bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of flow and peristaltic mixing on bacterial growth in a gut-like channel
Authors: Cremer Jonas , Segota Igor , Yang Chih-yu , Arnoldini Markus , Sauls John T. , Zhang Zhongge , Gutierrez Edgar , Groisman Alex , Hwa Terence 
Published: September 2016

Significance
The human colon is occupied by trillions of microbial cells. Recent sequencing studies have shown that many diseases lead to substantial changes in the composition of this gut microbiota and suggest a strong influence of composition on host physiology. However, not much is known about the underlying physiological factors shaping the gut microbiota. Here, we focus on the role of flow and mixing by colonic wall contractions. To grow in the proximal colon, microbes have to continuously overcome flow. Our in vitro study suggests that mixing helps to overcome flow, and controlled contractions by the colon strongly influence microbiota density and composition; flow and mixing are essential components toward developing a predictive understanding of the gut microbiota.
Functional receptor molecules CD300lf and CD300ld within the CD300 family enable murine noroviruses to infect cells
Authors: Haga Kei , Fujimoto Akira , Takai-Todaka Reiko , Miki Motohiro , Doan Yen Hai , Murakami Kosuke , Yokoyama Masaru , Murata Kazuyoshi , Nakanishi Akira , Katayama Kazuhiko 
Published: September 2016

Significance
Norovirus is the leading cause of acute gastroenteritis worldwide. Since the discovery of norovirus, a receptor for norovirus internalization into cells has not been identified. Murine norovirus (MNV) binding to cells that were originally not susceptible to the virus can be mediated by ectopically expressed CD300 molecule like family members f or d (CD300lf or CD300ld). The expression of CD300lf or CD300ld is sufficient to render cells permissive to infection by the virus. We conclude that CD300lf and CD300ld are essential for MNV infection and that each molecule can function independently as the viral receptor.
Early somatic mosaicism is a rare cause of long-QT syndrome
Authors: Priest James Rush , Gawad Charles , Kahlig Kristopher M. , Yu Joseph K. , O’Hara Thomas , Boyle Patrick M. , Rajamani Sridharan , Clark Michael J. , Garcia Sarah T. K. , Ceresnak Scott , Harris Jason , Boyle Sean , Dewey Frederick E. , Malloy-Walton Lindsey , Dunn Kyla , Grove Megan , Perez Marco V. , Neff Norma F. , Chen Richard , Maeda Katsuhide , Dubin Anne , Belardinelli Luiz , West John , Antolik Christian , Macaya Daniela , Quertermous Thomas , Trayanova Natalia A. , Quake Stephen R. , Ashley Euan A. 
Published: September 2016

Significance
Most genetic studies and clinical genetic testing do not look for the possibility of mosaic variation. The genetic form of long-QT syndrome (LQTS) can result in life-threatening arrhythmias, but 30% of patients do not have a genetic diagnosis. We performed deep characterization of a mosaic variant in an infant with perinatal LQTS and developed a computational model showing how abnormal cellular repolarization in only 8% of heart cells may cause arrhythmia. Finally we looked at the prevalence of mosaicism among patients with LQTS; in a population of 7,500 individuals we found evidence of pathogenic early somatic mosaicism in approximately 0.17% of LQTS patients without a genetic diagnosis. Together these data establish an unreported mechanism for LQTS and other genetic arrhythmias.
A spectral line survey from 17.5–250 nm of plasmas created in a magnetic confinement device
Authors: McCarthy K J , Zurro B , Hollmann E M , Sánchez J Hernández 
Published: September 2016

