bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vulgarisation scientifique et médiatisation de la science
Authors: Ledouble Hélène 
Published: July 2019

AbstractThis article explores terminological variation, in particular denominative variation, in popular science discourse. Our objective is to analyse the terminological complexity and instability of terms referring to the controversial notion ofbiocontrol (lutte biologiquein French) in two types of publications. The analysis is based on the identification of the different denominations used in this interdisciplinary subject field, both in a Journal specialized in plant protection and in the most popular French daily newspapers. Our study aims to give an in-depth linguistic and cognitive analysis of French terms and explain the reasons for the observed variation. As most scientific research topics gaining public attention, biological control (or biocontrol) is prone to a multiplication of terms. In this study, we show how the profusion of terms, in a domain with important scientific and societal implications, can maintain or even exacerbate terminological and conceptual confusion.
TermEnsembler
Authors: Repar Andraž , Podpečan Vid , Vavpetič Anže , Lavrač Nada , Pollak Senja 
Published: July 2019

Abstract
This paper describes TermEnsembler, a bilingual term extraction and alignment system utilizing a novel ensemble learning
approach to bilingual term alignment. In the proposed system, the processing starts with monolingual term extraction from a language
industry standard file type containing aligned English and Slovenian texts. The two separate term lists are then automatically aligned using
an ensemble of seven bilingual alignment methods, which are first executed separately and then merged using the weights learned with an
evolutionary algorithm. In the experiments, the weights were learned on one domain and tested on two other domains. When evaluated on the
top 400 aligned term pairs, the precision of term alignment is over 96%, while the number of correctly aligned multi-word unit terms exceeds
30% when evaluated on the top 400 term pairs.
Interpreting for Soviet leaders
Authors: Rogatchevski Andrei 
Published: July 2019

AbstractTop interpreters are rarely able to discuss publicly negotiations between their bosses-cum-clients. Yet the downfall of Nazi Germany and the USSR allowed some interpreters to speak, in interviews and memoirs, without fear of retribution. In the end, only a few told their story, and some did not always tell it correctly, either because of memory lapses or because of a desire to appear more informed or to distance themselves from the people for whom they had worked. Still, these publications contain material to investigate to what degree, in the service of an all-powerful client, interpreters remained “invisible” or exercised a “special interactional power, […] as a result of his or her bilingual and bicultural expertise” (Mason and Ren 2012: 238). This article presents a case study of Soviet interpreters for Stalin, Khrushchev, Brezhnev and Gorbachev and their associates, with memoirs by the interpreters for Hitler and British PMs consulted for cross-correlation.
Laboratory Blood-Based Testing for Non-Lyme Disease Tick-Borne Infections at a National Reference Laboratory
Authors: Lee-Lewandrowski Elizabeth , Chen Zhen , Branda John , Baron Jason , Kaufman Harvey W 
Published: July 2019

AbstractObjectivesWe evaluated trends in non-Lyme disease tick-borne disease (NLTBI) testing at a national reference laboratory.MethodsTesting data performed at Quest Diagnostics during 2010 to 2016 were analyzed nationally and at the state level.ResultsTesting and positivity for most NLTBIs increased dramatically from 2010 through 2016 based on testing from a large reference laboratory. The number of positive cases, though not as stringent as criteria for public health reporting, generally exceeds that reported by the Centers for Disease Control and Prevention. The frequency of NLTBI in the US is seasonal but testing activity and positive test results are observed throughout all months of the year. Positive results for NLTBI testing mostly originated from a limited number of states, indicating the geographic concentration and distribution of NLTBIs reported in this study.ConclusionsThis report provides an important complementary source of data to best understand trends in and spread of NLTBI.
Below-ground biomass of plants, with a key contribution of buried shoots, increases foredune resistance to wave swash
Authors: De Battisti Davide , Griffin John N 
Published: July 2019

