bluuebunny/crossref_metadata_2025_split huggingface dataset:
H3K4me3 induces allosteric conformational changes in the DNA-binding and catalytic regions of the V(D)J recombinase
Authors: Bettridge John , Na Chan Hyun , Pandey Akhilesh , Desiderio Stephen 
Published: February 2017

Significance
Accessibility of antigen receptor gene segments to recombination-activating gene (RAG), the V(D)J recombinase, is correlated with marks of active chromatin. One mark, histone H3 at lysine 4 (H3K4me3), binds to a plant homeodomain (PHD) in the RAG-2 subunit; mutations that abolish binding of the PHD to H3K4me3 also impair V(D)J recombination. Engagement of H3K4me3 by RAG-2 enhances substrate binding and catalysis, which are functions of RAG-1. We show that H3K4me3 acts through the PHD to induce conformational changes in an autoinhibitory domain residing within RAG-2 as well as in substrate-binding and catalytic regions of RAG-1. Our data suggest that H3K4me3 promotes displacement of the autoinhibitory domain as well as concomitant conformational alterations in RAG-1 that favor increased substrate affinity and catalytic rate.
A statics-dynamics equivalence through the fluctuation–dissipation ratio provides a window into the spin-glass phase from nonequilibrium measurements
Authors: Baity-Jesi Marco , Calore Enrico , Cruz Andres , Fernandez Luis Antonio , Gil-Narvión José Miguel , Gordillo-Guerrero Antonio , Iñiguez David , Maiorano Andrea , Marinari Enzo , Martin-Mayor Victor , Monforte-Garcia Jorge , Muñoz Sudupe Antonio , Navarro Denis , Parisi Giorgio , Perez-Gaviro Sergio , Ricci-Tersenghi Federico , Ruiz-Lorenzo Juan Jesus , Schifano Sebastiano Fabio , Seoane Beatriz , Tarancón Alfonso , Tripiccione Raffaele , Yllanes David 
Published: February 2017

Significance
The unifying feature of glass formers (such as polymers, supercooled liquids, colloids, granulars, spin glasses, superconductors, etc.) is a sluggish dynamics at low temperatures. Indeed, their dynamics are so slow that thermal equilibrium is never reached in macroscopic samples: in analogy with living beings, glasses are said to age. Here, we show how to relate experimentally relevant quantities with the experimentally unreachable low-temperature equilibrium phase. This relation is made quantitative via a statics-dynamics dictionary, established for spin glasses. In our dictionary, the aging response to a magnetic field is related to the spin-glass order parameter as obtained on samples small enough to equilibrate. We remark that all of the observables we consider can be measured with current experimental methods.
Bidirectional cross-linguistic influence in late bilingualism
Authors: Azaz Mahmoud , Frank Joshua 
Published: February 2017

AbstractThe container-content relation represents a set of nominal configurations unexplored in the acquisition literature. Whereas in English the switch from a noun-noun compound (water bottle) to a noun-prepositional phrase (bottle of water) is associated with a semantic shift from container to content, Spanish and Arabic adopt single canonical configurations for both conditions, noun-prepositional phrase and noun phrase, respectively. Importantly, Spanish, Arabic, and English display structural overlap in the content condition maintained by head-first isomorphic strings. In the container condition, they show structural dissimilarity; whereas English uses a head-final construction, Arabic and Spanish consistently use head-first constructions. Results from an elicited sentence-reordering task demonstrate that advanced late learners pattern native speakers when tested in Spanish but not when tested in English. Additionally, when tested in English, Arabic-speaking and Spanish-speaking learners overextend their L1 canonical configurations to both conditions. Furthermore, bilingual native speakers do not perform at ceiling, suggesting bidirectional cross-linguistic influence.
Identification of bilingual children with Specific Language Impairment in France
Authors: Almeida Laetitia de , Ferré Sandrine , Morin Eléonore , Prévost Philippe , Santos Christophe dos , Tuller Laurie , Zebib Racha , Barthez Marie-Anne 
Published: February 2017