Abstract
Spectral emission lines continue to be a powerful tool for studying astrophysical, process, laser-produced, and magnetically confined plasmas, among others. Hence, numerous spectroscopy-based plasma diagnostics, from the x-ray to the infrared, make use of the relative intensity, width, displacement in wavelength, or temporal evolution of such emission lines emitted by the atoms and ions present in such plasmas. In this work, a spectral line survey, from 17.5–250 nm, is presented for electron cyclotron resonance heated (ECRH) and neutral beam injection (NBI) heated plasmas created and maintained in the TJ-II stellarator, a medium-sized magnetically confined plasma device. In these plasmas, for which hydrogen, deuterium or helium have been used as the working gas, central electron temperatures and densities up to 1 keV and 5 × 1019 m−3, respectively, are achieved. This work is a compilation of the identified spectral emission lines emitted by the working gas as well by the intrinsic and injected impurity ions in the above wavelength range. For this, spectra were recorded, over the past fifteen years of TJ-II operation, using a 1 m focal length normal incidence spectrometer equipped with a charge-coupled detector at its output focal plane. In total, almost 400 spectral emission lines from eighteen different elements have been identified using a number of atomic line emission databases.
Babylonia: A Very Short Introduction
Authors: Bryce Trevor 
Published: September 2016

Abstract
Babylonia: A Very Short Introduction takes us on a journey of more than 2,000 years across the history and civilization of ancient Babylonia, from the emergence of its chief city, Babylon, as a village on the Euphrates in the 3rd millennium bc through phases of triumph, decline, and resurgence until its royal capital faded into obscurity in the Roman imperial era. Exploring key historical events as well as the day-to-day life of an ancient Babylonian—including the great Hammurabic, Kassite, and Nebuchadnezzar’s Neo-Babylonian empires as well as the periods of Persian and Macedonian rule under Alexander the Great—it provides a comprehensive guide to one of history’s most profound civilizations.
Cognitive Neuroscience: A Very Short Introduction
Authors: Passingham Richard 
Published: September 2016

Abstract
Cognitive neuroscience was born in the late 1970s when the study of patients who had suffered brain damage or injury to limited parts of the brain revealed different components and the processes taking place in the brain. Cognitive Neuroscience: A Very Short Introduction outlines the nature and scope of this relatively new field and the techniques available, focusing on investigation of the human brain. It explains what brain imaging shows, points out common misconceptions, and gives a brief overview of the different aspects of human cognition: perceiving, attending, remembering, reasoning, deciding, and acting. It concludes with a discussion of the exciting advances that may lie ahead.
The START App: a web-based RNAseq analysis and visualization resource
Authors: Nelson Jonathan W , Sklenar Jiri , Barnes Anthony P , Minnier Jessica 
Published: September 2016

Abstract

Summary
Transcriptional profiling using RNA sequencing (RNAseq) has emerged as a powerful methodology to quantify global gene expression patterns in various contexts from single cells to whole tissues. The tremendous amount of data generated by this profiling technology presents a daunting challenge in terms of effectively visualizing and interpreting results. Convenient and intuitive data interfaces are critical for researchers to easily upload, analyze and visualize their RNAseq data. We designed the START (Shiny Transcriptome Analysis Resource Tool) App with these requirements in mind. This application has the power and flexibility to be resident on a local computer or serve as a web-based environment, enabling easy sharing of data between researchers and collaborators.

Availability and Implementation
Source Code for the START App is written entirely in R and can be freely available to download at https://github.com/jminnier/STARTapp with the code licensed under GPLv3. It can be launched on any system that has R installed. The START App is also hosted on https://kcvi.shinyapps.io/START for researchers to temporarily upload their data.
Comprehensive evaluation of de novo transcriptome assembly programs and their effects on differential gene expression analysis
Authors: Wang Sufang , Gribskov Michael 
Published: September 2016

Abstract

Motivation
With the decreased cost of RNA-Seq, an increasing number of non-model organisms have been sequenced. Due to the lack of reference genomes, de novo transcriptome assembly is required. However, there is limited systematic research evaluating the quality of de novo transcriptome assemblies and how the assembly quality influences downstream analysis.

Results
We used two authentic RNA-Seq datasets from Arabidopsis thaliana, and produced transcriptome assemblies using eight programs with a series of k-mer sizes (from 25 to 71), including BinPacker, Bridger, IDBA-tran, Oases-Velvet, SOAPdenovo-Trans, SSP, Trans-ABySS and Trinity. We measured the assembly quality in terms of reference genome base and gene coverage, transcriptome assembly base coverage, number of chimeras and number of recovered full-length transcripts. SOAPdenovo-Trans performed best in base coverage, while Trans-ABySS performed best in gene coverage and number of recovered full-length transcripts. In terms of chimeric sequences, BinPacker and Oases-Velvet were the worst, while IDBA-tran, SOAPdenovo-Trans, Trans-ABySS and Trinity produced fewer chimeras across all single k-mer assemblies. In differential gene expression analysis, about 70% of the significantly differentially expressed genes (DEG) were the same using reference genome and de novo assemblies. We further identify four reasons for the differences in significant DEG between reference genome and de novo transcriptome assemblies: incomplete annotation, exon level differences, transcript fragmentation and incorrect gene annotation, which we suggest that de novo assembly is beneficial even when a reference genome is available.

