a significant influence on the structures and relative stabilities of the stable lowenergy conformations of [dGuo+H]+ versus [Guo+H]+ but does provide additional opportunities for hydrogen bonding such that more low-energy structures are found for [Guo+H]+. [dGuo+H]+ and [Guo+H]+ share very parallel IRMPD spectral features in the FELIX and OPO regions, whereas the effect of the 2′-hydroxyl substituent is primarily seen in the relative intensities of the measured IR bands. The measured OPO/OPA spectral signatures, primarily reflecting the IR features associated with the O -H and N-H stretches, provide complementary information to that of the FELIX region and enable the conformers that arise from different protonation sites to be more readily distinguished. Insight gained from this and parallel studies of other DNA and RNA nucleosides and nucleotides should help better elucidate the effects of the local environment on the overall structures of DNA and RNA. (Graph Presented). © 2014 American Chemical Society.


O'Reilly M.,University of Texas at Austin | Rispoli M.,Texas A&M University | Davis T.,Baylor University | Machalicek W.,University of Wisconsin - Madison | And 6 more authors.
Research in Autism Spectrum Disorders | Year: 2010

Children with autism spectrum disorders (ASDs) often present with challenging behavior, such as aggression and self-injury. In studies of children with other types of developmental disabilities challenging behavior appears more often to be maintained by attention or escape from demands. Less is known about the operant function of challenging behavior in children with ASD. The aim of the present study was to provide an analysis of the function of challenging behaviors in 10 children with ASD or PDD-NOS. Each child was assessed across five conditions (i.e., attention, escape, tangible, alone, and play). Each condition was presented 8-10 times in a multielement design while the percentage of 10-s intervals with challenging behavior (e.g., aggression, self-injury) was recorded. The results showed that for 8 of the 10 children, challenging behavior was maintained by automatic reinforcement, but by multiple sources of reinforcement for the other 2 children. The overall findings differ from the results of studies on children with other types of developmental disabilities, suggesting the possibility of a characteristically more non-social function to the challenging behavior of children with ASD. © 2010 Elsevier Ltd. All rights reserved.


Bouwman J.,Max Planck Institute for Astronomy | Lawson W.A.,Australian Defence Force Academy | Juhasz A.,Max Planck Institute for Astronomy | Dominik C.,University of Amsterdam | And 6 more authors.
Astrophysical Journal Letters | Year: 2010

We present Spitzer Space Telescope low-resolution spectroscopy of the protoplanetary disk around the M4 star RECX 5, a low-mass member of the ≈8 Myr old η Chamaeleontis star cluster. Two features of the disk around RECX 5 set it apart from other young, low-mass stars with protoplanetary disks: its mineralogy and its disk geometry. Band strengths of the crystalline silicate forsterite are a factor of two higher than that typically observed in T Tauri star disks, indicative of a high forsterite mass fraction. Continuum fluxes of the disk are inconsistent with either a flaring or flattened structure, suggesting a complex disk geometry. Radiative transfer modeling of the spectrum suggests that the disk has a gap at a radius of r = 0.6 AU, and that the disk density at r ≤ 33 AU is a factor of 100 lower than that of a continuous disk. A second disk gap might be centered at r = 24 AU. The RECX 5 disk has properties that are remarkably similar to the disk surrounding the Herbig Be star HD 100546, which is noted for having extreme mineralogy and geometry among Herbig star disks. Similar to a solution proposed for HD 100546, we speculate that the clearance of the RECX 5 disk at r ≤ 33 AU is a consequence of the formation of a Saturn-mass planet, with the planet being responsible for the striking difference in both the spectral energy distribution and chemical composition of the dust around RECX 5.©2010. The American Astronomical Society. All rights reserved.


