julilili42/papers huggingface dataset:
P776 Dysbiosis in Nlrp6/Asc-deficient mice does not result from inflammasome deficiency
2017-01-26

&lt;b&gt;Background:&lt;/b&gt; Shifts in intestinal microbial composition, termed dysbiosis, have been associated with Inflammatory Bowel Diseases (IBD). Genetic mouse models lacking Nlrp6 or Asc, which were proposed to regulate intestinal inflammasome activation, were reported with dysbiosis when compared to unrelated C57BL/6 controls, which conferred increased susceptibility to colon inflammation [1]. The Nlrp6/ASC inflammasome therefore was proposed as a host-encoded machinery that determines gut microbiota composition and thereby regulates intestinal health, suggesting that Nlrp6/ASC inflammasome deregulation may be a causal factor in eliciting dysbiosis-associated IBD. &lt;b&gt;Methods:&lt;/b&gt; Using unrelated separately housed wild-type mice as controls is prone to non-genetic factors such as housing conditions and maternal inheritance influencing the gut microbiota. We therefore subjected littermate and ex-germfree mice from distinct breeding schemes and housing conditions to faecal 16S sequencing in order to thoroughly delineate the contributions of host genetics, housing conditions and maternal inheritance to the gut microbiota composition in Nlrp6- or Asc-deficient mice. &lt;b&gt;Results:&lt;/b&gt; When comparing separately housed offspring from unrelated homozygous C57BL/6 and Nlrp6KO breeding couples, Nlrp6KO mice did not display overall gut microbial dysbiosis but did show statistically significant alterations in a number of individual bacterial taxa. In addition, cage and mother co-variates had bigger effects on the gut microbiota composition than the host genetic Nlrp6 status. Therefore, to minimise differential maternal inheritance as a confounding factor we next generated Nlrp6 and Asc+/− mice and inter-crossed those to obtain littermates of the three distinct +/+, +/− and −/− genotypes. Upon weaning, we housed these littermates separately according to their +/+, +/− and −/− genotype, thus avoiding coprophagy-mediated balancing of the gut microbiota. This tightly controlled experimental set-up allowed investigating whether the host Nlrp6 or Asc genetic status exerts an impact on the gut microbiota composition. In this controlled experimental set-up, Nlrp6−/− and Asc−/− mice did not display gut microbial dysbiosis when compared with wild-type littermates and none of the individual bacterial taxa differences in gut microbial alterations observed in Nlrp6KO vs C57BL/6 mice could be reproduced in these littermates. &lt;b&gt;Conclusions:&lt;/b&gt; These results show that the Nlrp6/Asc host genetic status does not influence the composition of the faecal microbiota and suggest that prior dysbiosis findings in inflammasome-deficient mice may result rather from differential maternal inheritance and/or long-term separate housing. References: [1] Elinav E, Strowig T, Kau AL, Henao-Mejia J, Thaiss CA, Booth CJ, Peaper DR, Bertin J, Eisenbarth SC, Gordon JI, Flavell RA (2011), NLRP6 inflammasome regulates colonic microbial ecology and risk for colitis. Cell
Antenatal management in fetal and neonatal alloimmune thrombocytopenia: a systematic review
2017-01-27

Key Points The systematic review suggests that first-line antenatal management in FNAIT is weekly IVIG administration. Noninvasive management is effective without the relatively high rate of adverse outcomes seen in invasive strategies.
Affinity of Rimantadine Enantiomers against Influenza A/M2 Protein Revisited
2017-01-27

Recent findings from solid state NMR (ssNMR) studies suggested that the (<i>R</i>)-enantiomer of rimantadine binds to the full M2 protein with higher affinity than the (<i>S</i>)-enantiomer. Intrigued by these findings, we applied functional assays, such as antiviral assay and electrophysiology (EP), to evaluate the binding affinity of rimantadine enantiomers to the M2 protein channel. Unexpectedly, no significant difference was found between the two enantiomers. Our experimental data based on the full M2 protein function were further supported by alchemical free energy calculations and isothermal titration calorimetry (ITC) allowing an evaluation of the binding affinity of rimantadine enantiomers to the M2TM pore. Both enantiomers have similar channel blockage, affinity, and antiviral potency.
Grid cells show field-to-field variability and this explains the aperiodic response of inhibitory interneurons
2017-01-27