Abstract
We report on the usefulness of three LITMUS tools in distinguishing bilingual children with SLI (Bi-SLI) from bilingual children with typical development (Bi-TD), in France: LITMUS-NWR-FR (non-word repetition), LITMUS-SR-FR (sentence repetition), and LITMUS-PABIQ (parental questionnaire). 82 bilingual children, aged 5–8, who had all been exposed to both French and either Arabic, Portuguese or Turkish, recruited both in ordinary schools and in SLP practices, were divided into Bi-TD (n = 61) and Bi-SLI (n = 21) groups based on parental questionnaire (LITMUS-PABIQ) information and standardized language scores in each language. Monolingual controls included 17 children with SLI and 37 TD children. NWR and SR significantly distinguished between the Bi-TD and the Bi-SLI children, and there was minimal impact of different factors related to bilingual development on children’s performance.
Glimpses of semantic restructuring of English emotion-laden words of American English L1 users residing outside the USA
Authors: Dewaele Jean-Marc 
Published: February 2017

Abstract
The present exploratory study focuses on the effect of living outside the USA on the understanding of the meaning, the perceived offensiveness and the self-reported frequency of use of four English emotion-laden words of British origin and four English emotion-laden words of American origin among 556 first (L1) users of American English. Statistical analyses revealed that the scores of the Americans living in the UK or in non-English-speaking countries differed significantly from those of compatriots living in the USA. Positive relationships emerged between multilingualism and scores on the dependent variables for the four British words, but no link emerged between languages known and the dependent variables for the American words. This is interpreted as an indication that semantic representations of emotion-laden words originating from another variety of the L1 are relatively weaker and are more likely to shift as a result of exposure to their use in other varieties, and the knowledge of other languages.
The environmental impacts of home and community gardening.
Authors: Wang XianZhong Wang XianZhong , Clark P. B. 
Published: February 2017

Abstract
Gardening has been practiced by humans for food and aesthetic purposes for thousands of years. As urbanization intensifies globally, gardening is increasing in both popularity and extent in urban and suburban regions of the world, thus increasing its impact on the environments. Here we discuss the health benefits and risks of home-grown vegetables followed by an in-depth examination of how home and community gardening impacts the biological and physical environments of the world with a focus on North America. In addition to offering multiple health benefits, gardens may promote biodiversity by providing critical habitats for a variety of native plant and animal species. At the same time, gardening has the potential to alter cycles of carbon, nutrients and water in urban and suburban areas, consequently contributing to global environmental changes. Conversely, gardening may have a range of adverse impacts on the environment, for instance, higher nutrient runoff and increased risk of eutrophication in aquatic ecosystems. Intensive lawn care, particularly in North America because of its large lawn areas, could divert essential resources, such as manpower, fertilizers and water, away from more ecologically and economically important activities. Exotic plants commonly grown in home gardens could escape cultivation and become noxious in their non-native habitats as already demonstrated by an increasing number of ornamental species, such as Callery pear and non-native honeysuckle, in the USA. As the world becomes more and more urbanized, the increasingly popular gardening will have greater impact on the abiotic and biotic environments of the world.
Potential Reservoirs and Risk Factors for VHSV IVb in an Enzootic System: Budd Lake, Michigan
Authors: Throckmorton Elizabeth , Brenden Travis , Peters Amber K. , Newcomb Tammy J. , Whelan Gary E. , Faisal Mohamed 
Published: February 2017