Availability and Implementation
Software used in this study are publicly available at the authors' websites.

Supplementary information
Supplementary data are available at Bioinformatics online.
SEQualyzer: interactive tool for quality control and exploratory analysis of high-throughput RNA structural profiling data
Authors: Choudhary Krishna , Ruan Luyao , Deng Fei , Shih Nathan , Aviran Sharon 
Published: September 2016

Abstract

Summary
To serve numerous functional roles, RNA must fold into specific structures. Determining these structures is thus of paramount importance. The recent advent of high-throughput sequencing-based structure profiling experiments has provided important insights into RNA structure and widened the scope of RNA studies. However, as a broad range of approaches continues to emerge, a universal framework is needed to quantitatively ensure consistent and high-quality data. We present SEQualyzer, a visual and interactive application that makes it easy and efficient to gauge data quality, screen for transcripts with high-quality information and identify discordant replicates in structure profiling experiments. Our methods rely on features common to a wide range of protocols and can serve as standards for quality control and analyses.

Availability and Implementation
SEQualyzer is written in R, is platform-independent, and is freely available at http://bme.ucdavis.edu/aviranlab/SEQualyzer.

Supplementary information
Supplementary data are available at Bioinformatics online.
bTSSfinder: a novel tool for the prediction of promoters in cyanobacteria and Escherichia coli
Authors: Shahmuradov Ilham Ayub , Mohamad Razali Rozaimi , Bougouffa Salim , Radovanovic Aleksandar , Bajic Vladimir B 
Published: September 2016

Abstract

Motivation
The computational search for promoters in prokaryotes remains an attractive problem in bioinformatics. Despite the attention it has received for many years, the problem has not been addressed satisfactorily. In any bacterial genome, the transcription start site is chosen mostly by the sigma (σ) factor proteins, which control the gene activation. The majority of published bacterial promoter prediction tools target σ70 promoters in Escherichia coli. Moreover, no σ-specific classification of promoters is available for prokaryotes other than for E. coli.

Results
Here, we introduce bTSSfinder, a novel tool that predicts putative promoters for five classes of σ factors in Cyanobacteria (σA, σC, σH, σG and σF) and for five classes of sigma factors in E. coli (σ70, σ38, σ32, σ28 and σ24). Comparing to currently available tools, bTSSfinder achieves higher accuracy (MCC = 0.86, F1-score = 0.93) compared to the next best tool with MCC = 0.59, F1-score = 0.79) and covers multiple classes of promoters.

Availability and Implementation
bTSSfinder is available standalone and online at http://www.cbrc.kaust.edu.sa/btssfinder.

Supplementary information
Supplementary data are available at Bioinformatics online.
Genetic mixed-stock analysis disentangles spatial and temporal variation in composition of the West Greenland Atlantic Salmon fishery
Authors: Bradbury Ian R. , Hamilton Lorraine C. , Sheehan Timothy F. , Chaput Gerald , Robertson Martha J. , Dempson J. Brian , Reddin David , Morris Vicki , King Timothy , Bernatchez Louis 
Published: September 2016

