julilili42/papers huggingface dataset:
Henkin semantics for reasoning with natural language
2016-02-11

The frequency of intensional and non-first-order definable operators in natural languages constitutes a challenge for automated reasoning with the kind of logical translations that are deemed adequate by formal semanticists. Whereas linguists employ expressive higher-order logics in their theories of meaning, the most successful logical reasoning strategies with natural language to date rely on sophisticated first-order theorem provers and model builders. In order to bridge the fundamental mathematical gap between linguistic theory and computational practice, we present a general translation from a higher-order logic frequently employed in the linguistics literature, two-sorted Type Theory, to first-order logic under Henkin semantics. We investigate alternative formulations of the translation, discuss their properties, and evaluate the availability of linguistically relevant inferences with standard theorem provers in a test suite of inference problems stated in English. The results of the experiment indicate that translation from higher-order logic to first-order logic under Henkin semantics is a promising strategy for automated reasoning with natural languages.The paper is accompanied by the source code (cf. SUPP. FILES) of the grammar and reasoning architecture described in the paper.
Increased Frequency of T Follicular Helper Cells and Elevated Interleukin-27 Plasma Levels in Patients with Pemphigus
2016-02-12

Pemphigus is an autoimmune disease in which IgG auto-antibodies (auto-ab) against the desmosomal cadherins desmoglein (Dsg) 3 and Dsg1 cause loss of epidermal keratinocyte adhesion. Aim of this study was to investigate cytokines derived from antigen-presenting cells (APC) and their relation to CD4+ T cell subpopulations and to the auto-ab response in pemphigus. In this regard, patients with pemphigus were compared to patients with myasthenia gravis (MG), an unrelated auto-ab-mediated autoimmune disease, and healthy controls. In pemphigus and MG, the plasma concentrations of the APC-derived immunomodulatory cytokine IL-27 were highly increased. Strikingly, IL-27 strongly correlated with Dsg-specific IgG auto-ab titers. T helper (Th) 17 cells were augmented in both pemphigus and MG patients while T follicular helper (Tfh) cells, which are essential in providing B cell help, were increased only in pemphigus along with increasing plasma concentrations of IL-21, a cytokine produced by Th17 and Tfh cells. Moreover, we could detect Dsg3-specific autoreactive T cells producing IL-21 upon ex vivo stimulation with Dsg3. These findings suggest that IL-27 and IL-21-producing T cells, are involved in the pathogenesis of pemphigus. The further characterization of IL-21-producing T cells and of the role of IL-27 will lead to a more defined understanding of the auto-ab response in pemphigus.
Small-scale disturbances in the stratigraphy of the NEEM ice core: observations and numerical model simulations
2016-02-12

Abstract. Disturbances on the centimetre scale in the stratigraphy of the North Greenland Eemian Ice Drilling (NEEM) ice core (North Greenland) can be mapped by an optical line scanner as long as the ice has visual layering, such as, for example, cloudy bands. Different focal depths allow, to a certain extent, a three-dimensional view of the structures. In this study we present a detailed analysis of the visible folds, discuss their characteristics and frequency, and present examples of typical fold structures. We also analyse the structures with regard to the deformation boundary conditions under which they formed. The structures evolve from gentle waves at about 1500 m to overturned z folds with increasing depth. Occasionally, the folding causes significant thickening of layers. Their similar fold shape indicates that they are passive features and are probably not initiated by rheology differences between alternating layers. Layering is heavily disturbed and tracing of single layers is no longer possible below a depth of 2160 m. C axes orientation distributions for the corresponding core sections were analysed, where available, in addition to visual stratigraphy. The data show axial-plane parallel strings of grains with c axis orientations that deviate from that of the matrix, which shows a single maximum fabric at the depth where the folding occurs. Numerical modelling of crystal viscoplastic deformation and dynamic recrystallisation was used to improve the understanding of the formation of the observed structures during deformation. The modelling reproduces the development of bands of grains with a tilted-lattice orientation relative to the single maximum fabric of the matrix, and also the associated local deformation. We conclude from these results that the observed folding can be explained by formation of these tilted-lattice bands.
The ignoble savage in urban Yerevan
2016-02-12

