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Li C.,European Bioinformatics Institute | Liakata M.,European Bioinformatics Institute | Liakata M.,University of Warwick | Rebholz-Schuhmann D.,European Bioinformatics Institute | Rebholz-Schuhmann D.,University of Zuerich
Briefings in Bioinformatics | Year: 2013

Networks of molecular interactions explain complex biological processes, and all known information on molecular events is contained in a number of public repositories including the scientific literature. Metabolic and signalling pathways are often viewed separately, even though both types are composed of interactions involving proteins and other chemical entities. It is necessary to be able to combine data from all available resources to judge the functionality, complexity and completeness of any given network overall, but especially the full integration of relevant information from the scientific literature is still an ongoing and complex task. Currently, the text-mining research community is steadily moving towards processing the full body of the scientific literature by making use of rich linguistic features such as full text parsing, to extract biological interactions. The next step will be to combine these with information from scientific databases to support hypothesis generation for the discovery of new knowledge and the extension of biological networks. The generation of comprehensive networks requires technologies such as entity grounding, coordination resolution and co-reference resolution, which are not fully solved and are required to further improve the quality of results. Here, we analyse the state of the art for the extraction of network information from the scientific literature and the evaluation of extraction methods against reference corpora, discuss challenges involved and identify directions for future research. © The Author 2013.


Ziegler G.,Friedrich - Schiller University of Jena | Dahnke R.,Friedrich - Schiller University of Jena | Jancke L.,University of Zuerich | Yotter R.A.,Friedrich - Schiller University of Jena | And 2 more authors.
Human Brain Mapping | Year: 2012

The aim of this large-sample cross-sectional voxel-based morphometry (VBM) study of anatomical brain data was to investigate linear and nonlinear age-related trajectories of grey matter volume in the human brain during the adult lifespan. To date, there are only a few structural brain studies investigating local nonlinear aspects at the voxel level, i.e., without using anatomical ROIs as a priori hypothesis. Therefore, we analyzed 547 T1-weighted MR images of healthy adult brains with an age range of 19 to 86 years, including 161 scans of subjects with ages 60 and older. We found that the gray matter volume in some regions did not linearly decrease over time, but rather exhibited a delayed decline. Nonlinear age trajectories were observed in the medial temporal lobe regions, the basal ganglia, and parts of the cerebellum. Their trajectories indicated a preservation of grey matter volume during the early adult lifespan. Interestingly, we found nonlinear grey matter structural dynamics specifically in parts of the brain that have been extensively discussed in the context of learning and memory. We propose a hypothesis in relation to the functional role of these brain regions that may explain these results. © 2011 Wiley Periodicals, Inc.


Langguth B.,University of Regensburg | Landgrebe M.,University of Regensburg | Kleinjung T.,University of Regensburg | Kleinjung T.,University of Zuerich | And 2 more authors.
World Journal of Biological Psychiatry | Year: 2011

Objectives. Depressive symptoms are common in individuals with tinnitus and may substantially aggravate their distress. The mechanisms, however, by which depression and tinnitus mutually interact are still not fully understood. Methods. Here we review neurobiological knowledge relevant for the interplay between depression and tinnitus. Results. Neuroimaging studies confirm the existence of neural circuits that are activated both in depression and tinnitus. Studies of neuroendocrine function demonstrate alterations of the HPA-axis in depression and, more recently, in tinnitus. Studies addressing neurotransmission suggest that the dorsal cochlear nucleus that is typically hyperactive in tinnitus, is also involved in the control of attention and emotional responses via projections to the locus coeruleus, the reticular formation and the raphe nuclei. Impaired hippocampal neurogenesis has been documented in animals with tinnitus after noise trauma, as in animal models of depression. Finally, from investigations of human candidate genes, there is some evidence to suggest that variant BDNF may act as a common susceptibility factor in both disorders. Conclusions. These parallels in the pathophysiology of tinnitus and depression argue against comorbidity by chance and against depression as pure reaction on tinnitus. Instead, they stand for a complex interplay between tinnitus and depression. Implications for tinnitus treatment are discussed. © 2011 Informa Healthcare.