Abstract
Viral hemorrhagic septicemia virus genotype IVb (VHSV IVb) has caused major, sporadic fish die-offs in the Laurentian Great Lakes region of North America since 2005. Presently, factors affecting VHSV IVb persistence in enzootic systems are not well understood. Even with annual surveillance, the virus can go undetected for several years after an outbreak before again re-emerging, which suggests that the virus is maintained in the system either below detectable levels or in untested reservoirs. The aim of this study was to identify potential reservoirs of VHSV IVb in Budd Lake, Michigan; VHSV IVb was first detected in Budd Lake in 2007 but remained undetected until 2011. Additionally, we explored the susceptibility of naive fish introduced into a water body enzootic for VHSV IVb by stocking age-0 Largemouth Bass Micropterus salmoides at varying densities into enclosures in the lake. The virus was not detected among samples of the fishes Notropis spp. and Lepomis spp., cylindrical papershell mussels Anodontoides ferussacianus, leeches (subclass Hirudinea), sediment, or water. However, the virus was successfully isolated from amphipods (family Hyalellidae) and Largemouth Bass held in the enclosures. Our finding of VHSV IVb in Hyalellidae amphipods in combination with other research that has detected the virus in Diporeia spp., a large benthic amphipod important as a food resource to Great Lake fishes, suggests that benthic macroinvertebrates are a reservoir for VHSV IVb in infected systems. If there are environmental reservoirs for VHSV IVb in infected systems, they are likely unevenly distributed. Findings of this study add to our understanding of the seemingly complex ecology of this deadly and economically detrimental virus.
Received February 22, 2016; accepted October 16, 2016 Published online February 6, 2017
Biochemical synthesis of uniformly 13C-labeled diterpene hydrocarbons and their bioconversion to diterpenoid phytoalexins in planta
Authors: Ye Zhongfeng , Nakagawa Kazuya , Natsume Masahiro , Nojiri Hideaki , Kawaide Hiroshi , Okada Kazunori 
Published: February 2017

Abstract
Phytocassanes and momilactones are the major diterpenoid phytoalexins inductively produced in rice as bioactive substances. Regardless of extensive studies on the biosynthetic pathways of these phytoalexins, bioconversion of diterpene hydrocarbons is not shown in planta. To elucidate the entire biosynthetic pathways of these phytoalexins, uniformly 13C-labeled ent-cassadiene and syn-pimaradiene were enzymatically synthesized with structural verification by GC–MS and 13C-NMR. Application of the 13C-labeled substrates on rice leaves led to the detection of 13C-labeled metabolites using LC-MS/MS. Further application of this method in the moss Hypnum plumaeforme and the nearest out-group of Oryza species Leersia perrieri, respectively, resulted in successful bioconversion of these labeled substrates into phytoalexins in these plants. These results demonstrate that genuine biosynthetic pathways from these diterpene hydrocarbons to the end product phytoalexins occur in these plants and that enzymatically synthesized [U-13C20] diterpene substrates are a powerful tool for chasing endogenous metabolites without dilution with naturally abundant unlabeled compounds.
Performing Prudence: Barack Obama’s Defense of NSA Surveillance Programs
Authors: Trifonov Svilen Veselinov 
Published: February 2017

ABSTRACT
With this essay, I present an argument about the performative and perceptual nature of prudence. I support my argument through a case study in which I examine Barack Obama’s response to Edward Snowden’s unauthorized disclosures about NSA surveillance programs as a way to observe prudence in practice. In my analysis, I identify three ways in which Obama performed prudence. First, he established his image as a prudent and informed leader. Second, he established surveillance as a prudent and historically effective practice ensuring national security. Third, he established the contemporary policy of surveillance as a prudent and deliberate choice reached through discussion and participation by all citizens.
Jeannette Rankin’s Democratic Errand to Washington
Authors: Stob Paul 
Published: February 2017

ABSTRACT
In this essay, I argue that Jeannette Rankin’s 1917 address at Carnegie Hall recast a religious rhetorical form—the Puritan errand—for the democratic needs of the early twentieth century. Rankin’s “democratic errand” positioned the American West as a place that nurtured the truths of democracy and could help purge the nation of its political sins.
Video Stabilization Using Feature Point Matching
Authors: Kulkarni Shamsundar , Bormane D.S , Nalbalwar S.L 
Published: February 2017

Abstract
Video capturing by non-professionals will lead to unanticipated effects. Such as image distortion, image blurring etc. Hence, many researchers study such drawbacks to enhance the quality of videos. In this paper an algorithm is proposed to stabilize jittery videos. A stable output video will be attained without the effect of jitter which is caused due to shaking of handheld camera during video recording. Firstly, salient points from each frame from the input video is identified and processed followed by optimizing and stabilize the video. Optimization includes the quality of the video stabilization. This method has shown good result in terms of stabilization and it discarded distortion from the output videos recorded in different circumstances.
RelExplain—integrating data and networks to explain biological processes
Authors: Berchtold Evi , Csaba Gergely , Zimmer Ralf 
Published: February 2017

Abstract

Motivation
The goal of many genome-wide experiments is to explain the changes between the analyzed conditions. Typically, the analysis is started with a set of differential genes DG and the first step is to identify the set of relevant biological processes BP. Current enrichment methods identify the involved biological process via statistically significant overrepresentation of differential genes in predefined sets, but do not further explain how the differential genes interact with each other or which other genes might be important for the enriched process. Other network-based methods determine subnetworks of interacting genes containing many differential genes, but do not employ process knowledge for a more focused analysis.

