bluuebunny/crossref_metadata_2025_split huggingface dataset:
PHYLUCE is a software package for the analysis of conserved genomic loci
Authors: Faircloth Brant C. 
Published: November 2015

Abstract
Summary: Targeted enrichment of conserved and ultraconserved genomic elements allows universal collection of phylogenomic data from hundreds of species at multiple time scales (&lt;5 Ma to &gt; 300 Ma). Prior to downstream inference, data from these types of targeted enrichment studies must undergo preprocessing to assemble contigs from sequence data; identify targeted, enriched loci from the off-target background data; align enriched contigs representing conserved loci to one another; and prepare and manipulate these alignments for subsequent phylogenomic inference. PHYLUCE is an efficient and easy-to-install software package that accomplishes these tasks across hundreds of taxa and thousands of enriched loci.
Availability and Implementation: PHYLUCE is written for Python 2.7. PHYLUCE is supported on OSX and Linux (RedHat/CentOS) operating systems. PHYLUCE source code is distributed under a BSD-style license from https://www.github.com/faircloth-lab/phyluce/. PHYLUCE is also available as a package (https://binstar.org/faircloth-lab/phyluce) for the Anaconda Python distribution that installs all dependencies, and users can request a PHYLUCE instance on iPlant Atmosphere (tag: phyluce). The software manual and a tutorial are available from http://phyluce.readthedocs.org/en/latest/ and test data are available from doi: 10.6084/m9.figshare.1284521.
Contact: brant@faircloth-lab.org
Supplementary information: Supplementary data are available at Bioinformatics online.
Exact quantification of cellular robustness in genome-scale metabolic networks
Authors: Gerstl Matthias P. , Klamt Steffen , Jungreuthmayer Christian , Zanghellini Jürgen 
Published: November 2015

Abstract
Motivation: Robustness, the ability of biological networks to uphold their functionality in spite of perturbations, is a key characteristic of all living systems. Although several theoretical approaches have been developed to formalize robustness, it still eludes an exact quantification. Here, we present a rigorous and quantitative approach for the structural robustness of metabolic networks by measuring their ability to tolerate random reaction (or gene) knockouts.
Results: In analogy to reliability theory, based on an explicit consideration of all possible knockout sets, we exactly quantify the probability of failure for a given network function (e.g. growth). This measure can be computed if the network’s minimal cut sets (MSCs) are known. We show that even in genome-scale metabolic networks the probability of (network) failure can be reliably estimated from MSCs with lowest cardinalities. We demonstrate the applicability of our theory by analyzing the structural robustness of multiple Enterobacteriaceae and Blattibacteriaceae and show a dramatically low structural robustness for the latter. We find that structural robustness develops from the ability to proliferate in multiple growth environments consistent with experimentally found knowledge.
Conclusion: The probability of (network) failure provides thus a reliable and easily computable measure of structural robustness and redundancy in (genome-scale) metabolic networks.
Availability and implementation: Source code is available under the GNU General Public License at https://github.com/mpgerstl/networkRobustnessToolbox.
Contact: juergen.zanghellini@boku.ac.at
Supplementary information: Supplementary data are available at Bioinformatics online.
A hidden Markov random field-based Bayesian method for the detection of long-range chromosomal interactions in Hi-C data
Authors: Xu Zheng , Zhang Guosheng , Jin Fulai , Chen Mengjie , Furey Terrence S. , Sullivan Patrick F. , Qin Zhaohui , Hu Ming , Li Yun 
Published: November 2015