Groch S.,University of Tübingen | Groch S.,University of Lübeck | Wilhelm I.,University of Zuerich | Lange T.,University of Lübeck | And 2 more authors.
Psychoneuroendocrinology | Year: 2013

Corticosteroids are known to modulate the consolidation of memories during sleep, specifically in the hippocampus-dependent declarative memory system. However, effects of the major human corticosteroid cortisol are conveyed via two different receptors, i.e., mineralocorticoid (MRs) and glucocorticoid receptors (GRs) whose specific contributions to memory consolidation are unclear. Whereas a shift in the balance between MR and GR activation toward predominant GR activation has been found to impair sleep-dependent consolidation of declarative memories, the effect of predominant MR activation is not well characterized. Here, we examined differential corticosteroid receptor contributions to memory consolidation during post-learning sleep in two placebo-controlled double-blind studies in humans, by comparing the effects of the selective MR agonist fludrocortisone (0.2. mg, orally, Study 1) and of hydrocortisone (22. mg, intravenously, Study 2) with strong binding affinity to both MR and GR. We hypothesized increased activation of MRs during sleep to enhance declarative memory consolidation, but the joint MR/GR activation to impair it. Participants (16 men in each study) learned a declarative (word pair associates) and a procedural task (mirror tracing) before a 7-h period of nocturnal retention sleep, with the substances administered before sleep (Study 1) and during sleep (Study 2), respectively. As hypothesized, retention of word pairs, but not of mirror tracing skill, was selectively enhanced by the MR agonist fludrocortisone. An impairing effect of hydrocortisone on word pair retention remained non-significant possibly reflecting that hydrocortisone administration failed to establish robust predominance of GR activation. Our results show that predominant MR activation benefits declarative memory consolidation presumably by enhancing the sleep-dependent reactivation of hippocampal memories and resultant synaptic plastic processes. The effect is counteracted by additional GR activation. Insufficient MR activation, like GR overactivation, might be a factor contributing to memory impairment in pathological conditions. © 2013 Elsevier Ltd.


Gebhart F.T.F.,University of Bern | Brogdon B.G.,University of South Alabama | Zech W.-D.,University of Bern | Thali M.J.,University of Zuerich | Germerott T.,Hannover Medical School
Forensic Science International | Year: 2012

Postmortem computed tomography (PMCT) has become an important complement in investigating forensic cases allowing an accurate detection of gas accumulations. The present study investigated the presence and distribution of gas in a large number of non-putrefied cases of traumatic and non-traumatic deaths. Furthermore the possibility of pneumobilia secondary to blunt abdominal trauma was studied. Retrospectively, 73 cases, underwent a whole-body PMCT prior to autopsy. These were divided into four groups: penetrating trauma (20 gunshot cases, 13 stabbing cases), blunt abdominal trauma (20 cases) and a control group of 20 non-trauma cases. Exclusion criteria were visible signs of decomposition. Each group was screened for gas accumulations in the vascular system, internal organs, soft tissues and body cavities. Gas accumulations were present in 98% of the trauma cases, compared to 80% of the control group. The most affected structures and/or organs in the trauma group were soft tissues, vessels and the liver. In most cases of the trauma group gas was associated with open injuries and lacerations of vessels. Furthermore, in the gunshot group gas was frequently seen in the intracranial cavity. Pneumobilia occurred in one case of the blunt trauma group; in that control group gas was also seen, but less frequently. Gas accumulation showed a strong association with traumatic events, but even the majority of non-trauma cases showed gas accumulations. Despite the exclusion of cases with visible decomposition signs, a putrefactive origin of gas was assumed in some cases. Gas accumulations are a frequent finding in PMCT with a higher incidence in (open) trauma cases. Even though a differentiation between putrefactive and traumatic gas accumulations is still difficult, knowledge of the circumstance surrounding the case may help identify the origin of gas. © 2012 Elsevier Ireland Ltd.


Garcia-Santos G.,VU University Amsterdam | Garcia-Santos G.,University of Zuerich | Garcia-Santos G.,University of Zürich | Bruijnzeel L.A.,VU University Amsterdam
Hydrological Processes | Year: 2011

Mixed tree-heath/beech forest is a type of subtropical montane cloud forest found on wind- and fog-exposed ridges in the Canary Islands. With a dry season of 5 months and an annual precipitation of 600-700 mm, the extra water inputs through fog interception assume particular importance in this environment. Measurements were made of rainfall, fog occurrence, wind speed and direction as well as of throughfall (TF) in a ridge top cloud forest located near the centre of the National Park of Garajonay on the island of La Gomera. Measured amounts of incident rainfall were corrected for wind-induced losses around the gauge and for topographic effects. Amounts of fog water as collected by a 0·25-m2 fog screen were corrected for changes in effective screen surface collection area depending on wind direction. No such corrections were taken into account in most if not all previous studies of rainfall and fog water inputs in the Canary Islands. TF fractions differed between events with rain-only (87% of wind-corrected rainfall), fog-only (∼6% of wind-corrected fog) and mixed precipitation (110%). It is concluded that the fog screen was more efficient at capturing fog water than the forest canopy, whereas previous wetting of the canopy and bryophytes by rain may have caused the higher TF fraction found on days with rainfall and fog. Copyright © 2010 John Wiley & Sons, Ltd.