AbstractBackground and aimsSand dunes reduce the impact of storms on shorelines and human infrastructure. The ability of these ecosystems to provide sustained coastal protection under persistent wave attack depends on their resistance to erosion. Although flume experiments show that roots of perennial plants contribute to foredune stabilization, the role of other plant organs, and of annual species, remains poorly studied. Furthermore, it remains unknown if restored foredunes provide the same level of erosion resistance as natural foredunes. We investigated the capacity of three widespread pioneer foredune species (the perennial Ammophila arenaria and the annuals Cakile maritima and Salsola kali) to resist dune erosion, and compared the erosion resistance of Ammophila at natural and restored sites.MethodsCores collected in the field were tested in a flume that simulated a wave swash. A multi-model inference approach was used to disentangle the contributions of different below-ground compartments (i.e. roots, rhizomes, buried shoots) to erosion resistance.Key ResultsAll three species reduced erosion, with Ammophila having the strongest effect (36 % erosion reduction versus unvegetated cores). Total below-ground biomass (roots, rhizomes and shoots), rather than any single compartment, most parsimoniously explained erosion resistance. Further analysis revealed that buried shoots had the clearest individual contribution. Despite similar levels of total below-ground biomass, coarser sediment reduced erosion resistance of Ammophila cores from the restored site relative to the natural site.ConclusionsThe total below-ground biomass of both annual and perennial plants, including roots, rhizomes and buried shoots, reduced dune erosion under a swash regime. Notably, we show that (1) annual pioneer species offer erosion protection, (2) buried shoots are an important plant component in driving sediment stabilization, and (3) management must consider both biological (plants and their traits) and physical (grain size) factors when integrating dunes into schemes for coastal protection.
Universal concept signature analysis: genome-wide quantification of new biological and pathological functions of genes and pathways
Authors: Chi Xu , Sartor Maureen A , Lee Sanghoon , Anurag Meenakshi , Patil Snehal , Hall Pelle , Wexler Matthew , Wang Xiao-Song 
Published: July 2019

Abstract
Identifying new gene functions and pathways underlying diseases and biological processes are major challenges in genomics research. Particularly, most methods for interpreting the pathways characteristic of an experimental gene list defined by genomic data are limited by their dependence on assessing the overlapping genes or their interactome topology, which cannot account for the variety of functional relations. This is particularly problematic for pathway discovery from single-cell genomics with low gene coverage or interpreting complex pathway changes such as during change of cell states. Here, we exploited the comprehensive sets of molecular concepts that combine ontologies, pathways, interactions and domains to help inform the functional relations. We first developed a universal concept signature (uniConSig) analysis for genome-wide quantification of new gene functions underlying biological or pathological processes based on the signature molecular concepts computed from known functional gene lists. We then further developed a novel concept signature enrichment analysis (CSEA) for deep functional assessment of the pathways enriched in an experimental gene list. This method is grounded on the framework of shared concept signatures between gene sets at multiple functional levels, thus overcoming the limitations of the current methods. Through meta-analysis of transcriptomic data sets of cancer cell line models and single hematopoietic stem cells, we demonstrate the broad applications of CSEA on pathway discovery from gene expression and single-cell transcriptomic data sets for genetic perturbations and change of cell states, which complements the current modalities. The R modules for uniConSig analysis and CSEA are available through https://github.com/wangxlab/uniConSig.
Bayesian estimation of genetic regulatory effects in high-throughput reporter assays
Authors: Majoros William H , Kim Young-Sook , Barrera Alejandro , Li Fan , Wang Xingyan , Cunningham Sarah J , Johnson Graham D , Guo Cong , Lowe William L , Scholtens Denise M , Hayes M Geoffrey , Reddy Timothy E , Allen Andrew S 
Published: July 2019