Results
RelExplain is a method to analyze a given biological process bp (e.g. identified by enrichment) in more detail by computing an explanation using the measured DG and a given network. An explanation is a subnetwork that contains the differential genes in the process bp and connects them in the best way given the experimental data using also genes that are not differential or not in bp. RelExplain takes into account the functional annotations of nodes and the edge consistency of the measurements. Explanations are compact networks of the relevant part of the bp and additional nodes that might be important for the bp. Our evaluation showed that RelExplain is better suited to retrieve manually curated subnetworks from unspecific networks than other algorithms. The interactive RelExplain tool allows to compute and inspect sub-optimal and alternative optimal explanations.

Availability and Implementation
A webserver is available at https://services.bio.ifi.lmu.de/relexplain.

Supplementary information
Supplementary data are available at Bioinformatics online.
An efficient concordant integrative analysis of multiple large-scale two-sample expression data sets
Authors: Lai Yinglei , Zhang Fanni , Nayak Tapan K , Modarres Reza , Lee Norman H , McCaffrey Timothy A 
Published: February 2017

Abstract

Motivation
We have proposed a mixture model based approach to the concordant integrative analysis of multiple large-scale two-sample expression datasets. Since the mixture model is based on the transformed differential expression test P-values (z-scores), it is generally applicable to the expression data generated by either microarray or RNA-seq platforms. The mixture model is simple with three normal distribution components for each dataset to represent down-regulation, up-regulation and no differential expression. However, when the number of datasets increases, the model parameter space increases exponentially due to the component combination from different datasets.

Results
In this study, motivated by the well-known generalized estimating equations (GEEs) for longitudinal data analysis, we focus on the concordant components and assume that the proportions of non-concordant components follow a special structure. We discuss the exchangeable, multiset coefficient and autoregressive structures for model reduction, and their related expectation-maximization (EM) algorithms. Then, the parameter space is linear with the number of datasets. In our previous study, we have applied the general mixture model to three microarray datasets for lung cancer studies. We show that more gene sets (or pathways) can be detected by the reduced mixture model with the exchangeable structure. Furthermore, we show that more genes can also be detected by the reduced model. The Cancer Genome Atlas (TCGA) data have been increasingly collected. The advantage of incorporating the concordance feature has also been clearly demonstrated based on TCGA RNA sequencing data for studying two closely related types of cancer.

Availability and Implementation
Additional results are included in a supplemental file. Computer program R-functions are freely available at http://home.gwu.edu/∼ylai/research/Concordance.

Supplementary information
Supplementary data are available at Bioinformatics online.
cooccurNet: an R package for co-occurrence network construction and analysis
Authors: Zou Yuanqiang , Wu Zhiqiang , Deng Lizong , Wu Aiping , Wu Fan , Li Kenli , Jiang Taijiao , Peng Yousong 
Published: February 2017

Abstract

Motivation
Previously, we developed a computational model to identify genomic co-occurrence networks that was applied to capture the coevolution patterns within genomes of influenza viruses. To facilitate easy public use of this model, an R package ‘cooccurNet’ is presented here.

Results
‘cooccurNet’ includes functionalities of construction and analysis of residues (e.g. nucleotides, amino acids and SNPs) co-occurrence network. In addition, a new method for measuring residues coevolution, defined as residue co-occurrence score (RCOS), is proposed and implemented in ‘cooccurNet’ based on the co-occurrence network.