Abstract Research on network mechanisms and coding properties of grid cells assume that the firing rate of a grid cell in each of its fields is the same. Furthermore, proposed network models predict spatial regularities in the firing of inhibitory interneurons that are inconsistent with experimental data. In this paper, by analyzing the response of grid cells recorded from rats during free navigation, we first show that there are strong variations in the mean firing rate of the fields of individual grid cells and thus show that the data is inconsistent with the theoretical models that predict similar peak magnitudes. We then build a two population excitatory-inhibitory network model in which sparse spatially selective input to the excitatory cells, presumed to arise from e.g. salient external stimuli, hippocampus or a combination of both, leads to the variability in the firing field amplitudes of grid cells. We show that, when combined with appropriate connectivity between the excitatory and inhibitory neurons, the variability in the firing field amplitudes of grid cells results in inhibitory neurons that do not exhibit regular spatial firing, consistent with experimental data. Finally, we show that even if the spatial positions of the fields are maintained, variations in the firing rates of the fields of grid cells are enough to cause remapping of hippocampal cells.
Conversion of nitriles to 1-aminophosphonic acids and preparation of phosphahomocysteines of high enantiomeric excess
2017-01-27

GRAPHICAL ABSTRACTConversion of nitriles to 1-aminophosphonic acids and preparation of phosphahomocysteines of high enantiomeric excessAll authorsRenzhe Qian, Jeannie Horak & Friedrich Hammerschmidthttps://doi.org/10.1080/10426507.2017.1284844Published online:25 May 2017
A comprehensive quality control workflow for paired tumor-normal NGS experiments
2017-01-27

Abstract Summary Quality control (QC) is an important part of all NGS data analysis stages. Many available tools calculate QC metrics from different analysis steps of single sample experiments (raw reads, mapped reads and variant lists). Multi-sample experiments, as sequencing of tumor-normal pairs, require additional QC metrics to ensure validity of results. These multi-sample QC metrics still lack standardization. We therefore suggest a new workflow for QC of DNA sequencing of tumor-normal pairs. With this workflow well-known single-sample QC metrics and additional metrics specific for tumor-normal pairs can be calculated. The segmentation into different tools offers a high flexibility and allows reuse for other purposes. All tools produce qcML, a generic XML format for QC of -omics experiments. qcML uses quality metrics defined in an ontology, which was adapted for NGS. Availability and Implementation All QC tools are implemented in C ++ and run both under Linux and Windows. Plotting requires python 2.7 and matplotlib. The software is available under the ‘GNU General Public License version 2’ as part of the ngs-bits project: https://github.com/imgag/ngs-bits Supplementary information Supplementary data are available at Bioinformatics online.
“Nonspatial” Attentional Deficits Interact with Spatial Position in Neglect
2017-01-27

Abstract A widely debated question concerns whether or not spatial and nonspatial components of visual attention interact in attentional performance. Spatial neglect is a common consequence of brain injury where individuals fail to respond to stimuli presented on their contralesional side. It has been argued that, beyond the spatial bias, these individuals also tend to exhibit nonspatial perceptual deficits. Here we demonstrate that the “nonspatial” deficits affecting the temporal dynamics of attentional deployment are in fact modulated by spatial position. Specifically, we observed that the pathological attentional blink of chronic neglect is enhanced when stimuli are presented on the contralesional side of the trunk while keeping retinal and head-centered coordinates constant. We did not find this pattern in right brain-damaged patients without neglect or in patients who had recovered from neglect. Our work suggests that the nonspatial attentional deficits observed in neglect are heavily modulated by egocentric spatial position. This provides strong evidence against models that suggest independent modules for spatial and nonspatial attentional functions while also providing strong evidence that trunk position plays an important role in neglect.
On the combined effect of soil fertility and topography on tree growth in subtropical forest ecosystems—a study from SE China
2017-01-28