AbstractMotivationHigh-throughput reporter assays dramatically improve our ability to assign function to noncoding genetic variants, by measuring allelic effects on gene expression in the controlled setting of a reporter gene. Unlike genetic association tests, such assays are not confounded by linkage disequilibrium when loci are independently assayed. These methods can thus improve the identification of causal disease mutations. While work continues on improving experimental aspects of these assays, less effort has gone into developing methods for assessing the statistical significance of assay results, particularly in the case of rare variants captured from patient DNA.ResultsWe describe a Bayesian hierarchical model, called Bayesian Inference of Regulatory Differences, which integrates prior information and explicitly accounts for variability between experimental replicates. The model produces substantially more accurate predictions than existing methods when allele frequencies are low, which is of clear advantage in the search for disease-causing variants in DNA captured from patient cohorts. Using the model, we demonstrate a clear tradeoff between variant sequencing coverage and numbers of biological replicates, and we show that the use of additional biological replicates decreases variance in estimates of effect size, due to the properties of the Poisson-binomial distribution. We also provide a power and sample size calculator, which facilitates decision making in experimental design parameters.Availability and implementationThe software is freely available from www.geneprediction.org/bird. The experimental design web tool can be accessed at http://67.159.92.22:8080Supplementary informationSupplementary data are available at Bioinformatics online.
ISoLDE: a data-driven statistical method for the inference of allelic imbalance in datasets with reciprocal crosses
Authors: Reynès Christelle , Kister Guilhem , Rohmer Marine , Bouschet Tristan , Varrault Annie , Dubois Emeric , Rialle Stéphanie , Journot Laurent , Sabatier Robert 
Published: July 2019

Abstract

Motivation
Allelic imbalance (AI), i.e. the unequal expression of the alleles of the same gene in a single cell, affects a subset of genes in diploid organisms. One prominent example of AI is parental genomic imprinting, which results in parent-of-origin-dependent, mono-allelic expression of a limited number of genes in metatherian and eutherian mammals and in angiosperms. Currently available methods for identifying AI rely on data modeling and come with the associated limitations.

Results
We have designed ISoLDE (Integrative Statistics of alleLe Dependent Expression), a novel nonparametric statistical method that takes into account both AI and the characteristics of RNA-seq data to infer allelic expression bias when at least two biological replicates are available for reciprocal crosses. ISoLDE learns the distribution of a specific test statistic from the data and calls genes ‘allelically imbalanced’, ‘bi-allelically expressed’ or ‘undetermined’. Depending on the number of replicates, predefined thresholds or permutations are used to make calls. We benchmarked ISoLDE against published methods, and showed that ISoLDE compared favorably with respect to sensitivity, specificity and robustness to the number of replicates. Using ISoLDE on different RNA-seq datasets generated from hybrid mouse tissues, we did not discover novel imprinted genes (IGs), confirming the most conservative estimations of IG number.

Availability and implementation
ISoLDE has been implemented as a Bioconductor package available at http://bioconductor.org/packages/ISoLDE/.

Supplementary information
Supplementary data are available at Bioinformatics online.
The nPYc-Toolbox, a Python module for the pre-processing, quality-control and analysis of metabolic profiling datasets
Authors: Sands Caroline J , Wolfer Arnaud M , Correia Gonçalo D S , Sadawi Noureddin , Ahmed Arfan , Jiménez Beatriz , Lewis Matthew R , Glen Robert C , Nicholson Jeremy K , Pearce Jake T M 
Published: July 2019

Abstract

Summary
As large-scale metabolic phenotyping studies become increasingly common, the need for systemic methods for pre-processing and quality control (QC) of analytical data prior to statistical analysis has become increasingly important, both within a study, and to allow meaningful inter-study comparisons. The nPYc-Toolbox provides software for the import, pre-processing, QC and visualization of metabolic phenotyping datasets, either interactively, or in automated pipelines.

Availability and implementation
The nPYc-Toolbox is implemented in Python, and is freely available from the Python package index https://pypi.org/project/nPYc/, source is available at https://github.com/phenomecentre/nPYc-Toolbox. Full documentation can be found at http://npyc-toolbox.readthedocs.io/ and exemplar datasets and tutorials at https://github.com/phenomecentre/nPYc-toolbox-tutorials.
TFEA.ChIP: a tool kit for transcription factor binding site enrichment analysis capitalizing on ChIP-seq datasets
Authors: Puente-Santamaria Laura , Wasserman Wyeth W , del Peso Luis 
Published: July 2019

Abstract

Summary
The computational identification of the transcription factors (TFs) [more generally, transcription regulators, (TR)] responsible for the co-regulation of a specific set of genes is a common problem found in genomic analysis. Herein, we describe TFEA.ChIP, a tool that makes use of ChIP-seq datasets to estimate and visualize TR enrichment in gene lists representing transcriptional profiles. We validated TFEA.ChIP using a wide variety of gene sets representing signatures of genetic and chemical perturbations as input and found that the relevant TR was correctly identified in 126 of a total of 174 analyzed. Comparison with other TR enrichment tools demonstrates that TFEA.ChIP is an highly customizable package with an outstanding performance.