Availability and Implementation
‘cooccurNet’ is publicly available on CRAN repositories under the GPL-3 Open Source License (http://cran.r-project.org/package=cooccurNet)

Supplementary information
Supplementary data are available at Bioinformatics online.
CPSS 2.0: a computational platform update for the analysis of small RNA sequencing data
Authors: Wan Changlin , Gao Jianing , Zhang Huan , Jiang Xiaohua , Zang Qiguang , Ban Rongjun , Zhang Yuanwei , Shi Qinghua 
Published: February 2017

Abstract

Summary
Next-generation sequencing has been widely applied to understand the complexity of non-coding RNAs (ncRNAs) in the last decades. Here, we present CPSS 2.0, an updated version of CPSS 1.0 for small RNA sequencing data analysis, with the following improvements: (i) a substantial increase of supported species from 10 to 48; (ii) improved strategies applied to detect ncRNAs; (iii) more ncRNAs can be detected and profiled, such as lncRNA and circRNA; (iv) identification of differentially expressed ncRNAs among multiple samples; (v) enhanced visualization interface containing graphs and charts in detailed analysis results. The new version of CPSS is an efficient bioinformatics tool for users in non-coding RNA research.

Availability and implementation
CPSS 2.0 is implemented in PHP + Perl + R and can be freely accessed at http://114.214.166.79/cpss2.0/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Genome sequence of a rice pest, the white-backed planthopper (Sogatella furcifera)
Authors: Wang Lin , Tang Nan , Gao Xinlei , Chang Zhaoxia , Zhang Liqin , Zhou Guohui , Guo Dongyang , Zeng Zhen , Li Wenjie , Akinyemi Ibukun A. , Yang Huanming , Wu Qingfa 
Published: February 2017

Abstract
Background: Sogatella furcifera is an important phloem sap-sucking and plant virus-transmitting migratory insect of rice. Because of its high reproductive potential, dispersal capability and transmission of plant viral diseases, S. furcifera causes considerable damage to rice grain production and has great economical and agricultural impacts. Comprehensive studies into ecological aspects and virus–host interactions of S. furcifera have been limited because of the lack of a well-assembled genome sequence.
Findings: A total of 241.3 Gb of raw reads from the whole genome of S. furcifera were generated by Illumina sequencing using different combinations of mate-pair and paired-end libraries from 17 insert libraries ranging between 180 bp and 40 kbp. The final genome assembly (0.72 Gb), with average N50 contig size of 70.7 kb and scaffold N50 of 1.18 Mb, covers 98.6 % of the estimated genome size of S. furcifera. Genome annotation, assisted by eight different developmental stages (embryos, 1st-5th instar nymphs, 5-day-old adults and 10-day-old adults), generated 21 254 protein-coding genes, which captured 99.59 % (247/248) of core CEGMA genes and 91.7 % (2453/2675) of BUSCO genes.
Conclusions: We report the first assembled and annotated whole genome sequence and transcriptome of S. furcifera. The assembled draft genome of S. furcifera will be a valuable resource for ecological and virus–host interaction studies of this pest.
Constitutional Antecedents
Authors: De Rohit 
Published: February 2017

Abstract
This chapter focuses on the antecedents of the Indian Constitution. It first examines the various charters and laws that established the structure of power in colonial India from 1600 to 1947. It then considers the attempts by Indian groups during the freedom struggle to draw up constitutions or articulate claims against the State, before turning to a discussion of constitutional practice in colonial India. The article treats the Indian Constitution as a set of interactions between constitutional texts, constitutional aspirations, and the quotidian practice of constitutional law, rather than a succession of legislation. This approach shifts from the idea that the Constitution was a product of grand ‘consensus underwritten by nationalism’ to that of the Constitution as a product of a series of conflicts.
Language
Authors: Choudhry Sujit 
Published: February 2017

Abstract
This chapter examines the constitutional politics of official language status in India. It gives an overview of the debates in the Indian Constituent Assembly over issues such as the official language of the Central Government and the Indian Constitution’s distinction between the language of parliamentary deliberations and the language of legislation. It considers the disaggregation of official language status into different linguistic states within the context of the relationship between federalism and language. It also discusses the implications of linguistic federalism for linguistic minorities in India and the legal controversy regarding the extent to which Article 30(1) of the Indian Constitution grants linguistic minorities the right to exclude instruction in the regional language.