bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mass occurrence of seep-specific bivalves in the oldest-known cold seep metazoan community
Authors: Jakubowicz Michal , Hryniewicz Krzysztof , Belka Zdzislaw 
Published: October 2017

AbstractOne of the most striking features of modern chemosynthesis-based ecosystems surrounding methane seeps is the presence of abundant chemosymbiotic bivalves. However, such accumulations have rarely been reported from Palaeozoic to mid-Mesozoic seeps, and it is widely thought that general trends in the evolution of chemosynthetic communities paralleled those typifying most marine environments, with the bivalve prevalence starting in the Mesozoic and with Palaeozoic seeps being dominated by brachiopods. Here, we report a discovery of bivalve clusters in the oldest-known methane seep that hosted metazoan fauna, dated to the late Silurian. We identify the bivalves, externally very similar to modern chemosymbiotic forms, as members of the extinct family Modiomorphidae, known previously from a younger, Devonian seep. The bivalves inhabited the seep at a stage of increased fluid flow, when they co-occurred with atrypid brachiopods, and display a set of morphological characteristics suggesting a seep-obligate lifestyle. We conclude that bivalves colonised chemosynthesis-based ecosystems at least as early as brachiopods and apparently first developed specialized lineages able to thrive in seep-related habitats for a prolonged period of time. Rather than being simple ecological successors of brachiopods, rich bivalve communities represent an ancient and recurring theme in the evolution of chemosynthetic assemblages.
Species traits and connectivity constrain stochastic community re-assembly
Authors: Holt Rebecca E. , Brown Christopher J. , Schlacher Thomas A. , Sheldon Fran , Balcombe Stephen R. , Connolly Rod M. 
Published: October 2017

AbstractAll communities may re-assemble after disturbance. Predictions for re-assembly outcomes are, however, rare. Here we model how fish communities in an extremely variable Australian desert river re-assemble following episodic floods and drying. We apply information entropy to quantify variability in re-assembly and the dichotomy between stochastic and deterministic community states. Species traits were the prime driver of community state: poor oxygen tolerance, low dispersal ability, and high fecundity constrain variation in re-assembly, shifting assemblages towards more stochastic states. In contrast, greater connectivity, while less influential than the measured traits, results in more deterministic states. Ecology has long recognised both the stochastic nature of some re-assembly trajectories and the role of evolutionary and bio-geographic processes. Our models explicitly test the addition of species traits and landscape linkages to improve predictions of community re-assembly, and will be useful in a range of different ecosystems.
Heterogeneous circRNA expression profiles and regulatory functions among HEK293T single cells
Authors: Zhong Chaofang , Yu Shaojun , Han Maozhen , Chen Jiahuan , Ning Kang 
Published: October 2017

AbstractThe single-cell analysis is becoming a powerful method for early detection of the abnormal variant in tissues, especially for profiling a small number of heterogeneous cells. With the advancement of sequencing technologies, many types of non-coding elements including miRNAs and lncRNAs which shed light on their heterogeneous patterns and functions among cells, have been profiled at the single-cell level. However, the complete picture of circRNA profile at single-cell level is still lacking. In this study, RNA-Seq data obtained from single HEK293T cells have been used to analyze expressions and functions of heterogeneous circRNA profiles. The enrichment patterns of circRNAs, interactions with miRNAs and pathways such as ErbB signaling pathway and protein processing in endoplasmic reticulum, have also been investigated. The results showed that circRNAs had a specific distribution pattern which was implicated with expression, miRNA and functional profiles at single-cell level. This assessment study of the expressions and functions of circRNAs at single-cell level shed light on heterogeneities among single cells.
Genetic footprint of population fragmentation and contemporary collapse in a freshwater cetacean
Authors: Chen Minmin , Fontaine Michael C. , Ben Chehida Yacine , Zheng Jinsong , Labbé Frédéric , Mei Zhigang , Hao Yujiang , Wang Kexiong , Wu Min , Zhao Qingzhong , Wang Ding 
Published: October 2017