Availability and implementation
TFEA.ChIP is implemented as an R package available at Bioconductor https://www.bioconductor.org/packages/devel/bioc/html/TFEA.ChIP.html and github https://github.com/LauraPS1/TFEA.ChIP_downloads. A web-based GUI to the package is also available at https://www.iib.uam.es/TFEA.ChIP/

Supplementary information
Supplementary data are available at Bioinformatics online.
Predicting promoters in phage genomes using PhagePromoter
Authors: Sampaio Marta , Rocha Miguel , Oliveira Hugo , Dias Oscar 
Published: July 2019

Abstract

Summary
The growing interest in phages as antibacterial agents has led to an increase in the number of sequenced phage genomes, increasing the need for intuitive bioinformatics tools for performing genome annotation. The identification of phage promoters is indeed the most difficult step of this process. Due to the lack of online tools for phage promoter prediction, we developed PhagePromoter, a tool for locating promoters in phage genomes, using machine learning methods. This is the first online tool for predicting promoters that uses phage promoter data and the first to identify both host and phage promoters with different motifs.

Availability and implementation
This tool was integrated in the Galaxy framework and it is available online at: https://bit.ly/2Dfebfv.

Supplementary information
Supplementary data are available at Bioinformatics online.
geneCo: a visualized comparative genomic method to analyze multiple genome structures
Authors: Jung Jaehee , Kim Jong Im , Yi Gangman 
Published: July 2019

Abstract

Summary
In comparative and evolutionary genomics, a detailed comparison of common features between organisms is essential to evaluate genetic distance. However, identifying differences in matched and mismatched genes among multiple genomes is difficult using current comparative genomic approaches due to complicated methodologies or the generation of meager information from obtained results. This study describes a visualized software tool, geneCo (gene Comparison), for comparing genome structure and gene arrangements between various organisms. User data are aligned, gene information is recognized, and genome structures are compared based on user-defined GenBank files. Information regarding inversion, gain, loss, duplication and gene rearrangement among multiple organisms being compared is provided by geneCo, which uses a web-based interface that users can easily access without any need to consider the computational environment.

Availability and implementation
Users can freely use the software, and the accessible URL is https://bigdata.dongguk.edu/geneCo. The main module of geneCo is implemented by Python and the web-based user interface is built by PHP, HTML and CSS to support all browsers.

Supplementary information
Supplementary data are available at Bioinformatics online.
The Changing Uses of Herbarium Data in an Era of Global Change: An Overview Using Automated Content Analysis
Authors: Heberling J Mason , Prather L Alan , Tonsor Stephen J 
Published: July 2019

Abstract
Widespread specimen digitization has greatly enhanced the use of herbarium data in scientific research. Publications using herbarium data have increased exponentially over the last century. Here, we review changing uses of herbaria through time with a computational text analysis of 13,702 articles from 1923 to 2017 that quantitatively complements traditional review approaches. Although maintaining its core contribution to taxonomic knowledge, herbarium use has diversified from a few dominant research topics a century ago (e.g., taxonomic notes, botanical history, local observations), with many topics only recently emerging (e.g., biodiversity informatics, global change biology, DNA analyses). Specimens are now appreciated as temporally and spatially extensive sources of genotypic, phenotypic, and biogeographic data. Specimens are increasingly used in ways that influence our ability to steward future biodiversity. As we enter the Anthropocene, herbaria have likewise entered a new era with enhanced scientific, educational, and societal relevance.
A Critical Perspective on Advance Care Planning for Older People
Authors: Duffy Francis 
Published: July 2019