Janssen M.J.,Radboud University Nijmegen | Waanders E.,Radboud University Nijmegen | Te Morsche R.H.M.,Radboud University Nijmegen | Xing R.,Radboud University Nijmegen | And 3 more authors.
Gastroenterology | Year: 2011

Background & Aims: Heterozygous germline mutations in PRKCSH cause autosomal dominant polycystic liver disease (PCLD), but it is not clear how they lead to cyst formation. We investigated whether mutations in cyst epithelial cells and corresponding loss of the PRKCSH gene product (hepatocystin) contributed to cyst development. Methods: Liver cyst material was collected through laparoscopic cyst fenestration from 8 patients with PCLD who had a heterozygous germline mutation in PRKCSH. Tissue sections from 71 cysts (214 per patient) were obtained for hepatocystin staining and mutation analysis. Cyst epithelium was acquired using laser microdissection; DNA was isolated and analyzed for loss of heterozygosity (LOH) and somatic mutations using restriction analysis and sequencing. Common single nucleotide polymorphisms (SNPs) in a 70-kilobase region surrounding the germline mutation were used to determine variations in the genomic region with LOH. Results: The wild-type allele of PRKCSH was lost (LOH) in 76% of cysts (54/71). Hepatocystin was not detected in cyst epithelia with LOH, whereas heterozygous cysts still expressed hepatocystin. The variation observed in the LOH region analysis indicates that cysts develop independently. We also detected somatic mutations in PRKCSH in 17% (2/12) of the cysts without LOH. Trans-heterozygous mutations in SEC63 were not observed. Conclusions: Among patients with PCLD who have a heterozygous germline mutation in PRKCSH, we found secondary, somatic mutations (second hits) in more than 76% of the liver cyst epithelia. PCLD is recessive at the cellular level, and loss of functional PRKCSH is an important step in cystogenesis. © 2011 AGA Institute.


Bakir A.,University of Plymouth | Bakir A.,University of Portsmouth | O'Connor I.A.,Radbound University Nijmegen | Rowland S.J.,University of Plymouth | And 2 more authors.
Environmental Pollution | Year: 2016

It has been hypothesised that, if ingested, plastic debris could act as vector for the transfer of chemical contaminants from seawater to organisms, yet modelling suggest that, in the natural environment, chemical transfer would be negligible compared to other routes of uptake. However, to date, the models have not incorporated consideration of the role of gut surfactants, or the influence of pH or temperature on desorption, whilst experimental work has shown that these factors can enhance desorption of sorbed contaminants several fold. Here, we modelled the transfer of sorbed organic contaminants dichlorodiphenyltrichloroethane (DDT), phenanthrene (Phe) and bis-2-ethylhexyl phthalate (DEHP) from microscopic particles of polyvinylchloride (PVC) and polyethylene (PE) to a benthic invertebrate, a fish and a seabird using a one-compartment model OMEGA (Optimal Modelling for EcotoxicoloGical Applications) with different conditions of pH, temperature and gut surfactants. Environmental concentrations of contaminants at the bottom and the top of published ranges were considered, in combination with ingestion of either 1 or 5% by weight of plastic. For all organisms, the combined intake from food and water was the main route of exposure for Phe, DEHP and DDT with a negligible input from plastic. For the benthic invertebrate, predictions including the presence of contaminated plastic resulted in very small increases in the internal concentrations of DDT and DEHP, while the net change in the transfer of Phe was negligible. While there may be scenarios in which the presence of plastic makes a more important contribution, our modelling study suggests that ingestion of microplastic does not provide a quantitatively important additional pathway for the transfer of adsorbed chemicals from seawater to biota via the gut. © 2016


Meijer H.J.M.,Radbound University Nijmegen | Fortuin A.S.,Radbound University Nijmegen | Van Lin E.N.J.T.,Radbound University Nijmegen | Debats O.A.,Radbound University Nijmegen | And 3 more authors.
Radiotherapy and Oncology | Year: 2013

Purpose: To investigate the pattern of lymph node spread on magnetic resonance lymphography (MRL) in prostate cancer patients and compare this pattern to the clinical target volume for elective pelvis irradiation as defined by the radiation therapy oncology group (RTOG-CTV). Methods and materials: The charts of 60 intermediate and high risk prostate cancer patients with non-enlarged positive lymph nodes on MRL were reviewed. Positive lymph nodes were assigned to a lymph node region according to the guidelines for delineation of the RTOG-CTV. Five lymph node regions outside this RTOG-CTV were defined: the para-aortal, proximal common iliac, pararectal, paravesical and inguinal region. Results: Fifty-three percent of the patients had an MRL-positive lymph node in a lymph node region outside the RTOG-CTV. The most frequently involved aberrant sites were the proximal common iliac, the pararectal and para-aortal region, which were affected in 30%, 25% and 18% respectively. Conclusion: More than half of the patients had an MRL-positive lymph node outside the RTOG-CTV. To reduce geographical miss while minimizing the toxicity of radiotherapy, image based definition of an individual target volume seems to be necessary. © 2013 Elsevier Ireland Ltd. All rights reserved. Radiotherapy and Oncology.