AbstractUnderstanding demographic trends and patterns of gene flow in an endangered species is crucial for devising conservation strategies. Here, we examined the extent of population structure and recent evolution of the critically endangered Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis). By analysing genetic variation at the mitochondrial and nuclear microsatellite loci for 148 individuals, we identified three populations along the Yangtze River, each one connected to a group of admixed ancestry. Each population displayed extremely low genetic diversity, consistent with extremely small effective size (≤92 individuals). Habitat degradation and distribution gaps correlated with highly asymmetric gene-flow that was inefficient in maintaining connectivity between populations. Genetic inferences of historical demography revealed that the populations in the Yangtze descended from a small number of founders colonizing the river from the sea during the last Ice Age. The colonization was followed by a rapid population split during the last millennium predating the Chinese Modern Economy Development. However, genetic diversity showed a clear footprint of population contraction over the last 50 years leaving only ~2% of the pre-collapsed size, consistent with the population collapses reported from field studies. This genetic perspective provides background information for devising mitigation strategies to prevent this species from extinction.
On-demand optogenetic activation of human stem-cell-derived neurons
Authors: Klapper Simon D. , Sauter Evelyn J. , Swiersy Anka , Hyman Max A. E. , Bamann Christian , Bamberg Ernst , Busskamp Volker 
Published: October 2017

AbstractThe widespread application of human stem-cell-derived neurons for functional studies is impeded by complicated differentiation protocols, immaturity, and deficient optogene expression as stem cells frequently lose transgene expression over time. Here we report a simple but precise Cre-loxP-based strategy for generating conditional, and thereby stable, optogenetic human stem-cell lines. These cells can be easily and efficiently differentiated into functional neurons, and optogene expression can be triggered by administering Cre protein to the cultures. This conditional expression system may be applied to stem-cell-derived neurons whenever timed transgene expression could help to overcome silencing at the stem-cell level.
Central Blood Pressure Monitoring via a Standard Automatic Arm Cuff
Authors: Natarajan Keerthana , Cheng Hao-Min , Liu Jiankun , Gao Mingwu , Sung Shih-Hsien , Chen Chen-Huan , Hahn Jin-Oh , Mukkamala Ramakrishna 
Published: October 2017

AbstractCurrent oscillometric devices for monitoring central blood pressure (BP) maintain the cuff pressure at a constant level to acquire a pulse volume plethysmography (PVP) waveform and calibrate it to brachial BP levels estimated with population average methods. A physiologic method was developed to further advance central BP measurement. A patient-specific method was applied to estimate brachial BP levels from a cuff pressure waveform obtained during conventional deflation via a nonlinear arterial compliance model. A physiologically-inspired method was then employed to extract the PVP waveform from the same waveform via ensemble averaging and calibrate it to the brachial BP levels. A method based on a wave reflection model was thereafter employed to define a variable transfer function, which was applied to the calibrated waveform to derive central BP. This method was evaluated against invasive central BP measurements from patients. The method yielded central systolic, diastolic, and pulse pressure bias and precision errors of −0.6 to 2.6 and 6.8 to 9.0 mmHg. The conventional oscillometric method produced similar bias errors but precision errors of 8.2 to 12.5 mmHg (p ≤ 0.01). The new method can derive central BP more reliably than some current non-invasive devices and in the same way as traditional cuff BP.
Plasticity of intrinsic excitability during LTD is mediated by bidirectional changes in h-channel activity
Authors: Gasselin Célia , Inglebert Yanis , Ankri Norbert , Debanne Dominique 
Published: October 2017

AbstractThe polarity of excitability changes associated with induction of Long-Term synaptic Depression (LTD) in CA1 pyramidal neurons is a contentious issue. Postsynaptic neuronal excitability after LTD induction is found to be reduced in certain cases (i.e. synergistic changes) but enhanced in others (i.e. compensatory or homeostatic). We examined here whether these divergent findings could result from the activation of two separate mechanisms converging onto a single learning rule linking synergistic and homeostatic plasticity. We show that the magnitude of LTD induced with low frequency stimulation (LFS) of the Schaffer collaterals determines the polarity of intrinsic changes in CA1 pyramidal neurons. Apparent input resistance (Rin) is reduced following induction of moderate LTD (<20–30%). In contrast, Rin is increased after induction of large LTD (>40%) induced by repetitive episodes of LFS. The up-regulation of Ih observed after moderate LTD results from the activation of NMDA receptors whereas the down-regulation of Ih is due to activation of mGluR1 receptors. These changes in Rin were associated with changes in intrinsic excitability. In conclusion, our study indicates that changes in excitability after LTD induction follow a learning rule describing a continuum linking synergistic and compensatory changes in excitability.
Mesiolingual root rotation for horizontal mandibular third molar extraction: position classification and surgical simulation
Authors: Ye Zhou-Xi , Yang Chi 
Published: October 2017

