bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antibody repertoire diversification through VH gene replacement in mice cloned from an IgA plasma cell
Authors: Kumar Rashmi , Bach Martina P. , Mainoldi Federica , Maruya Mikako , Kishigami Satoshi , Jumaa Hassan , Wakayama Teruhiko , Kanagawa Osami , Fagarasan Sidonia , Casola Stefano 
Published: January 2015

SignificanceAntibodies produced by B cells provide a protective barrier to our organism against the penetration and dissemination of microorganisms. Each antibody recognizes a specific antigen through variable (V) region domains of pairs of immunoglobulin (Ig) heavy (H) and light (L) chains. In mammals, VDJ recombination generates a highly diversified preimmune pool of VHand VLdomains. Acquisition of a functional VHrearrangement is thought to prevent further VDJ recombination at the IgH locus. Instead, mice cloned from a terminally differentiated B cell unravel the ability of VDJ recombination to revise a functionally rearranged VHgene through VH replacement. We show that up to 20% of the antibody V gene repertoire of mature B-lymphocytes can be generated through VH replacement.
Structural insight into the active site of a Bombyx mori unclassified glutathione transferase
Authors: Tofazzal Hossain M D , Yamamoto Kohji 
Published: January 2015

Abstract
Glutathione transferases (GSTs) are major detoxification enzymes that play central roles in the defense against various environmental toxicants as well as oxidative stress. Here, we identify amino acid residues of an unclassified GST from Bombyx mori, bmGSTu-interacting glutathione (GSH). Site-directed mutagenesis of bmGSTu mutants indicated that amino acid residues Asp103, Ser162, and Ser166 contribute to catalytic activity.
Venetians in America: Nicolò Zen and the Virtual Exploration of the New World*
Authors: Horodowich Elizabeth 
Published: January 2015

AbstractIn 1558, the Venetian patrician Nicolò Zen publishedDello scoprimento, a text that suggested that his Venetian ancestors had made landfall in the Americas before Columbus. Generations of scholars have pored over Zen’s text and accompanying map with the hopes of determining whether or not this voyage took place. Zen’s text, however, cannot be classified as either history or fiction; like many other early modern travel accounts, it was a combination of both. Shifting the focus about what is significant from the text’s truthfulness to its tactics, from the historicity of the voyage to the mechanics of the composition, reveals a series of fascinating textual strategies surrounding the European production of knowledge about the New World. Specifically, Zen followed well-established patterns for European travel writing, playing with quotation, pastiche, and temporality in order to depict his fellow Venetians as experts on the Americas and as viable contestants in the race to New World empire.
Where the Spirit (of Violence) Leads
Authors: Bauman Chad M. 
Published: January 2015

AbstractThere is certainly some truth to the assertion that Pentecostal proselytization is provocative, and that this provocation alone occasionally leads to attacks against Indian Pentecostals. But this explanation of the disproportionate targeting of Pentecostals is only part of the story, and its persuasiveness derives, in part, from certain prejudices about Pentecostalism that one finds consciously or unconsciously held by both non-Christians and “mainstream” Christians. The point of this chapter, therefore, is to provide a more nuanced enumeration of the many factors that together conspire to make Pentecostals more vulnerable to anti-Christian violence. While some of these factors are related to the nature of Pentecostal faith and belief, others have more to do with the social location of Pentecostals and the subtle ways in which Pentecostals—not uniquely but certainly more so than most other Indian Christians—challenge or run afoul of hegemonic (if not uncontested) Indian cultural norms and mores.
Missions and the Pentecostalization of Indian Christianity
Authors: Bauman Chad M. 
Published: January 2015