Background: Moderate salt stress, which often occurs in most saline agriculture land, suppresses crop growth and reduces crop yield. Rice, as an important food crop, is sensitive to salt stress and rice genotypes differ in their tolerance to salt stress. Despite extensive studies on salt tolerance of rice, a few studies have specifically investigated the mechanism by which rice plants respond and tolerate to moderate salt stress. Two rice genotypes differing in their tolerance to saline-alkaline stress, Dongdao-4 and Jigeng-88, were used to explore physiological and molecular mechanisms underlying tolerance to moderate salt stress. Results: Dongdao-4 plants displayed higher biomass, chlorophyll contents, and photosynthetic rates than Jigeng-88 under conditions of salt stress. No differences in K+ concentrations, Na+ concentrations and Na+/K+ ratio in shoots between Dongdao-4 and Jigeng-88 plants were detected when challenged by salt stress, suggesting that Na+ toxicity may not underpin the greater tolerance of Dongdao-4 to salt stress than that of Jigeng-88. We further demonstrated that Dongdao-4 plants had greater capacity to accumulate soluble sugars and proline (Pro) than Jigeng-88, thus conferring greater tolerance of Dongdao-4 to osmotic stress than Jigeng-88. Moreover, Dongdao-4 suffered from less oxidative stress than Jigeng-88 under salt stress due to higher activities of catalase (CAT) in Dongdao-4 seedlings. Finally, RNA-seq revealed that Dongdao-4 and Jigeng-88 differed in their gene expression in response to salt stress, such that salt stress changed expression of 456 and 740 genes in Dongdao-4 and Jigeng-88, respectively. Conclusion: Our results revealed that Dongdao-4 plants were capable of tolerating to salt stress by enhanced accumulation of Pro and soluble sugars to tolerate osmotic stress, increasing the activities of CAT to minimize oxidative stress, while Na+ toxicity is not involved in the greater tolerance of Dongdao-4 to moderate salt stress.
Tracer‐based characterization of hyporheic exchange and benthic biolayers in streams
2017-01-28

Abstract Shallow benthic biolayers at the top of the streambed are believed to be places of enhanced biogeochemical turnover within the hyporheic zone. They can be investigated by reactive stream tracer tests with tracer recordings in the streambed and in the stream channel. Common in‐stream measurements of such reactive tracers cannot localize where the processing primarily takes place, whereas isolated vertical depth profiles of solutes within the hyporheic zone are usually not representative of the entire stream. We present results of a tracer test where we injected the conservative tracer bromide together with the reactive tracer resazurin into a third‐order stream and combined the recording of in‐stream breakthrough curves with multidepth sampling of the hyporheic zone at several locations. The transformation of resazurin was used as an indicator of metabolism, and high‐reactivity zones were identified from depth profiles. The results from our subsurface analysis indicate that the potential for tracer transformation (i.e., the reaction rate constant) varied with depth in the hyporheic zone. This highlights the importance of the benthic biolayer, which we found to be on average 2 cm thick in this study, ranging from one third to one half of the full depth of the hyporheic zone. The reach‐scale approach integrated the effects of processes along the reach length, isolating hyporheic processes relevant for whole‐stream chemistry and estimating effective reaction rates.
Long-term functional outcome in patients with acquired infections after acute spinal cord injury
2017-01-28

Hospital-acquired Pn/Wi are predictive of propagated disability and mortality after SCI. Pn/Wi qualify as a potent and targetable outcome-modifying factor. Pn/Wi prevention constitutes a viable strategy to protect functional recovery and reduce mortality. Pn/Wi can be considered as rehabilitation confounders in clinical trials.
Deciphering topographic signals of glaciation and rock uplift in an active orogen: a case study from the Olympic Mountains, USA
2017-01-28