This article focuses on a recent development in the Armenian capital, Yerevan, described by its urban population as a ruralization process. I explore what it means to call something or someone ‘rural’ or ‘urban’, and I compare the social category of ‘rural people’ with the social category of the (old) urban intelligentsia. This includes an analysis and reconsideration of the traditional ‘nature–culture dichotomy’ and its meaning for the architecture and urban planning of Yerevan. It also interrogates the classification of people into newcomers from the countryside, urban dwellers, new elites, and young men called rabiz.
The chloride‐channel blocker 9‐anthracenecarboxylic acid reduces the nonlinear capacitance of prestin‐associated charge movement
2016-02-12

The basis of the extraordinary sensitivity and frequency selectivity of the cochlea is a chloride-sensitive protein called prestin which can produce an electromechanical response and which resides in the basolateral plasma membrane of outer hair cells (OHCs). The compound 9-anthracenecarboxylic acid (9-AC), an inhibitor of chloride channels, has been found to reduce the electromechanical response of the cochlea and the OHC mechanical impedance. To elucidate these 9-AC effects, the functional electromechanical status of prestin was assayed by measuring the nonlinear capacitance of OHCs from the guinea-pig cochlea and of prestin-transfected human embryonic kidney 293 (HEK 293) cells. Extracellular application of 9-AC caused reversible, dose-dependent and chloride-sensitive reduction in OHC nonlinear charge transfer, Qmax . Prestin-transfected cells also showed reversible reduction in Qmax . For OHCs, intracellular 9-AC application as well as reduced intracellular pH had no detectable effect on the reduction in Qmax by extracellularly applied 9-AC. In the prestin-transfected cells, cytosolic application of 9-AC approximately halved the blocking efficacy of extracellularly applied 9-AC. OHC inside-out patches presented the whole-cell blocking characteristics. Disruption of the cytoskeleton by preventing actin polymerization with latrunculin A or by decoupling of spectrin from actin with diamide did not affect the 9-AC-evoked reduction in Qmax . We conclude that 9-AC acts on the electromechanical transducer principally by interaction with prestin rather than acting via the cytoskeleton, chloride channels or pH. The 9-AC block presents characteristics in common with salicylate, but is almost an order of magnitude faster. 9-AC provides a new tool for elucidating the molecular dynamics of prestin function.
Monitoring carcinogenesis in a case of oral squamous cell carcinoma using a panel of new metabolic blood biomarkers as liquid biopsies
2016-02-13

A combination strategy using a standardized panel of established (metabolic) blood biomarkers (TKTL1, LDH, LDH isoenzymes) is worth and can be recommended among others (apoptosis resistance-related Apo10, SCC-Ag) for early detection and diagnosis of primary, secondary, and recurrent OSCC. A tandem strategy utilizing (metabolic pronounced) routine liquid biopsies with imaging techniques may enhance diagnosis of OSCC in the future. Although we demonstrated the diagnostic utility of separated liquid biopsies in our previous study cohorts, further investigations in a larger patient cohort are necessary to recommend this combination strategy (EDIM blood test, LDH value, metabolic shift of LDH isoenzymes, and others, e.g., SCC-Ag or immunophenotyping) as a diagnostic tool for the addition to the OSCC staging system and as a routine procedure in the aftercare.
Development of the synganglion and morphology of the adult nervous system in the mite Archegozetes longisetosus Aoki (Chelicerata, Actinotrichida, Oribatida)
2016-02-13