AbstractIn the rhetoric of Indian critics of Christianity, “missionaries” often symbolically stand in for Christianity more generally. The work of missionaries, it is implied by these critics, reveals the true and truly sinister nature of Christianity as an expansionist and anti-national religion. And, of course, Pentecostals are deemed by many, both Christian and non-Christian, to be consummate and particularly provocative missionaries. This chapter examines the transnational missionary movement, looking especially closely at data on American mission societies and their support for evangelism in India, and in the end makes the claim that a variety of global trends favor the increasing Pentecostalization of Indian Christianity, and of Christian missions in India, and therefore—since Pentecostals are disproportionately targeted in anti-Christian violence—portend a likely increase in Hindu–Christian conflict.
Animate object fronting in Dutch: A production study
Authors: Lamers Monique J. A. , de Hoop Helen 
Published: January 2015

AbstractIn Dutch, there is a preference for starting a sentence with an animate noun phrase. At the same time, as in many other languages, there is a strong tendency to start a sentence with the grammatical subject. These two tendencies coincide when the subject is animate, as is usually the case. If, however, the subject is inanimate while the object is animate, they compete, with the latter tendency being stronger than the first one. In this chapter, a sentence production study is presented with two classes of psych verbs which require their object to be animate. It is found that object fronting is relatively frequent for unaccusative psych verbs, but not for causative psych verbs. It is argued that this pattern results from the grammatical differences between the verbs (i.e. the possibility of passivization), which in turn provide the speaker with the possibility to satisfy word order preferences.
Patterns in competing motivations and the interaction of principles
Authors: Hawkins John A. 
Published: January 2015

AbstractThis chapter examines empirical patterns in data from language performance and in the distribution of grammatical variants across languages and uses them to shed light on how multiple principles work together. Some data from (second) language acquisition are also briefly considered. Three types of general patterns are observed. The first set illustrate a Degree of Preference generalization for individual principles. The second set illustrate Cooperation, whereby the more principles there are that define a collective preference for a common set of outputs {P}, the greater is the preference for and size of that {P}. The third set involve Competition and they suggest that when there is competition between two principles A and B, the relative strength of their outputs, {A} from A and {B} from B, will be in proportion to the degree of preference for their respective outputs.
A statistical model of competing motivations affecting relative clause extraposition in German
Authors: Strunk Jan 
Published: January 2015

AbstractRelative clause extraposition has been studied by both generativists and functionalists. Whereas generativists have concentrated on structural and semantic factors, such as syntactic locality, definiteness, and restrictiveness, functionalists have investigated surface‐oriented factors, like the length of the relative clause and the distance between it and its antecedent. Most studies, however, have only looked at individual factors and not tried to account for extraposition as a syntactic alternation using an integrated model. This chapter presents a statistical investigation of relative clause extraposition in German that considers multiple competing motivations in order to predict extraposition. It concludes that the decision whether to extrapose a relative clause cannot be attributed to only one factor and that multiple motivations have to be taken into account. It also reports on an acceptability study showing that constraints against extraposition can sometimes be overridden by increasing the antecedent's salience and the predictability of the relative clause.
Six competing motives for repetition
Authors: Haiman John 
Published: January 2015

AbstractMost discussions of competing have implicitly adopted the point of view of the speaker. One may, however, also take the point of view of the hearer, and ask the question: given a specific linguistic structure, specifically a repetition of a form F, what (competing) meanings could lie behind that repetition, and how can the hearer tell which one was intended by the speaker? Intertextually, a speaker may repeat another speaker's F in order to fool yet another hearer that he is that other speaker, to voice his agreement with the other speaker, or to mock him. All of these are familiar, and have been more or less conventionalized in at least some grammars. Yet they may be distinguished from each other by the use of disambiguating “diacritics”—minor signs that are added to the fundamental diagram F(…)F to clarify what was intended.
The category of roots
Authors: Borer Hagit 
Published: January 2015

AbstractThis chapter focuses on the categorial properties of roots and proposes that, just like event structure, these emerge in the context of particular functional structure and as a consequence of it. For Borer, functors, whether segments of extended projections or derivational categorizers, are viewed as elements that partition the categorial space. Borer explicitly argues against linking the emergence of a category to zero-realized n, v, and a.
The scope of plant population ecology
Authors: Gibson David J. 
Published: January 2015