Abstract Estimating recent patterns of erosion and rock uplift within Cenozoic orogens has proven difficult as signals of these processes have been obfuscated by Plio‐Pleistocene glaciation. The topography of many mountain ranges integrates the effects of long‐lived rock uplift, Late‐Cenozoic climate variation, and post‐glacial landscape adjustment. In this study, we employ a suite of topographic analyses to study the relief of an active mountain range on a sub‐catchment scale in an effort to the separate the long‐term signal of rock uplift from perturbations due to shorter‐lived climate signals. We focus on the Olympic Mountains, USA, where patterns of exhumation and glaciation have been previously estimated; however, our methods and results are broadly applicable to other orogens. Our analysis shows that Plio‐Pleistocene alpine glaciers and the Cordilleran Ice Sheet have reduced the elevations of channel profiles and created anomalously low channel relief in the Olympic Mountains. Large low‐gradient areas formed at lower elevations where ice sheets were present and alpine glaciers widened and deepened valleys. In the more rugged core of the range, near‐threshold hillslopes along the margins of the oversteepened glacially‐carved valleys, dominate the range. This implies a strong Plio‐Pleistocene glacial climate control on the topography over the more recent evolution of the Olympic Mountains. However, the broad relief structure of the range appears to still record the regional rock uplift pattern and is suggestive of an east‐plunging antiform, consistent with folding of the subducting plate or underplating of accreted rocks. Copyright © 2017 John Wiley &amp; Sons, Ltd.
Vertex-Coloring with Defects
2017-01-29

Defective coloring is a variant of the traditional vertex-coloring in which adjacent vertices are allowed to have the same color, as long as the induced monochromatic components have a certain structure. Due to its important applications, as for example in the bipartisation of graphs, this type of coloring has been extensively studied, mainly with respect to the size, degree, diameter, and acyclicity of the monochromatic components. We focus on defective colorings with colors in which the monochromatic components are acyclic and have small diameter, namely we consider (edge, )-colorings, in which the monochromatic components have diameter , and (star, )-colorings, in which they have diameter . We prove that the (edge, )-coloring problem remains NP-complete even for graphs with maximum vertex-degree , hence answering an open question posed by Cowen et al. [Cowen, Goddard, Jesurum, J. Graph Theory, 1997], and for planar graphs with maximum vertex-degree , and we prove that the (star, )-coloring problem is NP-complete even for planar graphs with bounded maximum vertex-degree. On the other hand, we give linear-time algorithms for testing the existence of (edge, )-colorings and of (star, )-colorings of partial -trees. Finally, we prove that outerpaths, a notable subclass of outerplanar graphs, always admit (star, )-colorings.
Needs and Requirements of Modern Biobanks on the Example of Dystonia Syndromes
2017-01-29

Dystonia belongs to a group of rare diseases (RDs) characterized by etiologic heterogeneity, affection often in childhood, severe and variable clinical manifestation. The burden of this disease is aggravated by the lack of effective and specific treatment. In the field of dystonia as in other RDs the number of available biospecimens is, in general, limited. Here, we report a new approach to collect clinical and genetic data in biospecimens maintained collaboratively by researchers and their associated institutions in a decentralized system. Allowing researchers to have access to significant numbers of samples and corresponding clinical data, biobanking in dystonia might not only provide a powerful tool in the identification of disease genes but also the classification of variants detected in known genes with respect to their clinical relevance. Growing data in genetics due to the technical progress demand for well-annotated and well-managed biobanks, which in near future hold even the potential for biomarker research and generating medical treatment based on clinical and genetic data currently summarized as "personalized medicine."
Aortic elongation and the risk for dissection: the Tübingen Aortic Pathoanatomy (TAIPAN) project†
2017-01-30

TAD-prediction based on the aortic diameter is ineffective. Besides circumferential dilatation, ascending aorta elongation precedes TAD and appears to be a useful additional parameter for prognostication. We propose a diagnostic score involving ascending aorta diameter and length.
Impact of end-stage renal disease on glucose metabolism—a matched cohort analysis
2017-01-30