Landsbergen K.M.,Radbound University Nijmegen | Brunner E.G.,Radbound University Nijmegen | Manders P.,Radbound University Nijmegen | Hoogerbrugge N.,Radbound University Nijmegen | Prins J.B.,Radbound University Nijmegen
Genetic Counseling | Year: 2010

Introduction: Due to high cancer risks, women carrying a BRCA 1/2 mutation face a complex choice between breast and ovarian cancer surveillance and prophylactic surgery. The aim of this study is to evaluate educational-support groups, which are offered to facilitate mutual support between BRCA mutation carriers and to provide adequate information. Methods: Female BRCA mutation carriers were approached by a social worker after genetic test disclosure and offered participation in educational-support groups. Data regarding emotional well-being, breast cancer risk knowledge and perception, cancer risk management behaviour and family communication were collected both before (T1) and after group participation (T2). Results: Of the 34 participants, mean levels of negative mood states at TI were significantly higher compared to those of a norm group (depression p<0.001, anger p<0.001, fatigue p=0.04, tension p=0.03) and remained high at T2. Self-perceived breast cancer risk and frequency of cancer thoughts were high both at T1 and T2. Breast cancer risk knowledge was accurate both at T1 and T2; women either followed current surveillance advices or obtained prophylactic surgery. Communication with the family of origin was significantly reduced at T2 compared to T1 (p=0.02). At T2, all women indicated that group participation highly met their needs of BRCA-related information to support their decision-making processes regarding cancer surveillance or prophylactic surgery. Conclusion: After following an educational support group female BRCA mutation carriers were able to make cancer risk management decisions but still reported high levels of emotional distress while family communication appeared diminished.


Lucassen P.,Radbound University Nijmegen
BMJ clinical evidence | Year: 2010

INTRODUCTION: Colic in infants causes one in six families (17%) with children to consult a health professional. One systematic review of 15 community-based studies found a wide variation in prevalence, which depended on study design and method of recording.METHODS AND OUTCOMES: We conducted a systematic review and aimed to answer the following clinical question: What are the effects of treatments for colic in infants? We searched: Medline, Embase, The Cochrane Library, and other important databases up to September 2009 (Clinical Evidence reviews are updated periodically, please check our website for the most up-to-date version of this review). We included harms alerts from relevant organisations such as the US Food and Drug Administration (FDA) and the UK Medicines and Healthcare products Regulatory Agency (MHRA).RESULTS: We found 27 systematic reviews, RCTs, or observational studies that met our inclusion criteria. We performed a GRADE evaluation of the quality of evidence for interventions.CONCLUSIONS: In this systematic review we present information relating to the effectiveness and safety of the following interventions: advice to increase carrying, advice to reduce stimulation, casein hydrolysate milk, cranial osteopathy, crib vibrator device, focused counselling, gripe water, infant massage, low-lactose milk, simethicone, soya-based infant feeds, spinal manipulation, and whey hydrolysate milk.


Huijgens H.,Technical University of Delft | Gousios G.,Radbound University Nijmegen | Van Deursen A.,Technical University of Delft
International Symposium on Empirical Software Engineering and Measurement | Year: 2015

A medium-sized west-European telecom company experienced a worsening trend in performance, indicating that the organization did not learn from history, in combination with much time and energy spent on preparation and review of project proposals. In order to create more transparency in the supplier proposal pro-cess a pilot was started on Functional Size Measurement pricing (FSM-pricing). In this paper we evaluate the implementation of FSM-pricing in the software engineering domain of the company, as an instrument useful in the context of software management and supplier proposal pricing. We analyzed 77 finalized software engineering projects, covering 14 million Euro project cost and a project portfolio size of more than 5,000 function points. We found that a statistical, evidence-based pricing approach for software engineering, as a single instrument (without a connec-tion with expert judgment), can be used in the subject companies to create cost transparency and performance management of software project portfolios. © 2015 IEEE.

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