Abstract
Motivation: Advances in chromosome conformation capture and next-generation sequencing technologies are enabling genome-wide investigation of dynamic chromatin interactions. For example, Hi-C experiments generate genome-wide contact frequencies between pairs of loci by sequencing DNA segments ligated from loci in close spatial proximity. One essential task in such studies is peak calling, that is, detecting non-random interactions between loci from the two-dimensional contact frequency matrix. Successful fulfillment of this task has many important implications including identifying long-range interactions that assist interpreting a sizable fraction of the results from genome-wide association studies. The task – distinguishing biologically meaningful chromatin interactions from massive numbers of random interactions – poses great challenges both statistically and computationally. Model-based methods to address this challenge are still lacking. In particular, no statistical model exists that takes the underlying dependency structure into consideration.
Results: In this paper, we propose a hidden Markov random field (HMRF) based Bayesian method to rigorously model interaction probabilities in the two-dimensional space based on the contact frequency matrix. By borrowing information from neighboring loci pairs, our method demonstrates superior reproducibility and statistical power in both simulation studies and real data analysis.
Availability and implementation: The Source codes can be downloaded at: http://www.unc.edu/∼yunmli/HMRFBayesHiC.
Contact: ming.hu@nyumc.org or yunli@med.unc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
IL-28B down-regulates regulatory T cells but does not improve the protective immunity following tuberculosis subunit vaccine immunization
Authors: Luo Yanping , Ma Xingming , Liu Xun , Lu Xiaoling , Niu Hongxia , Yu Hongjuan , Bai Chunxiang , Peng Jinxiu , Xian Qiaoyang , Wang Yong , Zhu Bingdong 
Published: November 2015

AbstractRegulatory T cells (Tregs), which could be down-regulated by IL-28B, were reported to suppress T-cell-mediated immunity. The aim of this study was to investigate the role of IL-28B on the immune responses and protective efficacy of a tuberculosis (TB) subunit vaccine. First, a recombinant adenoviral vector expressing mouse IL-28B (rAd-mIL-28B) was constructed; then C57BL/6 mice were immunized with subunit vaccine ESAT6-Ag85B-Mpt64 (190–198) -Mtb8.4-HspX (EAMMH) and rAd-mIL-28B together thrice or primed with Mycobacterium bovis bacillus Calmette–Gue′rin (BCG) and boosted by EAMMH and rAd-mIL-28B twice. At last the immune responses were evaluated, and the mice primed with BCG and boosted by subunit vaccines were challenged with virulent Mycobacterium tuberculosis H37Rv to evaluate the protective efficacy. The results showed that rAd-mIL-28B treatment significantly down-regulated the frequency of Tregs at 4 weeks after the last immunization but did not increase the T h 1-type immune responses. Moreover, in the regimen of BCG priming and EAMMH boosting, rAd-mIL-28B treatment did not increase the antigen-specific cellular and humoral immune responses, and consequently did not reduce the bacteria load following H37Rv challenge. Instead, it induced more serious pathology reaction. In conclusion, IL-28B down-regulates Tregs following EAMMH vaccination but does not improve the protective immune responses.
Multilayered temporal modeling for the clinical domain
Authors: Lin Chen , Dligach Dmitriy , Miller Timothy A , Bethard Steven , Savova Guergana K 
Published: November 2015

Abstract
Objective To develop an open-source temporal relation discovery system for the clinical domain. The system is capable of automatically inferring temporal relations between events and time expressions using a multilayered modeling strategy. It can operate at different levels of granularity—from rough temporality expressed as event relations to the document creation time (DCT) to temporal containment to fine-grained classic Allen-style relations.
Materials and Methods We evaluated our systems on 2 clinical corpora. One is a subset of the Temporal Histories of Your Medical Events (THYME) corpus, which was used in SemEval 2015 Task 6: Clinical TempEval. The other is the 2012 Informatics for Integrating Biology and the Bedside (i2b2) challenge corpus. We designed multiple supervised machine learning models to compute the DCT relation and within-sentence temporal relations. For the i2b2 data, we also developed models and rule-based methods to recognize cross-sentence temporal relations. We used the official evaluation scripts of both challenges to make our results comparable with results of other participating systems. In addition, we conducted a feature ablation study to find out the contribution of various features to the system’s performance.
Results Our system achieved state-of-the-art performance on the Clinical TempEval corpus and was on par with the best systems on the i2b2 2012 corpus. Particularly, on the Clinical TempEval corpus, our system established a new F1 score benchmark, statistically significant as compared to the baseline and the best participating system.
Conclusion Presented here is the first open-source clinical temporal relation discovery system. It was built using a multilayered temporal modeling strategy and achieved top performance in 2 major shared tasks.
Transgluteal Approach for Drainage of Obturator Internus Abscess in Pediatric Patients
Authors: White Stephen , Stopka Stephanie , Nimityongskul Prasit , Jorgensen Dennis 
Published: November 2015

Background:
Of the locations of peripelvic pyomyositis, infection of the obturator musculature poses a difficult challenge for operative drainage. The anatomic location of the obturator muscles, especially the obturator internus, complicates operative debridement as the surgical approach must safely bypass a large number of neurovascular structures. Realizing the challenges and risks of approaches to the obturator musculature, the purpose of our study was to review a novel, yet simple, posterior approach to the obturator internus.