ABSTRACT Small arthropods show a highly condensed central nervous system, which is accompanied by the loss of the ancestral metameric organization. This results in the formation of one solid mass, a synganglion. Although numerous studies investigated the morphology of Archegozetes longisetosus , the organization of the nervous system is to date unknown. Using synchrotron X‐ray microtomography, we investigated the organization of the nervous system in the adult stage and the development of the synganglion over all five free‐living life stages (larva, proto‐, deuto‐, tritonymph and adult). The general morphology of the synganglion resembles that of other studied mites (in the classic sense) and ticks, being subdivided into a sub‐ and supraesophageal region, and consisting of cortex and neuropil. All nerves entering the walking legs except the first consist of two rami. This split is not based on a functional division into a motor and a sensory ramus, but both rami contain motor and sensory neurites. Within the synganglion, we found structures that resemble the ancestral metameric organization of the nervous system of arthropods. The development of the synganglion of A. longisetosus shows a more or less linear increase in volume, but cortex and neuropil grow at different rates over the five life stages. Between the second and third nymphal stage, the volume of the neuropil increases at a faster rate than the cortex. J. Morphol. 277:537–548, 2016. © 2016 Wiley Periodicals, Inc.
Eating disorder pathology in elite adolescent athletes
2016-02-15

ABSTRACT Objective We aimed to investigate eating disorder pathology in German elite adolescent athletes. Evidence suggests that eating disorder pathology is more common in adult elite sports, especially in female athletes and in sports emphasizing leanness. There is a scarcity of studies in elite adolescent athletes who are in a vulnerable developmental stage and are affected by general as well as sport‐specific risk factors. Method Our data was derived from the German Young Olympic Athletes' Lifestyle and Health Management Study (GOAL) which conducted a survey in 1138 elite adolescent athletes. In this sample, we assessed body weight, weight control behavior, body acceptance and screened overall for core symptoms of eating disorders, depression and anxiety. We performed a tree analysis to identify high risk groups for eating disorder pathology. Results High risk groups comprised (a) athletes competing in weight dependent sports, and among athletes competing in disciplines other than weight dependent sports (b) athletes who are high on negative affectivity, (c) female athletes and (d) male athletes competing in endurance, technical or power sports. Athletes competing in weight dependent disciplines reported wide spread use of compensatory behaviors to influence body weight. Athletes reporting eating disorder pathology showed higher levels of depression and anxiety than athletes without eating disorder pathology. Discussion Increased psychosocial burden in athletes with eating disorder pathology suggests that eating disorder symptoms should not be accepted as an unproblematic and functional part of elite sports. The prevention and management of eating disorder pathology is especially important in weight dependent sports. © 2016 Wiley Periodicals, Inc. (Int J Eat Disord 2016; 49:553–562)
Fibroblast growth factor (Fgf) 23 gene transcription depends on actin cytoskeleton reorganization
2016-02-15

FGF 23 regulates renal phosphate and vitamin D metabolism. Loss of FGF 23 results in massive calcification and rapid aging. FGF 23 production is stimulated by 1,25( OH ) 2 D 3 and NF κB signaling. Here, we report that treatment of UMR 106 osteoblast‐like cells with 1,25( OH ) 2 D 3 , inducing Fgf23 transcription, resulted in actin polymerization which was blocked by NF κB inhibitor wogonin. Interestingly, 1,25( OH ) 2 D 3 ‐induced Fgf23 gene transcription was abolished by the actin microfilament‐disrupting agent cytochalasin B, as well as by the inhibition of actin‐regulating Rac1/ PAK 1 signaling. Our results provide strong evidence that actin redistribution regulated by the Rac1/ PAK 1 pathway participates in 1,25( OH ) 2 D 3 ‐induced Fgf23 gene transcription.
Nutrient Addition Modifies Phosphatase Activities along an Altitudinal Gradient in a Tropical Montane Forest in Southern Ecuador
2016-02-15

