bluuebunny/crossref_metadata_2025 huggingface dataset:
Amorphous Family Nexus: An Analytical Tool in Considering Community/m-MGO Haritika's Ties in Bundelkhand, Central India
Authors: Saxena Gunjan , Singh Avani Mohan
Published: October 2014

In this paper we apply the notion of the amorphous family nexus (AFN) to examine the underinvestigated implications of family-like ties existing between minor NGOs (m-NGOs) and communities in sustaining the momentum of developmental activities despite resource scarcity and weak institutional support. AFN embodies symbolic connectedness and meaningful associations that actors enjoy with each other within and independently of the family nexus. Focusing on Bundelkhand-based m-NGO Haritika's (a non-profit-making research consultancy) initiatives centred on improving water quality and availability, we analyse the emotional dynamics inherent in the carefully crafted social bonds existing amongst fieldworkers, community members, and volunteers. Our findings reveal how their kindred camaraderie and displays of affection and trust, a result of their long-standing affiliations, are able to activate latent resources and creative energy as they seek to involve each other as active partners in enacting their daily routines.
Do Palestinians Live across the Road? Address and the Micropolitics of Home in Israeli Contested Urban Spaces
Authors: Fenster Tovi
Published: October 2014

This paper develops a substantive argument of the ‘home exchange as contact zone’ for addressing the ‘other’, focusing on Israeli–Palestinian mixed urban spaces. By analyzing original archival research of a specific address, along with personal narratives of Palestinian and Jewish inhabitants of this address, the paper aims to understand politics of nations through the microgeographies of home. Thus, the analysis of asymmetric power in the politics of Israeli urban planning becomes the context of analyzing the archaeology of the address—more specifically, 218 Yefet Street, Jaffa, originally the home of my mother and grandparents. The ‘home exchange as contact zone’ argument facilitates the examination of the language, conversation, and text derived from meetings with the Palestinian owners and with my mother, and exposes the complexities of the binary divisions of coloniality.
Fixed-Term and Temporary: Teaching Fellows, Tactics, and the Negotiation of Contingent Labour in the UK Higher Education System
Authors: Peters Kimberley , Turner Jennifer
Published: October 2014

This paper autobiographically considers the role of teaching-only staff as a contingent labour force in the contemporary higher education system in the UK. The aims are twofold. First, whilst much attention has been paid to the role of the research fellow, there has been less consideration, in the UK context, of the teaching fellow as an alternate form of postdoctoral experience. Accordingly, this paper gives voice to the teaching fellow—a member of academic staff who is not allocated writing and research time as part of their contract—whose views are often marginalised in ongoing debates concerning the plays of power in the neoliberalised academy. Second, the paper raises these voices to bring into consciousness the impacts of the teaching fellow experience for the fellows themselves and the faculties they work in. It is argued that teaching fellows face challenging circumstances with regard to their career trajectories in the academy. Accordingly, this paper considers the ways in which fellows, through tactics of place-making, presence and visibility, and collaboration, negotiate the challenging structural and institutional conditions that underscore their contracts. It is contended that exploring the teaching-only workforce is vital for critically assessing the workings of the contemporary academy and questioning the unequal power relations that shape work places in a culture where contingent labour is expanding; becoming less of a fixed-term and temporary feature of the university system but, rather, a stable and enduring one.
The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes
Authors: Mérai Zsuzsanna , Chumak Nina , García-Aguilar Marcelina , Hsieh Tzung-Fu , Nishimura Toshiro , Schoft Vera K. , Bindics János , Ślusarz Lucyna , Arnoux Stéphanie , Opravil Susanne , Mechtler Karl , Zilberman Daniel , Fischer Robert L. , Tamaru Hisashi
Published: October 2014

Significance

Centromeres are the fundamental unit required for segregation of chromosomes during mitosis and meiosis, and they are defined by the centromere-specific histone H3 variant (CenH3)/centromere protein A (CENP-A). In contrast to the relatively well-known process of de novo assembly of CenH3 at centromeres, little is known of how CenH3 is actively removed, leading to centromere disassembly, an essential biological process during the life of a cell. This study describes the process of centromere disassembly, demonstrating that it occurs via an active, proteolytic mechanism, which is also linked to major changes in chromosome dynamics: chromatin decondensation and bulk rRNA gene activation.
Polysemy and synonymy
Authors: Glynn Dylan
Published: October 2014