Our study is the first to provide metabolic phenotyping in patients with ESRD and to compare them with matched controls with normal renal function. Glucose metabolism differs substantially between cohorts, with insulin resistance and a compensatory increase in insulin secretion in ESRD patients.
Impact of tree diversity and environmental conditions on the survival of shrub species in a forest biodiversity experiment in subtropical China
2017-01-30

Forests of the Sierra Nevada (SN) mountain range are valuable natural heritages for the region and the country, and tree height is an important forest structure parameter for understanding the SN forest ecosystem. There is still a need in the accurate estimation of wall-to-wall SN tree height distribution at fine spatial resolution. In this study, we presented a method to map wall-to-wall forest tree height (defined as Lorey's height) across the SN at 70-m resolution by fusing multi-source datasets, including over 1600 in situ tree height measurements and over 1600 km(2) airborne light detection and ranging (LiDAR) data. Accurate tree height estimates within these airborne LiDAR boundaries were first computed based on in situ measurements, and then these airborne LiDAR-derived tree heights were used as reference data to estimate tree heights at Geoscience Laser Altimeter System (GLAS) footprints. Finally, the random forest algorithm was used to model the SN tree height from these GLAS tree heights, optical imagery, topographic data, and climate data. The results show that our fine-resolution SN tree height product has a good correspondence with field measurements. The coefficient of determination between them is 0.60, and the root-mean-squared error is 5.45 m.
Comparing sensitivity estimates from MLDS and forced-choice methods in a slant-from-texture experiment
2017-01-30

Maximum likelihood difference scaling (MLDS) is a method for the estimation of perceptual scales based on the judgment of differences in stimulus appearance (Maloney & Yang, 2003). MLDS has recently also been used to estimate near-threshold discrimination performance (Devinck & Knoblauch, 2012). Using MLDS as a psychophysical method for sensitivity estimation is potentially appealing, because MLDS has been reported to need less data than forced-choice procedures, and particularly naive observers report to prefer suprathreshold comparisons to JND-style threshold tasks. Here we compare two methods, MLDS and two-interval forced-choice (2-IFC), regarding their capability to estimate sensitivity assuming an underlying signal-detection model. We first examined the theoretical equivalence between both methods using simulations. We found that they disagreed in their estimation only when sensitivity was low, or when one of the assumptions on which MLDS is based was violated. Furthermore, we found that the confidence intervals derived from MLDS had a low coverage; i.e., they were too narrow, underestimating the true variability. Subsequently we compared MLDS and 2-IFC empirically using a slant-from-texture task. The amount of agreement between sensitivity estimates from the two methods varied substantially across observers. We discuss possible reasons for the observed disagreements, most notably violations of the MLDS model assumptions. We conclude that in the present example MLDS and 2-IFC could equally be used to estimate sensitivity to differences in slant, with MLDS having the benefit of being more efficient and more pleasant, but having the disadvantage of unsatisfying coverage.
Transitions to retirement – Learning to redesign one’s lifestyle
2017-01-30

With the ongoing political debate in many western countries on retirement age and ways of designing the transition into the post-professional phase of life, the transition from work to retirement seems to be on the agenda again. The research questions guiding this study are: how do older workers plan their retirement and how do they prepare themselves for it? Which facets of their current conditions of living and working and which biographical aspects have an impact on the way they learn and prepare for this new phase of life? How do retired adults sum up the transition and the significance of learning related to this process? To better understand the ways older workers prepare themselves for this next phase of life, on the one hand, and to contrast their expectations and plans with the actual experiences of those who already went through this transitional process, we collected data from 24 qualitative interviews and from a questionnaire answered by a representative quantitative sample of German adults aged 50 to 69. Some of the initial results derived from this data are presented here. We provide some empirical insight into the transition to retirement and, based on this, point to possible ways of supporting older workers faced with this transition through educational programs.