Atmospheric nutrient deposition and climate change are expected to endanger the diversity of tropical forest ecosystems. Nitrogen (N) deposition might influence nutrient fluxes beyond the N cycle by a concomitant increased demand for other nutritional elements such as phosphorus (P). Organisms might respond to the increased P demand by enhanced activity of enzymes involved in releasing inorganic P from organic matter (OM). Our aims were to assess the effect of i) climate shifts (approximated by an altitudinal gradient), and ii) nutrient addition (N, P, N+P) on phosphatase activity (PA) in organic layer and mineral soil of a tropical montane rainforest in Southern Ecuador. A nutrient manipulation experiment (NUMEX) was set up along an altitudinal gradient (1000, 2000, and 3000 m a.s.l.). We determined PA and inorganic and total P concentrations. PA at 1000 m was significantly lower (mean ± standard error: 48 ± 20 μmol p-NP g-1 dm h-1) as compared to 2000 m and 3000 m (119 ± 11 and 137 ± 19, respectively). One explanation might be that very rapid decomposition of OM at 1000 m results in very thin organic layers reducing the stabilization of enzymes and thus, resulting in leaching loss of enzymes under the humid tropical climate. We found no effect of N addition on PA neither in the organic layer nor in mineral soil, probably because of the low nutrient addition rates that showed ambiguous results so far on productivity measures as a proxy for P demand. In the organic layers of P and N+P treatments, we found decreased PA and increased concentrations of inorganic P. This indicates that the surplus of inorganic P reduced the biosynthesis of phosphatase enzymes. PA in megadiverse montane rainforests is likely to be unaffected by increased atmospheric N deposition but reduced upon atmospheric P deposition.
Reducing rainfall amount has a greater negative effect on the productivity of grassland plant species than reducing rainfall frequency
2016-02-15

The productivity of semiarid Australian grassland ecosystems is currently limited by water availability and may be impacted further by predicted changes in rainfall regimes associated with climate change. In this study, we established a rainfall manipulation experiment to determine the effects of reduced frequency (RF; 8 days between water events) and reduced magnitude (RM; 50% reduction in amount) of rainfall events on the physiology and above- and below-ground growth of five grassland plant species with differing traits. Native C4 grasses exhibited the highest productivity in well watered, control (Cont) conditions, as well as in RF and RM treatments. The RF treatment generally had little effect on total biomass, rooting distributions or photosynthesis, suggesting species were relatively tolerant of reduction in the frequency of rainfall events. However, the RM treatment had a negative effect on total biomass and physiology, and generally resulted in a shift towards shallower rooting profiles. Overall, the reduction in biomass was greater in RM than RF, suggesting that rainfall magnitude may be a more important determinant of grassland productivity and composition than the frequency of rainfall events under future climates.
BALL-SNPgp—from genetic variants toward computational diagnostics
2016-02-15

Abstract Summary: In medical research, it is crucial to understand the functional consequences of genetic alterations, for example, non-synonymous single nucleotide variants (nsSNVs). NsSNVs are known to be causative for several human diseases. However, the genetic basis of complex disorders such as diabetes or cancer comprises multiple factors. Methods to analyze putative synergetic effects of multiple such factors, however, are limited. Here, we concentrate on nsSNVs and present BALL-SNPgp, a tool for structural and functional characterization of nsSNVs, which is aimed to improve pathogenicity assessment in computational diagnostics. Based on annotated SNV data, BALL-SNPgp creates a three-dimensional visualization of the encoded protein, collects available information from different resources concerning disease relevance and other functional annotations, performs cluster analysis, predicts putative binding pockets and provides data on known interaction sites. Availability and implementation: BALL-SNPgp is based on the comprehensive C ++ framework Biochemical Algorithms Library (BALL) and its visualization front-end BALLView. Our tool is available at www.ccb.uni-saarland.de/BALL-SNPgp. Contact: ballsnp@milaman.cs.uni-saarland.de
BK K+ channel blockade inhibits radiation-induced migration/brain infiltration of glioblastoma cells
2016-02-16