This chapter introduces the field of polysemy and synonymy studies from a Cognitive Linguistic perspective. Firstly, the discussion explains and defines the object of research, showing that the study of semantic relations, traditionally restricted to the description of lexical semantics, needs to be extended to include all formal structures, including morpho-syntax. Secondly, given the theoretical assumptions of Cognitive Linguistics, it is argued that quantitative corpus-driven methods are essential for the description of semantic structures. Lastly, the chapter charts the development of Cognitive Semantic research in polysemy and synonymy and demonstrates how the current corpus-driven research in the field is inherently linked to the traditions of radial network analysis and prototype semantics. It is argued that instead of an empirical revolution (as has been suggested in recent commentaries), the current trends in the use of observational data are a natural extension of the Cognitive Semantic research tradition.
Competing ‘transfer’ constructions in Dutch
Authors: Delorge Martine , Plevoets Koen , Colleman Timothy
Published: October 2014

This paper zooms in on the semantic relations between the constructions of
“possessional transfer” (i.e. constructions used to encode events of possessional
transfer) in Dutch by zooming in on a specific morphological class of dispossession
verbs, viz. verbs with the prefix ont- ‘away’, such as ontnemen ‘take away’,
ontfutselen ‘fish out of ’, onttrekken ‘extract, withdraw’, ontheffen ‘relieve’, etc. A
database with several thousand attested ont-examples from various corpora of
present-day written Dutch will serve as the starting point for an investigation of
their constructional possibilities and preferences: the ont-verbs will be shown
to cluster into a number of subclasses in terms of alternation possibilities. In
addition, a comparison of these present-day Dutch results with data from a
diachronic corpus of 19th century Dutch will reveal a number of lexico-grammatical
shifts: the use of the double object construction and (especially) of the
aan-dative with ont-verbs is more heavily constrained now than it was in earlier
stages of the language.
Rethinking constructional polysemy
Authors: Perek Florent
Published: October 2014

This chapter examines the conative construction, e.g., I kicked at the ball, using
collexeme analysis. Previous studies report that strong collexemes of a construction
provide an indication of its central meaning, from which polysemic extensions
are derived. However, the conative construction does not seem to attract
a particular kind of verb that could be used to characterize its central meaning.
To address this problem, a variant of collexeme analysis is suggested that
consists in splitting the verbal distribution into semantic classes and consider
“verb-class-specific” constructions independently. For the three classes tested,
the most significant collexemes are found to be verbs whose inherent meaning
contains the semantic contribution of the construction in that class. Hence, the
most attracted collexemes do provide an indication of the constructional meaning,
albeit specific to each verb class.
Quantifying polysemy in Cognitive Sociolinguistics
Authors: Robinson Justyna A.
Published: October 2014

This chapter uses various statistical techniques to explore the extralinguistic grounding of individual conceptualisations of polysemous adjectives in English, such as awesome, gay, wicked. It considers the extent to which individual conceptualisations are non-random and can be related to the socio-demographic characteristics of the speaker. The experimental survey data collected from 72 speakers is analysed via hierarchical agglomerative clustering, decision tree analysis, and logistic regression analysis. The results reveal that not only individual adjectives, as indicated in Robinson (2010a), but whole groups of polysemous adjectives currently undergoing semantic change form usage patterns that can be explained by a very similar sociolinguistic distribution. This study demonstrates that employing a socio-cognitive perspective when researching polysemy is hugely advantageous.
The many uses of run
Authors: Glynn Dylan
Published: October 2014

Multifactorial usage-feature analysis (profile-based approach) has been successfully
applied to polysemy research (Gries 2006; Glynn 2009, 2010). This chapter
represents a repeat analysis of Gries (2006). The study has three aims: (i) to
verify the results of the previous study; (ii) to identify limitations in the applications
of the statistical technique employed (hierarchical cluster analysis) in the
previous study; and (iii) to demonstrate the need to account for sociolinguistic
dimensions in polysemy research. The study is based on a sample of 500 occurrences
of the lexeme to run, extracted in even proportions from British English
and American English and from online personal journals (blogs) and conversations
(American National Corpus and British National Corpus).
Visualizing distances in a set of near-synonyms
Authors: Desagulier Guillaume
Published: October 2014

I aim to uncover revealing aspects of the conceptual structure of four English
moderators (rather, quite, fairly, and pretty) and shed new light on previous
studies on degree modifiers. I develop an original methodology for handling
and visualizing measures of significant attraction between lexical items. This
methodology combines univariate and multivariate statistics. Collexeme analysis
is used as input for hierarchical agglomerative cluster analysis, and multiple
distinctive collexeme analysis is used as input for correspondence analysis. Visualizing
collexemes with exploratory tools does more than depict proximities
and distances between individuals and variables. It is also an accurate means to
(a) unveil fine semantic differences in a set of near-synonymous constructions,
(b) determine entrenchment continua, and (c) represent a significant part of the
complex inventory of intensifying constructions.
A case for the multifactorial assessment of learner language
Authors: Deshors Sandra C. , Gries Stefan Th.
Published: October 2014