Methods:
We reviewed a case series of children (age 0 to 18 y), who presented to our institution with obturator internus pyomyositis. The patients’ demographics, vital signs, laboratory data, and radiographic findings from the initial evaluation were reviewed. Blood and intraoperative culture results were collected. Duration of symptoms and length of hospital stay were also reviewed. Cases of suspected obturator internus abscess were confirmed by magnetic resonance imaging of the pelvis. All patients in this study who met the operative indications were debrided using the posterior transgluteal approach.

Results:
Five patients were identified who met criteria for isolated obturator internus pyomyositis. Four out of the 5 patients met operative indications and underwent drainage through a transgluteal approach. One patient responded well to antibiotic treatment; therefore, no surgery was indicated. Purulence was expressed in all 4 operative cases. Hospital length of stay ranged from 6 to 14 days. All patients were treated with an IV antibiotic course for 3 to 6 weeks. All patients returned to normal function and activity levels. There were no surgical complications.

Conclusions:
This case series has reviewed a new technique for the drainage of an isolated obturator internus abscess. The transgluteal posterior approach is a simple approach that is performed through a single incision with minimal soft-tissue dissection. It avoids the risks and challenges posed by other approaches. Most importantly, our case series, although small, in our experience, has shown that it is a safe and effective approach for drainage of obturator internus abscess.

Level of Evidence:
Level IV.
The Long-term Clinical Effect of Minimal-Invasive TLIF Technique in 1-Segment Lumbar Disease
Authors: Li Yi-bing , Wang Xiao-dong , Yan Hong-wei , Hao Ding-jun , Liu Zheng-hua 
Published: November 2015

Study Design:
A prospective cohort double-center study.

Objective:
To assess the clinical effect of minimally invasive transforaminal lumbar interbody fusion (miTLIF) using the tunnel technique.

Summary of Background Data:
A series of short-term studies have indicated that miTLIF could reduce blood loss and improve clinical results. However, long-term clinical study and magnetic resonance imaging research are still scare.

Methods:
From January 2008 to January 2009, 187 patients with 1-segment lumbar disease requiring intervertebral fusion were enrolled in this study. Patients were divided into 2 groups according to the operative methods. Postoperative low back pain (LBP), postoperative lumbar function, the fusion rate, lower extremity pain relief, variation of lumbar lordosis, and implant failure were assessed. At 48 months postoperation, the cross-sectional area of the paraspinal muscle was measured using magnetic resonance imaging.

Results:
The mean duration of follow-up was 54.4±5.9 months. The intermuscular pressure generated by the tunnel in the miTLIF group was lower than that generated in the oTLIF group. Patients in the miTLIF group reported a lower degree of LBP at all timepoints. The ODI scores were similar to the VAS scores. No significant differences were found in fusion rate, lower extremity pain relief, lumbar lordosis, or implant failure rate. A significant difference was found between the 2 groups in postoperative cross-sectional area.

Conclusions:
This study confirmed the advantages of miTLIF in reducing postoperative LBP, improving postoperative quality of life and preventing paraspinal muscle atrophy compared with oTLIF, while achieving a similar therapeutic outcome. The lower intermuscular pressure generated by minimally invasive tunnel and subsequent moderate muscle atrophy were presumed to be possible reasons for its superiority.
Whole-genome modeling accurately predicts quantitative traits, as revealed in plants
Authors: Gentzbittel Laurent , Ben Cécile , Mazurier Mélanie , Shin Min-Gyoung , Triska Martin , Rickauer Martina , Nikolsky Yuri , Marjoram Paul , Nuzhdin Sergey , Tatarinova Tatiana V. 
Published: November 2015