Infiltration of the brain by glioblastoma cells reportedly requires Ca2+ signals and BK K+ channels that program and drive glioblastoma cell migration, respectively. Ionizing radiation (IR) has been shown to induce expression of the chemokine SDF-1, to alter the Ca2+ signaling, and to stimulate cell migration of glioblastoma cells. Here, we quantified fractionated IR-induced migration/brain infiltration of human glioblastoma cells in vitro and in an orthotopic mouse model and analyzed the role of SDF-1/CXCR4 signaling and BK channels. To this end, the radiation-induced migratory phenotypes of human T98G and far-red fluorescent U-87MG-Katushka glioblastoma cells were characterized by mRNA and protein expression, fura-2 Ca2+ imaging, BK patch-clamp recording and transfilter migration assay. In addition, U-87MG-Katushka cells were grown to solid glioblastomas in the right hemispheres of immunocompromised mice, fractionated irradiated (6 MV photons) with 5 × 0 or 5 × 2 Gy, and SDF-1, CXCR4, and BK protein expression by the tumor as well as glioblastoma brain infiltration was analyzed in dependence on BK channel targeting by systemic paxilline application concomitant to IR. As a result, IR stimulated SDF-1 signaling and induced migration of glioblastoma cells in vitro and in vivo. Importantly, paxilline blocked IR-induced migration in vivo. Collectively, our data demonstrate that fractionated IR of glioblastoma stimulates and BK K+ channel targeting mitigates migration and brain infiltration of glioblastoma cells in vivo. This suggests that BK channel targeting might represent a novel approach to overcome radiation-induced spreading of malignant brain tumors during radiotherapy.
The Influence of Menstrual Cycle and Androstadienone on Female Stress Reactions: An fMRI Study
2016-02-16

Communicating threats and stress via biological signaling is common in animals. In humans, androstadienone (ANDR), a synthetic male steroid, is a socially relevant chemosignal exhibited to increase positive mood and cortisol levels specifically in (periovulatory) females in positively arousing contexts. In a negative context, we expected that such effects of ANDR could amplify social evaluative threat depending on the stress sensitivity, which differs between menstrual cycle phases. Therefore, this fMRI study aimed to examine psychosocial stress reactions on behavioral, hormonal and neural levels in 31 naturally cycling females, between 15 early follicular (EF) and 16 mid-luteal (ML) females tested with ANDR and placebo treatment in a repeated-measures design. Regardless of odor stimulation, psychosocial stress (i.e., mental arithmetic task with social evaluative threat) led to elevated negative mood and anxiety in all females. A negative association of social threat related amygdala activation and competence ratings appeared in ML-females, indicating enhanced threat processing by ANDR, particularly in ML-females who felt less competent early in the stress experience. Further, ML-females showed reduced performance and stronger stress-related hippocampus activation compared to EF-females under ANDR. Hippocampal activation in ML-females also correlated positively with post-stress subjective stress. Contrarily, such patterns were not observed in EF-females or under placebo in either group. Strikingly, unlike passive emotional processing, ANDR in a stressful context decreased cortisol concentration in all females. This points to a more complex interaction of ovarian/gonadal hormones in social threat processing and stress reactivity. Our findings suggest that ANDR enhanced initial evaluation of self-related social threat in ML-females. Female stress reactions are related to stress sensitivity through enhanced awareness and processing of social cues in a stressful context, with menstrual cycle phase being a critical factor.
ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis
2016-02-16

Bioinformatics analysis has become an integral part of research in biology. However, installation and use of scientific software can be difficult and often requires technical expert knowledge. Reasons are dependencies on certain operating systems or required third-party libraries, missing graphical user interfaces and documentation, or nonstandard input and output formats. In order to make bioinformatics software easily accessible to researchers, we here present a web-based platform. The Center for Bioinformatics Tuebingen (ZBIT) Bioinformatics Toolbox provides web-based access to a collection of bioinformatics tools developed for systems biology, protein sequence annotation, and expression data analysis. Currently, the collection encompasses software for conversion and processing of community standards SBML and BioPAX, transcription factor analysis, and analysis of microarray data from transcriptomics and proteomics studies. All tools are hosted on a customized Galaxy instance and run on a dedicated computation cluster. Users only need a web browser and an active internet connection in order to benefit from this service. The web platform is designed to facilitate the usage of the bioinformatics tools for researchers without advanced technical background. Users can combine tools for complex analyses or use predefined, customizable workflows. All results are stored persistently and reproducible. For each tool, we provide documentation, tutorials, and example data to maximize usability. The ZBIT Bioinformatics Toolbox is freely available at https://webservices.cs.uni-tuebingen.de/.