Abstract
How older people plan ahead for ageing in relation to accommodation, care arrangements, healthcare and medical treatment, and end of life decisions has attracted particular attention in recent years and as a result there has been considerable promotion of the importance of planning ahead and executing planning instruments with the aim of making one’s wishes and preferences known in advance. Planning ahead is promoted as allowing older people to have their voices heard, to advance their autonomy, choice and self-determination and to allow them to decide what treatment they may not want to receive. This article provides a critique of advance care planning, based on a subset of findings from a qualitative intergenerational study on ageing in Australia. The findings suggest that advance care planning is a much more complex and at times problematic endeavour, compared to what is promoted about advance care planning, in particular with regard to the use of planning instruments.
Asian Territorial Disputes and the 1951 San Francisco Peace Treaty: The Case of Dokdo
Authors: Schwartz Thomas , Yoo John 
Published: July 2019

Abstract
This Article analyzes whether the 1951 San Francisco Peace Treaty, the only multilateral international agreement that draws borders in East Asia, resolves the longstanding dispute over Dokdo between Korea and Japan. It uses the dispute to draw larger lessons about the nature of the treaty that ended World War II in the Pacific and how it structured the peace in Asia differently from that in Europe. It uses U.S. archival material to reconstruct the history of the making of the Treaty, which continues to be the most significant international legal instrument governing post-WWII Asia.
Although the Republic of Korea demonstrated a long history of control over Dokdo, Japan annexed the island on February 22, 1905. Japan places much importance on the Treaty’s silence because the Treaty otherwise required Japan to relinquish the territories it acquired before and during World War II. After the fall of the Nationalist government in China, the United States decided to rebuild Japan into a strong regional ally, and consequently negotiated a generous peace treaty with its former WWII enemy. This Article concludes that the Treaty left Dokdo, along with other important issues, open for future resolution.
Emergence of Polymyxin Resistance in Clinical Klebsiella pneumoniae Through Diverse Genetic Adaptations: A Genomic, Retrospective Cohort Study
Authors: Macesic Nenad , Nelson Brian , Mcconville Thomas H , Giddins Marla J , Green Daniel A , Stump Stephania , Gomez-Simmonds Angela , Annavajhala Medini K , Uhlemann Anne-Catrin 
Published: July 2019

AbstractBackgroundPolymyxins are antimicrobials of last resort for the treatment of carbapenem-resistant Enterobacteriaceae, but resistance in 5% to &gt;40% isolates has been reported. We conducted a genomic survey of clinical polymyxin-resistant (PR) Klebsiella pneumoniae to determine the molecular mechanisms of PR and the role of polymyxin exposure versus transmission in PR emergence.MethodsWe included 88 patients with PR K. pneumoniae from 2011–2018 and collected demographic, antimicrobial exposure, and infection data. Whole-genome sequencing was performed on 388 isolates, including 164 PR isolates. Variant calling and insertion sequence detection were performed, focusing on key genes associated with PR (mgrB, crrAB, phoPQ, and pmrAB). We conducted phylogenetic analyses of key K. pneumoniae multi-locus sequence types (ST258, ST17, ST307, and ST392).ResultsPolymyxin exposure was documented in 53/88 (60%) patients prior to PR detection. Through an analysis of key PR genes, we detected 129 individual variants and 72 unique variant combinations in PR isolates. This included multiple, distinct changes in 36% of patients with serial PR isolates. Insertion sequence disruption was limited to mgrB (P &lt; .001). Polymyxin minimum inhibitory concentrations showed stepwise increases with the number of PR genes affected (P &lt; .001). When clusters containing PR isolates in ≥2 patients were analyzed, 10/14 had multiple genetic events leading to PR.ConclusionsMolecular mechanisms leading to PR in clinical K. pneumoniae isolates are remarkably heterogenous, even within clusters or individual patients. Polymyxin exposure with de novo PR emergence led to PR in the majority of patients, rather than transmission. Optimizing polymyxin use should be a key strategy in stopping the spread of PR.