AbstractMany adaptive events in natural populations, as well as response to artificial selection, are caused by polygenic action. Under selective pressure, the adaptive traits can quickly respond via small allele frequency shifts spread across numerous loci. We hypothesize that a large proportion of current phenotypic variation between individuals may be best explained by population admixture.We thus consider the complete, genome-wide universe of genetic variability, spread across several ancestral populations originally separated. We experimentally confirmed this hypothesis by predicting the differences in quantitative disease resistance levels among accessions in the wild legumeMedicago truncatula. We discovered also that variation in genome admixture proportion explains most of phenotypic variation for several quantitative functional traits, but not for symbiotic nitrogen fixation. We shown that positive selection at the species level might not explain current, rapid adaptation.These findings prove the infinitesimal model as a mechanism for adaptation of quantitative phenotypes. Our study produced the first evidence that the whole-genome modeling of DNA variants is the best approach to describe an inherited quantitative trait in a higher eukaryote organism and proved the high potential of admixture-based analyses. This insight contribute to the understanding of polygenic adaptation, and can accelerate plant and animal breeding, and biomedicine research programs.
repgenHMM: a dynamic programming tool to infer the rules of immune receptor generation from sequence data
Authors: Elhanati Yuval , Marcou Quentin , Mora Thierry , Walczak Aleksandra M. 
Published: November 2015

The diversity of the immune repertoire is initially generated by random rearrangements of the receptor gene during early T and B cell development. Rearrangement scenarios are composed of random events – choices of gene templates, base pair deletions and insertions – described by probability distributions. Not all scenarios are equally likely, and the same receptor sequence may be obtained in several different ways. Quantifying the distribution of these rearrangements is an essential baseline for studying the immune system diversity. Inferring the properties of the distributions from receptor sequences is a computationally hard problem, requiring enumerating every possible scenario for every sampled receptor sequence. We present a Hidden Markov model, which accounts for all plausible scenarios that can generate the receptor sequences. We developed and implemented a method based on the Baum-Welch algorithm that can efficiently infer the parameters for the different events of the rearrangement process. We tested our software tool on sequence data for both the alpha and beta chains of the T cell receptor. To test the validity of our algorithm, we also generated synthetic sequences produced by a known model, and confirmed that its parameters could be accurately inferred back from the sequences. The inferred model can be used to generate synthetic sequences, to calculate the probability of generation of any receptor sequence, as well as the theoretical diversity of the repertoire. We estimate this diversity to be ≈ 1023for human T cells. The model gives a baseline to investigate the selection and dynamics of immune repertoires.Source code and sample sequence files are available athttps://bitbucket.org/yuvalel/repgenhmm/downloads.
Genome-wide association studies suggest limited immune gene enrichment in schizophrenia compared to five autoimmune diseases
Authors: Pouget Jennie G. , Gonçalves Vanessa F. ,   Schizophrenia Working Group of the Psychiatric Genomics Consortium, Spain Sarah L. , Finucane Hilary K. , Raychaudhuri Soumya , Kennedy James L. , Knight Jo 
Published: November 2015

AbstractThere has been intense debate over the immunological basis of schizophrenia, and the potential utility of adjunct immunotherapies. The major histocompatibility complex is consistently the most powerful region of association in genome-wide association studies (GWASs) of schizophrenia, and has been interpreted as strong genetic evidence supporting the immune hypothesis. However, global pathway analyses provide inconsistent evidence of immune involvement in schizophrenia, and it remains unclear whether genetic data support an immune etiologyper se. Here we empirically test the hypothesis that variation in immune genes contributes to schizophrenia. We show that there is no enrichment of immune loci outside of the MHC region in the largest genetic study of schizophrenia conducted to date, in contrast to five diseases of known immune origin. Among 108 regions of the genome previously associated with schizophrenia, we identify six immune candidates (DPP4, HSPD1, EGR1, CLU, ESAM, NFATC3) encoding proteins with alternative, nonimmune roles in the brain. While our findings do not refute evidence that has accumulated in support of the immune hypothesis, they suggest that genetically mediated alterations in immune function may not play a major role in schizophrenia susceptibility. Instead, there may be a role for pleiotropic effects of a small number of immune genes that also regulate brain development and plasticity. Whether immune alterations drive schizophrenia progression is an important question to be addressed by future research, especially in light of the growing interest in applying immunotherapies in schizophrenia.
The single-species metagenome: subtypingStaphylococcus aureuscore genome sequences from shotgun metagenomic data
Authors: Joseph Sandeep J. , Li Ben , Petit Robert A. , Qin Zhaohui S. , Darrow Lyndsey A. , Read Timothy D. 
Published: November 2015