AbstractExtracting horizontal mandibular 3rd molars face considerable difficulty due to the large bone and adjacent tooth resistances. This study aims at evaluating the effectiveness of a novel method-mesiolingual root rotation to extract wisdom teeth of this type. In this study, 73 horizontal teeth extracted using piezosurgery were reviewed and classified based on impaction depth: position I, II, III refers to the highest portion of the crown on a level with upper 1/3, middle 1/3, lower 1/3 of the 2rd molar’s root. Based on the surgical simulations on their 3D CBCT reconstructions, traditional method(crown distal rotation) and novel method(root mesiolingual rotation) are applied. 79.17% of teeth in position I and 57.89% of teeth in position II were designed using traditional method, 83.33% teeth in position III were designed using the novel method(p < 0.05). The surgeries were performed according to the designs. Two cases in position II using traditional method were found temporary inferior alveolar nerve(IAN) injury; while only one case in position III using novel method got temporary IAN and lingual nerve injury. Our study suggested that root mesiolingual rotation is an effective method to extract the horizontal mandibular 3rd molars, especially the deep impacted ones.
Fault-Tolerant Control of ANPC Three-Level Inverter Based on Order-Reduction Optimal Control Strategy under Multi-Device Open-Circuit Fault
Authors: Xu Shi-Zhou , Wang Chun-Jie , Lin Fang-Li , Li Shi-Xiang 
Published: October 2017

AbstractThe multi-device open-circuit fault is a common fault of ANPC (Active Neutral-Point Clamped) three-level inverter and effect the operation stability of the whole system. To improve the operation stability, this paper summarized the main solutions currently firstly and analyzed all the possible states of multi-device open-circuit fault. Secondly, an order-reduction optimal control strategy was proposed under multi-device open-circuit fault to realize fault-tolerant control based on the topology and control requirement of ANPC three-level inverter and operation stability. This control strategy can solve the faults with different operation states, and can works in order-reduction state under specific open-circuit faults with specific combined devices, which sacrifices the control quality to obtain the stability priority control. Finally, the simulation and experiment proved the effectiveness of the proposed strategy.
Personality in the chimpanzees of Gombe National Park
Authors: Weiss Alexander , Wilson Michael L. , Collins D. Anthony , Mjungu Deus , Kamenya Shadrack , Foerster Steffen , Pusey Anne E. 
Published: October 2017

AbstractResearchers increasingly view animal personality traits as products of natural selection. We present data that describe the personalities of 128 eastern chimpanzees (Pan troglodytes schweinfurthii) currently living in or who lived their lives in the Kasekela and Mitumba communities of Gombe National Park, Tanzania. We obtained ratings on 24 items from an established, reliable, well-validated questionnaire used to study personality in captive chimpanzee populations. Ratings were made by former and present Tanzanian field assistants who followed individual chimpanzees for years and collected detailed behavioral observations. Interrater reliabilities across items ranged from acceptable to good, but the personality dimensions they formed were not as interpretable as those from captive samples. However, the personality dimensions corresponded to ratings of 24 Kasekela chimpanzees on a different questionnaire in 1973 that assessed some similar traits. These correlations established the repeatability and construct validity of the present ratings, indicating that the present data can facilitate historical and prospective studies that will lead to better understanding of the evolution of personality in chimpanzees and other primates.
BASIC (BLI Adenoma Serrated International Classification) classification for colorectal polyp characterization with blue light imaging
Authors: Bisschops Raf , Hassan Cesare , Bhandari Pradeep , Coron Emmanuel , Neumann Helmut , Pech Oliver , Correale Loredana , Repici Alessandro 
Published: October 2017