AbstractThis introductory chapter defines the scope and breadth of the topic of plant population ecology as the study of plant populations in their habitat. A brief history of the topic is discussed followed by an outline of the goals of plant population ecology along with a list of important books and papers, and presentation of fourteen fundamental questions intended to guide the future direction of the discipline. Four case studies are introduced that are returned to throughout the rest of the book. A road map for using the book is outlined.
Abiotic and biotic measurements of a plant’s environment
Authors: Gibson David J. 
Published: January 2015

AbstractMethods for measuring components of the plant’s biotic and abiotic environment are described. It is stressed that quantifying the effects of the environment on a plant requires measurement of both the plant and environmental factors. Measurements of the biotic environment that are described in this chapter include herbivory, pathogens (including mycorrhizae), the soil microbial community, and allelochemicals. Measurements of the abiotic environment include the soil (structure, nutrients, and soil moisture), radiation, atmospheric water, and disturbance (area and extent, and fire). A methodological and statistical approach to assessing the importance of spatial variation in the environment on plant performance is described.
Planning, choosing, and using statistics
Authors: Gibson David J. 
Published: January 2015

AbstractUsing the correct statistics to analyse data is a matter of advance planning to collect the appropriate data. This chapter describes the background to planning and choosing appropriate statistical methods, and is a primer for the basic statistical tests that plant population ecologists will need to use. Topics include: choosing the right statistical test, kinds of distributions, goodness of fit tests and contingency tables, correlation and regression, analysis of variance and tests of differences among samples (including Generalized Linear Mixed Models), multivariate statistics (ordination, classification, discriminant functions), Bayesian statistics, and reporting statistics. The statistical tests used in the four case studies from Chapter 1 are reviewed.
GrammR: graphical representation and modeling of count data with application in metagenomics
Authors: Ayyala Deepak Nag , Lin Shili 
Published: January 2015

Abstract
Motivation: Microbiota compositions have great implications in human health, such as obesity and other conditions. As such, it is of great importance to cluster samples or taxa to visualize and discover community substructures. Graphical representation of metagenomic count data relies on two aspects, measure of dissimilarity between samples/taxa and algorithm used to estimate coordinates to study microbiota communities. UniFrac is a dissimilarity measure commonly used in metagenomic research, but it requires a phylogenetic tree. Principal coordinate analysis (PCoA) is a popular algorithm for estimating two-dimensional (2D) coordinates for graphical representation, although alternative and higher-dimensional representations may reveal underlying community substructures invisible in 2D representations.
Results: We adapt a new measure of dissimilarity, penalized Kendall’s τ-distance, which does not depend on a phylogenetic tree, and hence more readily applicable to a wider class of problems. Further, we propose to use metric multidimensional scaling (MDS) as an alternative to PCoA for graphical representation. We then devise a novel procedure for determining the number of clusters in conjunction with PAM (mPAM). We show superior performances with higher-dimensional representations. We further demonstrate the utility of mPAM for accurate clustering analysis, especially with higher-dimensional MDS models. Applications to two human microbiota datasets illustrate greater insights into the subcommunity structure with a higher-dimensional analysis.
Availability and implementation: GrammR is implemented as an R-package available at http://www.stat.osu.edu/∼statgen/SOFTWARE/GrammR/. It may also be downloaded from http://cran.rproject.org/web/packages/GrammR/.
Contact: shili@stat.osu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Enhancer modeling uncovers transcriptional signatures of individual cardiac cell states in Drosophila
Authors: Busser Brian W. , Haimovich Julian , Huang Di , Ovcharenko Ivan , Michelson Alan M. 
Published: January 2015