Abstract
The West Greenland Atlantic Salmon (Salmo salar) fishery represents the largest remaining mixed-stock fishery for Atlantic Salmon in the Northwest Atlantic and targets multi-sea-winter (MSW) salmon from throughout North America and Europe. We evaluated stock composition of salmon harvested in the waters off West Greenland (n = 5684 individuals) using genetic mixture analysis and individual assignment to inform conservation of North American populations, many of which are failing to meet management targets. Regional contributions to this fishery were estimated using 2169 individuals sampled throughout the fishery between 2011 and 2014. Of these, 22% were identified as European in origin. Major North American contributions were detected from Labrador (∼20%), the Southern Gulf/Cape Breton (29%), and the Gaspe Peninsula (29%). Minor contributions (∼5%) were detected from Newfoundland, Ungava, and Quebec regions. Region-specific catches were extrapolated using estimates of composition and fishery catch logs and harvests ranged from 300 to 600 and 2000 to 3000 individuals for minor and major constituents, respectively. To evaluate the temporal stability of the observed fishery composition, we extended the temporal coverage through the inclusion of previously published data (1995–2006, n = 3095) and data from archived scales (1968–1998, n = 420). Examination of the complete time-series (47 years) suggests relative stability in stock proportions since the late 1980s. Genetic estimates of stock composition were significantly associated with model-based estimates of returning MSW salmon (individual years r = 0.69, and overall mean r = 0.96). This work demonstrates that the analysis of both contemporary and archived samples in a mixed-stock context can disentangle levels of regional exploitation and directly inform assessment and conservation of Atlantic Salmon in the West Greenland interceptory Atlantic Salmon fishery.
Mark-recapture estimation of mortality and migration rates for sea trout (Salmo trutta) in the northern Baltic sea
Authors: Whitlock Rebecca E. , Kopra Juho , Pakarinen Tapani , Jutila Eero , Leach Adrian W. , Levontin Polina , Kuikka Sakari , Romakkaniemi Atso 
Published: September 2016

Knowledge of current fishing mortality rates is an important prerequisite for formulating management plans for the recovery of threatened stocks. We present a method for estimating migration and fishing mortality rates for anadromous fishes that combines tag return data from commercial and recreational fisheries with expert opinion in a Bayesian framework. By integrating diverse sources of information and allowing for missing data, this approach may be particularly applicable in data-limited situations.Wild populations of anadromous sea trout (Salmo trutta) in the northern Baltic Sea have undergone severe declines, with the loss of many populations. The contribution of fisheries to this decline has not been quantified, but is thought to be significant. We apply the Bayesian mark-recapture model to two reared sea trout stocks from the Finnish Isojoki and Lestijoki Rivers. Over the study period (1987–2012), the total harvest rate was estimated to average 0.82 y–1 for the Isojoki River stock and 0.74 y−1 for the Lestijoki River stock. Recreational gillnet fishing at sea was estimated to be the most important source of fishing mortality for both stocks, particularly during the 1980s and 1990s. Our results indicate a high probability of unsustainable levels of fishing mortality for both stocks, and illustrate the importance of considering the effect of recreational fisheries on fish population dynamics.
Uncertainty in empirical estimates of marine larval connectivity
Authors: Kaplan David M. , Cuif Marion , Fauvelot Cécile , Vigliola Laurent , Nguyen-Huu Tri , Tiavouane Josina , Lett Christophe 
Published: September 2016

Abstract
Despite major advances in our capacity to measure marine larval connectivity (i.e. the pattern of transport of marine larvae from spawning to settlement sites) and the importance of these measurements for ecological and management questions, uncertainty in experimental estimates of marine larval connectivity has been given little attention. We review potential uncertainty sources in empirical larval connectivity studies and develop Bayesian statistical methods for estimating these uncertainties based on standard techniques in the mark-recapture and genetics literature. These methods are implemented in an existing R package for working with connectivity data, ConnMatTools, and applied to a number of published connectivity estimates. We find that the small sample size of collected settlers at destination sites is a dominant source of uncertainty in connectivity estimates in many published results. For example, widths of 95% CIs for relative connectivity, the value of which is necessarily between 0 and 1, exceeded 0.5 for many published connectivity results, complicating using individual results to conclude that marine populations are relatively closed or open. This “small sample size” uncertainty is significant even for studies with near-exhaustive sampling of spawners and settlers. Though largely ignored in the literature, the magnitude of this uncertainty is straightforward to assess. Better accountability of this and other uncertainties is needed in the future so that marine larval connectivity studies can fulfill their promises of providing important ecological insights and informing management questions (e.g. related to marine protected area network design, and stock structure of exploited organisms). In addition to using the statistical methods developed here, future studies should consistently evaluate and report a small number of critical factors, such as the exhaustivity of spawner and settler sampling, and the mating structure of target species in genetic studies.
The cancer precision medicine knowledge base for structured clinical-grade mutations and interpretations
Authors: Huang Linda , Fernandes Helen , Zia Hamid , Tavassoli Peyman , Rennert Hanna , Pisapia David , Imielinski Marcin , Sboner Andrea , Rubin Mark A , Kluk Michael , Elemento Olivier 
Published: September 2016