Abstract
Background and study aim Advanced endoscopic imaging has revolutionized the characterization of lesions during colonoscopy. The aim of this study was to create a new classification for differentiating subcentimetric hyperplastic and adenomatous polyps, and deeply invasive malignant lesions using blue-light imaging (BLI) with high definition, with and without optical magnification, as well as to assess its interobserver concordance.
Methods A video library consisting of 48 videos/still images (with/without optical magnification) from 24 histologically verified polyps/cancer with BLI was prospectively created. In the first step, seven endoscopists with experience in electronic chromoendoscopy reviewed 12 BLI videos/still images with/without magnification representative of the different histotypes, and individually identified possible descriptors. In the second step, these descriptors were categorized and summarized with a modified Delphi methodology. In the third step, the seven endoscopists independently reviewed the remaining 36 videos/still images with/without optical magnification, and the interobserver agreement for the new descriptors was assessed. The interobserver agreement between endoscopists was assessed using Gwet’s AC1.
Results By reviewing the initial 12 videos/still images, 43 descriptors were proposed. By a modified Delphi process, the endoscopists eventually agreed on summarizing 12 descriptors into three main domains. The main domains identified were: polyp surface (mucus, yes/no; regular/irregular; [pseudo]depressed, yes/no), pit appearance (featureless, yes/no; round/nonround with/without dark spots; homogeneous/heterogeneous distribution with/without focal loss), and vessels (present/absent, lacy, pericryptal, irregular). Interobserver agreement for the polyp surface domain appeared to be almost perfect for mucus (AC1 0.92 with and 0.88 without optical magnification), substantial for the regular/irregular surface (AC1 0.67 with and 0.66 without optical magnification). For the pit appearance domain, interobserver agreement was good for featureless (AC1 0.9 with and 0.8 without optical magnification), and round/nonround (AC1 0.77 with and 0.69 without optical magnification) descriptors, but less consistent for the homogeneity of distribution (AC1 with/without optical magnification 0.58). Agreement was almost perfect for the vessel domain (AC1 0.81 – 0.85).
Conclusions The new BASIC classification takes into account both morphological features of the polyp, as well as crypt and vessel characteristics. A high concordance among the observers was shown for most of the summarized descriptors. Optical magnification had a beneficial effect in terms of interobserver agreement for most of the descriptors.
Effect of normalization methods on the performance of supervised learning algorithms applied to HTSeq-FPKM-UQ data sets: 7SK RNA expression as a predictor of survival in patients with colon adenocarcinoma
Authors: Shahriyari Leili 
Published: October 2017

Abstract
Motivation: One of the main challenges in machine learning (ML) is choosing an appropriate normalization method. Here, we examine the effect of various normalization methods on analyzing FPKM upper quartile (FPKM-UQ) RNA sequencing data sets. We collect the HTSeq-FPKM-UQ files of patients with colon adenocarcinoma from TCGA-COAD project. We compare three most common normalization methods: scaling, standardizing using z-score and vector normalization by visualizing the normalized data set and evaluating the performance of 12 supervised learning algorithms on the normalized data set. Additionally, for each of these normalization methods, we use two different normalization strategies: normalizing samples (files) or normalizing features (genes). Results: Regardless of normalization methods, a support vector machine (SVM) model with the radial basis function kernel had the maximum accuracy (78%) in predicting the vital status of the patients. However, the fitting time of SVM depended on the normalization methods, and it reached its minimum fitting time when files were normalized to the unit length. Furthermore, among all 12 learning algorithms and 6 different normalization techniques, the Bernoulli naive Bayes model after standardizing files had the best performance in terms of maximizing the accuracy as well as minimizing the fitting time. We also investigated the effect of dimensionality reduction methods on the performance of the supervised ML algorithms. Reducing the dimension of the data set did not increase the maximum accuracy of 78%. However, it leaded to discovery of the 7SK RNA gene expression as a predictor of survival in patients with colon adenocarcinoma with accuracy of 78%.
VecScreen_plus_taxonomy: imposing a tax(onomy) increase on vector contamination screening
Authors: Schäffer Alejandro A , Nawrocki Eric P , Choi Yoon , Kitts Paul A , Karsch-Mizrachi Ilene , McVeigh Richard 
Published: October 2017

Abstract

Motivation
Nucleic acid sequences in public databases should not contain vector contamination, but many sequences in GenBank do (or did) contain vectors. The National Center for Biotechnology Information uses the program VecScreen to screen submitted sequences for contamination. Additional tools are needed to distinguish true-positive (contamination) from false-positive (not contamination) VecScreen matches.