Abstract
Here we used discriminative training methods to uncover the chromatin, transcription factor (TF) binding and sequence features of enhancers underlying gene expression in individual cardiac cells. We used machine learning with TF motifs and ChIP data for a core set of cardiogenic TFs and histone modifications to classify Drosophila cell-type-specific cardiac enhancer activity. We show that the classifier models can be used to predict cardiac cell subtype cis-regulatory activities. Associating the predicted enhancers with an expression atlas of cardiac genes further uncovered clusters of genes with transcription and function limited to individual cardiac cell subtypes. Further, the cell-specific enhancer models revealed chromatin, TF binding and sequence features that distinguish enhancer activities in distinct subsets of heart cells. Collectively, our results show that computational modeling combined with empirical testing provides a powerful platform to uncover the enhancers, TF motifs and gene expression profiles which characterize individual cardiac cell fates.
Outcome of Bilateral C1 Laminar Hooks Combined With C2 Pedicle Screw Fixation for the Treatment of C1–C2 Instability
Authors: Lao Lifeng , Zhong Guibin , Li Qianyi , Li Xinfeng , Chen Bin , Qian Lie , Liu Zude 
Published: January 2015

Study Design:
A retrospective technical report.

Objective:
To assess the effect of bilateral C1 laminar hooks combined with C2 pedicle screw fixation for the treatment of C1–C2 instability.

Summary of Background Data:
Various posterior atlantoaxial fixations for C1–C2 instability have been developed. However, due to anatomic anomalies of the vertebral artery, the smallness of the pedicle, trajectories of broken screws, or a lack of surgical experience, a simple atlantoaxial fixation technique with good safety and effectiveness is urgently needed.

Materials and Methods:
From January 2007 to September 2012, 18 patients with C1–C2 instability who underwent posterior bilateral C1 laminar hooks combined with C2 pedicle screw fixation were evaluated. Six patients had acute odontoid fractures (Anderson IIc type), 8 patients had odontoid pseudarthrosis, 3 had os odontoideum, and 1 had a traumatic rupture of the transverse ligament. The mean age at the time of surgery was 34.1 years. The clinical and radiographic analyses were performed before and after the operation and at follow-up.

Results:
The follow-up period was 12–78 months (with an average follow-up period of 25.6 mo). All patients were relieved of pain and their neurological symptoms were substantially improved. The postoperative JOA score improved significantly (t=−7.234, P<0.001). No neurological or vascular complications occurred in these cases. The device was placed well and had not loosened or broken and plain radiographs revealed bony fusion in 17 patients. One patient had C1 posterior arch fracture 3 weeks postoperatively and she was followed up for 18 months without revision surgery.

Conclusions:
When appropriate patients were selected, bilateral C1 laminar hooks combined with C2 pedicle screw fixation can be an alternative method to treat C1–C2 instability effectively with a relatively simple procedure. Preoperative planning and evaluation were crucial for the solid atlantoaxial fusion.
A variant inTAF1is associated with a new syndrome with severe intellectual disability and characteristic dysmorphic features
Authors: Ou’Rawe Jason , Wu Yiyang , Rope Alan , Jimenez Barrón Laura T. , Swensen Jeffrey , Fang Han , Mittelman David , Highnam Gareth , Robison Reid , Yang Edward , Wang Kai , Lyon Gholson 
Published: January 2015