In this study, we apply Gries and Divjak’s Behavioral Profile approach to compare
native English can and may, learner English can and may, and French pouvoir.
We annotated over 3,700 examples across three corpora according to more
than 20 morphosyntactic and semantic features and we analysed the features’
distribution with a hierarchical cluster analysis and a logistic regression. The
cluster analysis shows that French English learners build up fairly coherent categories
that group the English modals together followed by pouvoir, but that they
also consider pouvoir to be semantically more similar to can than to may. The
regression strongly supports learners’ coherent categories; however, a variety of
interactions shows where learners’ modal use still deviates from that of native
speakers.
Dutch causative constructions
Authors: Levshina Natalia , Geeraerts Dirk , Speelman Dirk
Published: October 2014

This chapter is a multivariate corpus-based study of two near-synonymous periphrastic causatives with doen and laten in Dutch. Using multiple logistic regression and classification trees, the study explores the conceptual differences between the constructions. The results support the existing definition of doen as the direct causation auxiliary, and interpretation of laten as the indirect causative (e.g. Verhagen and Kemmer 1997). However, the analyses also reveal more specific patterns: the most distinctive semantic pattern of doen is affective causation, whereas the contexts with the highest probability of laten refer to inducive causation. These differences remain valid when we control for geographic and thematic variation, as well as for the individual Effected Predicates treated as random effects in a mixed model.
The semasiological structure of Polish myśleć ‘to think’
Authors: Fabiszak Malgorzata , Hebda Anna , Kokorniak Iwona , Krawczak Karolina
Published: October 2014

The aim of the present chapter is to investigate the semasiological structure of the Polish verb myśleć ‘to think’ relative to the construal imposed by its prefixes. It juxtaposes the results of cognitive linguistic corpus-based introspective analysis with the results of a series of statistical tests of almost 4,000 manually coded example sentences. Multiple cluster analysis employs the techniques presented in Glynn (this volume), hierarchical cluster analysis follows Divjak and Fieller (this volume) and logistic regression is based on Speelman (this volume). The study shows that the do- prefix has a strong preference for clausal, processual complements, while the wy- prefix opts for nominal complements suggesting objectifiable results of the thinking process.
Techniques and tools
Authors: Glynn Dylan
Published: October 2014

The use of corpora in semantic research is a rapidly developing method. However, the range of quantitative techniques employed in the field can make it difficult for the non-specialist to keep abreast with the methodological development. This chapter serves as an introduction to the use of corpus methods in Cognitive Semantic research and as an overview of the relevant statistical techniques and software needed for performing them. The discussion and description are intended for researches in semantics that are interested in adopting quantitative corpus-driven methods. The discussion argues that there are fundamentally two corpus-driven approaches to meaning, one based on observable formal patterns (collocation analysis) and another based on patterns of annotated usage-features of use (feature analysis). The discussion then introduces and explains each of the statistical techniques currently used in the field. Examples of the use of each technique are listed and a summary of the software packages available in R for performing the techniques is included.
Statistics in R
Authors: van de Weijer Joost , Glynn Dylan
Published: October 2014

The R Project for Statistical Computing is one of the most comprehensive and widely used software options for statistical analysis. Moreover, it is open source, freely available and entirely cross-platform. It is for these reasons that the following chapters all employ R to demonstrate the application and interpretation of statistics. Like the commercially available software SAS, but unlike three other widely used suites (SPSS, Stata, and Statistica), R is principally used in command line. The need to work with commands rather than a graphical user interface can be a challenge for novice users, especially when combined with the task of learning statistics. However, commands given in a step-by-step fashion is arguably simpler than a graphic interface, which can overwhelm the novice user with options. This chapter is an introduction to R focusing on how to import data and make sure those data are in the correct format for analysis. Knowledge of each of these steps is assumed in the following chapters.
Frequency tables
Authors: Gries Stefan Th.
Published: October 2014

This chapter provides an overview of statistical tests to analyze frequency data. Specifically, it discusses the use, logic, and interpretation of chi-squared tests of two-dimensional frequency tables as well as the computation of effect sizes for such tables, followed by several extensions and follow-up procedures that are not usually discussed (such as the analysis of sub-tables of tables and the Marascuilo procedure). In addition, there is a brief discussion of how Poisson/count regression can be used to analyze frequency data with more than two dimensions.
Collostructional analysis
Authors: Hilpert Martin
Published: October 2014

This chapter offers a practical introduction to a set of corpus-linguistic analytical methods that are referred to collectively as ‘collostructional analysis’. The overarching aim in conducting a collostructional analysis is to find out which lexical items form collocations with a given grammatical construction. The purpose of such an undertaking, in the context of this book, is to facilitate the semantic analysis of grammatical constructions. The chapter discusses several case studies in order to show that the semantic description of grammatical constructions benefits from a quantitative analysis of the lexical material that occurs with the respective constructions. A final discussion surveys advantages and pitfalls of collostructional methods.
Correspondence analysis
Authors: Glynn Dylan
Published: October 2014