Results
A principal reason for false-positive VecScreen matches is that the sequence and the matching vector subsequence originate from closely related or identical organisms (for example, both originate in Escherichia coli). We collected information on the taxonomy of sources of vector segments in the UniVec database used by VecScreen. We used that information in two overlapping software pipelines for retrospective analysis of contamination in GenBank and for prospective analysis of contamination in new sequence submissions. Using the retrospective pipeline, we identified and corrected over 8000 contaminated sequences in the nonredundant nucleotide database. The prospective analysis pipeline has been in production use since April 2017 to evaluate some new GenBank submissions.

Availability and implementation
Data on the sources of UniVec entries were included in release 10.0 (ftp://ftp.ncbi.nih.gov/pub/UniVec/). The main software is freely available at https://github.com/aaschaffer/vecscreen_plus_taxonomy.

Supplementary information
Supplementary data are available at Bioinformatics online.
ROSC-Pred: web-service for rodent organ-specific carcinogenicity prediction
Authors: Lagunin Alexey , Rudik Anastasia , Druzhilovsky Dmitry , Filimonov Dmitry , Poroikov Vladimir 
Published: October 2017

Abstract

Motivation
Identification of rodent carcinogens is an important task in risk assessment of chemicals. SAR methods were proposed to reduce the number of animal experiments. Most of these methods ignore information about organ-specificity of tumorigenesis. Our study was aimed at the creation of classification models and a freely available online service for prediction of rodent carcinogens considering the species (rats, mice), sex and tissue-specificity from structural formula of compounds.

Results
The data from Carcinogenic Potency Database for 1011 organic compounds evaluated on the standard two-year rodent carcinogenicity bioassay was used for the creation of training sets. Structure-activity relationships models for prediction of rodent organ-specific carcinogenicity were created by PASS software, which was based on Bayesian-like approach and Multilevel Neighborhoods of Atoms descriptors. The average prediction accuracy for training sets calculated by leave-one-out and 10-fold cross-validation was 79 and 78.2%, respectively.

Availability and implementation
Freely available on the web at http://www.way2drug.com/ROSC.

Supplementary information
Supplementary data are available at Bioinformatics online.
Estimating autoantibody signatures to detect autoimmune disease patient subsets
Authors: Wu Zhenke , Casciola-Rosen Livia , Shah Ami A , Rosen Antony , Zeger Scott L 
Published: October 2017

Abstract
Autoimmune diseases are characterized by highly specific immune responses against molecules in self-tissues. Different autoimmune diseases are characterized by distinct immune responses, making autoantibodies useful for diagnosis and prediction. In many diseases, the targets of autoantibodies are incompletely defined. Although the technologies for autoantibody discovery have advanced dramatically over the past decade, each of these techniques generates hundreds of possibilities, which are onerous and expensive to validate. We set out to establish a method to greatly simplify autoantibody discovery, using a pre-filtering step to define subgroups with similar specificities based on migration of radiolabeled, immunoprecipitated proteins on sodium dodecyl sulfate (SDS) gels and autoradiography [Gel Electrophoresis and band detection on Autoradiograms (GEA)]. Human recognition of patterns is not optimal when the patterns are complex or scattered across many samples. Multiple sources of errors—including irrelevant intensity differences and warping of gels—have challenged automation of pattern discovery from autoradiograms.
In this article, we address these limitations using a Bayesian hierarchical model with shrinkage priors for pattern alignment and spatial dewarping. The Bayesian model combines information from multiple gel sets and corrects spatial warping for coherent estimation of autoantibody signatures defined by presence or absence of a grid of landmark proteins. We show the pre-processing creates more clearly separated clusters and improves the accuracy of autoantibody subset detection via hierarchical clustering. Finally, we demonstrate the utility of the proposed methods with GEA data from scleroderma patients.