Objective: This paper describes the Precision Medicine Knowledge Base (PMKB; https://pmkb.weill.cornell.edu), an interactive online application for collaborative editing, maintenance, and sharing of structured clinical-grade cancer mutation interpretations.
Materials and Methods: PMKB was built using the Ruby on Rails Web application framework. Leveraging existing standards such as the Human Genome Variation Society variant description format, we implemented a data model that links variants to tumor-specific and tissue-specific interpretations. Key features of PMKB include support for all major variant types, standardized authentication, distinct user roles including high-level approvers, and detailed activity history. A REpresentational State Transfer (REST) application-programming interface (API) was implemented to query the PMKB programmatically.
Results: At the time of writing, PMKB contains 457 variant descriptions with 281 clinical-grade interpretations. The EGFR, BRAF, KRAS, and KIT genes are associated with the largest numbers of interpretable variants. PMKB’s interpretations have been used in over 1500 AmpliSeq tests and 750 whole-exome sequencing tests. The interpretations are accessed either directly via the Web interface or programmatically via the existing API.
Discussion: An accurate and up-to-date knowledge base of genomic alterations of clinical significance is critical to the success of precision medicine programs. The open-access, programmatically accessible PMKB represents an important attempt at creating such a resource in the field of oncology.
Conclusion: The PMKB was designed to help collect and maintain clinical-grade mutation interpretations and facilitate reporting for clinical cancer genomic testing. The PMKB was also designed to enable the creation of clinical cancer genomics automated reporting pipelines via an API.
A single-arm study evaluating bevacizumab, cisplatin, and paclitaxel followed by single-agent bevacizumab in Japanese patients with advanced cervical cancer
Authors: Sugiyama Toru , Mizuno Mika , Aoki Yoichi , Sakurai Manabu , Nishikawa Tadaaki , Ueda Eisuke , Tajima Kosei , Takeshima Nobuhiro 
Published: September 2016

Background
Adding bevacizumab to chemotherapy for recurrent, persistent or metastatic cervical cancer significantly improved overall survival (primary endpoint), progression-free survival and overall response rate in the randomized Phase III GOG-0240 trial. However, data for bevacizumab-containing therapy are scarce in Japanese patients with advanced cervical cancer.

Methods
The primary objective of the single-arm multicenter Phase II JO29569 study was to evaluate the tolerability of paclitaxel (135 mg/m2 over 24 h or 175 mg/m2 over 3 h), cisplatin (50 mg/m2) and bevacizumab (15 mg/kg), administered every 3 weeks until disease progression or unacceptable toxicity in Japanese patients with stage IVB, persistent or recurrent cervical cancer.

Results
The seven treated patients received a median of nine (range 7–12) bevacizumab cycles and six (range 4–12) chemotherapy cycles. None of the predefined adverse events occurred during the tolerability evaluation period. The most common all-grade adverse events were alopecia, hypertension, decreased appetite, nausea and peripheral sensory neuropathy. There were no cases of fistula. The most common grade ≥3 adverse events were hypertension, neutrophil count decreased and neutropenia. Only one patient experienced febrile neutropenia. The overall response rate was 86% (95% confidence interval, 42–100%), including a complete response in one patient. At data cutoff, disease had progressed in one patient; bevacizumab therapy was ongoing in the remaining six.

Conclusions
According to the specified primary objective, a regimen of cisplatin, paclitaxel and bevacizumab was tolerable in Japanese patients and demonstrated encouraging activity in this small single-arm study. Further study is warranted to confirm the safety and effectiveness of bevacizumab in Japanese patients with cervical cancer.