Artunc F.,University of Tübingen | Rossi C.,University of Zuerich | Boss A.,University of Zuerich
Current Opinion in Nephrology and Hypertension | Year: 2011

Purpose of Review: In addition to excellent anatomical depiction, MRI techniques have expanded to study functional aspects of renal physiology, such as renal perfusion, glomerular filtration rate (GFR) or tissue oxygenation. This review will focus on current developments with an emphasis on clinical applicability. Recent Findings: The method of GFR determination is largely heterogeneous and still has weaknesses. However, the technique of employing liver disappearance curves has been shown to be accurate in healthy persons and patients with chronic kidney disease. In potential kidney donors, complete evaluation of kidney anatomy and function can be accomplished in a single-stop investigation. Techniques without contrast media can be utilized to measure renal tissue oxygenation (blood oxygen level-dependent MRI) or perfusion (arterial spin labeling) and could aid in the diagnosis and treatment of ischemic renal diseases, such as renal artery stenosis. Diffusion imaging techniques may provide information on spatially restricted water diffusion and tumor cellularity. Summary: Functional MRI opens new horizons in studying renal physiology and pathophysiology in vivo. Although extensively utilized in research, labor-intensive postprocessing and lack of standardization currently limit the clinical applicability of functional MRI. Further studies are necessary to evaluate the clinical value of functional magnetic resonance techniques for early discovery and characterization of kidney disease. © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins.


Gabriel B.,University of Georgia | Beach S.R.H.,University of Georgia | Bodenmann G.,University of Zuerich
Behavior Therapy | Year: 2010

The correlation between depression and dysfunctional marital interaction is well documented, but only a few studies have examined gender-related differences in marital interaction patterns of couples with a depressed partner. In this paper we examined differences in observed marital communication in a sample of 62 Swiss couples presenting for treatment of depression. There were 16 maritally distressed couples with a depressed wife, 21 maritally nondistressed couples with a depressed wife, 18 maritally distressed couples with a depressed husband, and 7 maritally nondistressed couples with a depressed husband. Marital interaction behavior was found to depend on gender, depression, marital distress, as well as gender of the depressed partner. Our results suggest the need for a gender-sensitive model of the link between marital interaction and depression. © 2008.


Schiess R.,University of Zuerich | Haeusler M.,University of Zuerich
American Journal of Physical Anthropology | Year: 2013

The Nariokotome boy skeleton KNM-WT 15000 is the most complete Homo erectus fossil and therefore is key for understanding human evolution. Nevertheless, since Latimer and Ohman (2001) reported on severe congenital pathology in KNM-WT 15000, it is questionable whether this skeleton can still be used as reference for Homo erectus skeletal biology. The asserted pathologies include platyspondylic and diminutive vertebrae implying a disproportionately short stature; spina bifida; condylus tertius; spinal stenosis; and scoliosis. Based on this symptom complex, the differential diagnosis of spondyloepiphyseal dysplasia tarda, an extremely rare form of skeletal dysplasia, has been proposed. Yet, our reanalysis of these pathologies shows that the shape of the KNM-WT 15000 vertebrae matches that of normal modern human adolescents. The vertebrae are not abnormally flat, show no endplate irregularities, and thus are not platyspondylic. As this is the hallmark of spondyloepiphyseal dysplasia tarda and related forms of skeletal dysplasia, the absence of platyspondyly refutes axial dysplasia and disproportionate dwarfism. Furthermore, we neither found evidence for spina bifida occulta nor manifesta, whereas the condylus tertius, a developmental anomaly of the cranial base, is not related to skeletal dysplasias. Other fossils indicate that the relatively small size of the vertebrae and the narrow spinal canal are characteristics of early hominins rather than congenital pathologies. Except for the recently described signs of traumatic lumbar disc herniation, the Nariokotome boy fossil therefore seems to belong to a normal Homo erectus youth without pathologies of the axial skeleton. Copyright © 2013 Wiley Periodicals, Inc.


Disclosed is an antiviral agent which can be effectively used against Herpes virus. The agent includes siDNA that can bind to Herpes virus target RNA. The siDNA oligonucleotides comprise generally an antisense strand that is complementary to Herpes virus target RNA which is linked via a thymidine linker to a second strand that is partially complementary to the antisense-strand.

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