AbstractMetagenome shotgun sequence projects offer the potential for large scale biogeographic analysis of microbial species. In this project we developed a method for detecting 33 common subtypes of the pathogenic bacteriumStaphylococcus aureus.We used a binomial mixture model implemented in thebinstrainsoftware and the coverage counts at > 100,000 knownS. aureusSNP (single nucleotide polymorphism) sites derived from prior comparative genomic analysis to estimate the proportion of each subtype in metagenome samples. Using this pipeline we were able to obtain > 87% sensitivity and > 94% specificity when testing on low genome coverage samples of diverseS. aureusstrains (0.025X). We found that 321 and 149 metagenome samples from the Human Microbiome Project and metaSUB analysis of the New York City subway, respectively, containedS. aureusat genome coverage > 0.025. In both projects, CC8 and CC30 were the most commonS. aureussubtypes encountered. We found evidence that the subtype composition at different body sites of the same individual were more similar than random sampling and more limited evidence that certain body sites were enriched for particular subtypes. One surprising finding was the apparent high frequency of CC398, a lineage associated with livestock, in samples from the tongue dorsum. Epidemiologic analysis of the HMP subject population suggested that high BMI (body mass index) and health insurance are risk factors forS. aureusbut there was limited power to find factors linked to carriage of even the most common subtype. In the NYC subway data, we found a small signal of geographic distance affecting subtype clustering but other unknown factors influence taxonomic distribution of the species around the city. We argue that pathogen detection in metagenome samples requires the use of subtypes based on whole species population genomic analysis rather than using ad hoc collections of reference strains.
The entry drilling process of flexible printed circuit board and its influence on hole quality
Authors: Zheng Lijuan , Wang Chengyong , Zhang Xin , Song Yuexian , Zhang Lunqiang , Wang Kefeng 
Published: November 2015

Purpose
– The purpose of this study is to present the entry drilling process of flexible printed circuit board (FPCs) and its influence on hole quality, especially hole location accuracy. Compared with the traditional PCB drilling process, the technology of drilling FPCs is facing more problems, such as hole location accuracy, smear on the hole wall surface, burned hole wall surface, etc. Moreover, the materials of FPCs are quite different from the rigid printed circuit boards (RPCs). FPCs no longer contain glass fiber cloths to reinforce resin, resulting in flexibility. Micro-hole quality is the most important issue in FPC drilling. Suggestions were given to obtain higher hole qualities and higher FPC reliability.

Design/methodology/approach
– The entry drilling process of FPC with different kind of entry boards was observed by a high-speed camera. The hole qualities of FPC micro-drilling, especially hole location accuracy and hole entrance quality, were measured. The relationship between entry boards and hole quality was analyzed.

Findings
– Significant sliding occurred when drilling FPC with using no-entry board or pure aluminum plate entry board. On the contrary, no significant sliding occurred when using LC-110 or resin-coated aluminum foil (MVC) entry boards. The type, thickness and use-pattern of entry boards influenced hole location accuracy of FPCs seriously. In addition, entry board also influenced the micro-hole entrance quality and micro-hole diameter. The entrance quality of drilling FPC with LC-110 entry board was the best. The diameter variation of drilling FPC with MVC entry board was the smallest. The hole location accuracy decreased as the thickness of entry board increased. Thus, the best use-pattern of entry board was putting a LC-110 under MVC entry board, resulting in best entrance quality and hole location accuracy.

Originality/value
– The technology and manufacturing of FPCs in China are obviously behind. Research of FPCs micro-drilling and research data are lacking so far. Thus, it is most necessary to improve the technology level of FPCs micro-drilling in China. Researches on hole quality, especially hole location accuracy of FPCs drilling, were performed in this paper. Suggestions were given to obtain higher hole quality of FPCs.