AbstractWe describe the discovery of a new genetic syndrome, RykDax syndrome, driven by a whole genome sequencing (WGS) study of one family from Utah with two affected male brothers, presenting with severe intellectual disability (ID), a characteristic intergluteal crease, and very distinctive facial features including a broad, upturned nose, sagging cheeks, downward sloping palpebral fissures, prominent periorbital ridges, deep-set eyes, relative hypertelorism, thin upper lip, a high-arched palate, prominent ears with thickened helices, and a pointed chin. This Caucasian family was recruited from Utah, USA. Illumina-based WGS was performed on 10 members of this family, with additional Complete Genomics-based WGS performed on the nuclear portion of the family (mother, father and the two affected males). Using WGS datasets from 10 members of this family, we can increase the reliability of the biological inferences with an integrative bioinformatic pipeline. In combination with insights from clinical evaluations and medical diagnostic analyses, these DNA sequencing data were used in the study of three plausible genetic disease models that might uncover genetic contribution to the syndrome. We found a 2 to 5-fold difference in the number of variants detected as being relevant for various disease models when using different sets of sequencing data and analysis pipelines. We de-rived greater accuracy when more pipelines were used in conjunction with data encompassing a larger portion of the family, with the number of putative de-novo mutations being reduced by 80%, due to false negative calls in the parents. The boys carry a maternally inherited mis-sense variant in a X-chromosomal geneTAF1, which we consider as disease relevant. TAF1 is the largest subunit of the general transcription factor IID (TFIID) multi-protein complex, and our results implicate mutations inTAF1as playing a critical role in the development of this new intellectual disability syndrome.
IFRS adoption strategies and theories of economic development
Authors: Ben Othman Hakim , Kossentini Anas 
Published: January 2015

Purpose– The purpose of this paper is to explore the underlying assumptions of economic development theories that may support or constrain accounting standard-setting strategies related to IFRS adoption and their potential effects on emerging stock markets (ESMs) development. The authors investigate the country-level association between the extent of IFRS adoption and ESMs development.Design/methodology/approach– The empirical analysis is based on a dynamic panel model using the generalized method of moments for 50 emerging economies over a period spanning from 2001 to 2007.Findings– The authors find that a higher level of IFRS adoption affects positively and significantly stock market development (SMD). More specifically, full IFRS adoption for listed firms is substantially associated with SMD. However, the authors find that partial adoption of IFRS might be not only inappropriate and irrelevant, but also significantly harmful to ESMs development. In addition, it is shown that local GAAPs shaped on the basis of IFRS with major changes are at the origin of such counter-intuitive relationships.Practical implications– This paper has some policy implications for developing countries. In order to enhance ESMs development, it is important to improve financial information quality through full adoption of IFRS. In a global economic system, it is essential to standard-setters as well as market regulators in non-adopter developing countries to require full IFRS adoption.Originality/value– This paper extends previous work of Larson and Kenny (1996) in establishing relationships between standard-setting strategies faced to IFRS and theories of economic development. The authors investigate the effects of these standard-setting strategies on SMD using a sample of 50 emerging economies.
Comprehensiveness of internet reporting by Caribbean companies
Authors: Bowrin Anthony R. 
Published: January 2015

Purpose– The purpose of this paper is to examine the comprehensiveness and determinants of internet reporting by publicly listed Caribbean companies.Design/methodology/approach– In total, 65 companies with common shares listed on one of the four Caribbean stock exchanges, were included in the study. The study examined the relationship between firm characteristics (size, industry affiliation, listing status, and CEO role duality) and the comprehensiveness of corporate internet reporting (CIR), while controlling for the importance of public equity financing, company age and profitability. CIR was measured using an unweighted 107-item disclosure index that focussed on web site usability, disclosure timeliness, disclosure content, and several advanced CIR features. The data were subjected to content analysis using descriptive statistics, contingency tables, and multiple regression analysis.Findings– As a whole, publicly listed Caribbean firms seem to be in stage 2 of the internet evolutionary model presented by Hedlin (1999); most firms have a web presence, a majority of firms engage in CIR and very few firms are using social media, communication and processable reporting formats in their CIR. It was found that Caribbean companies, on average, satisfied only 63.1 percent of the items included in the index. As hypothesized company size and industry affiliation were positively related to the comprehensiveness of CIR. Conversely, both industry affiliation and listing status generated mixed results. Also, the importance of public equity financing was significantly and negatively related to the general content and timeliness dimensions of CIR.Practical implications– The findings suggest that Caribbean governments and regulators interested in raising the profile of regional stock exchanges may need to implement incentives for public companies to engage in internet reporting.Originality/value– This is the first study to examine the comprehensiveness and determinants of internet reporting by publicly listed Caribbean companies.