Correspondence analysis is an exploratory technique for complex categorical data, typical of corpus-driven research. It identifies patterns of association and disassociation in those data. For instance, it can map the correlations between different uses of a linguistic form and its various social and/or morpho-syntactic contexts. The technique presents its results in the form of a two-dimensional plot, which visualises these relationships in an intuitive manner. These plots offer rich representations of the relations between different facets of complex data. Using R, this chapter explains how the technique works and offers a step-by-step explanation of its application and the interpretation of its results. The technique is also compared to the better-known and comparable cluster analysis.
Corpus frequency and second language learners’ knowledge of collocations
Authors: Durrant Philip
Published: October 2014

Tests of second language learners’ knowledge of collocation have lacked a principled strategy for item selection, making claims about learners’ knowledge beyond the particular collocations tested difficult to evaluate. Corpus frequency may offer a good basis for item selection, if a reliable relationship can be demonstrated between frequency and learner knowledge. However, such a relationship is difficult to establish satisfactorily, given the small number of items and narrow range of test-takers involved in any individual study. In this study, a meta-analysis is used to determine the correlation between learner knowledge and frequency data across nineteen previously-reported tests. Frequency is shown to correlate moderately with knowledge, but the strength of this correlation varies widely across corpora. Strength of association measures (such as mutual information) do not to correlate with learner knowledge. These findings are discussed in terms of their implications for collocation testing and models of collocation learning.
Spurious effects in variational corpus linguistics
Authors: Tummers José , Speelman Dirk , Geeraerts Dirk
Published: October 2014

As repositories of spontaneously realized language, corpora generally have an uncontrolled and unbalanced structure where all variables operate simultaneously. Consequently, a variable’s real effect can be concealed when studied in isolation because of the exclusion of the impact of other potentially confounding variables. Analyzing a variational case study, the alternation between inflected and uninflected attributive adjectives in Dutch, it will be demonstrated how confounding variables alter the impact of explanatory variables on the response variable, resulting in spurious effects in the bivariate analyses. Multiple Correspondence Analysis will be used as a heuristic tool to unveil the association patterns between explanatory variables in the data matrix which induce the spurious effects. Based on these findings, we will argue for a thorough analysis of the database patterns to gain insight in the underlying associations between explanatory variables before modeling their real impact on the response variable in a multivariate model.
The have-it-that construction
Authors: Gómez-Moreno Pedro Ureña
Published: October 2014

Speakers do not always attribute agency straightforwardly when they communicate. While complying with the maxims of explicitness and relevance, they may depict states of affairs headed by an identifiable source. More often than not, however, it seems they leave out this source for a number of reasons and through different mechanisms. This paper is a corpus-based study of one such non-identifying structures, namely the extrapositional have-it-that construction, in examples such as Several hypotheses have it that land-use changes. Drawing on data from the BNC, this paper investigates the use, distribution and functioning of the have-it-that construction. The paper also highlights the usefulness of simple collexeme analysis in revealing systematic co-selection relationships within the construction.
Antihypertensive Drug Class and Adherence: An Electronic Monitoring Study
Authors: Moise Nathalie , Schwartz Joseph , Bring Rachel , Shimbo Daichi , Kronish Ian M.
Published: October 2014

BACKGROUND

Medication adherence is essential to optimizing blood pressure (BP) control. Prior research has demonstrated differences in pharmacy refill patterns according to antihypertensive drug class. No prior study has assessed the association between drug class and day-to-day adherence.

METHODS

Between 2011 and 2014, we enrolled a convenience sample of 149 patients with persistently uncontrolled hypertension from two inner-city clinics and concurrently measured adherence of up to four antihypertensive medications using electronic pillboxes during the interval between two primary care visits. The main outcome was mean percent of days adherent to each drug. Mixed effects regression analyses were used to assess the association between drug class and adherence adjusting for age, gender, race, ethnicity, education, health insurance, coronary artery disease, heart failure, chronic kidney disease, diabetes, number of medications, days monitored, and dosing frequency.

RESULTS

The mean age was 64 years; 72% women, 75% Hispanic, 88% prescribed ≥1 BP medication. In unadjusted analyses, adherence was lower for beta-blockers (70.9%) compared to angiotensin receptor blocking agents (75.0%, P = 0.11), diuretics (75.9%, P < 0.001), calcium channel blockers (77.6%, P < 0.001) and angiotensin-converting enzyme inhibitors (78.0%, P < 0.0001). In the adjusted analysis, only dosing frequency (P = 0.0001) but not drug class (P = 0.71) was associated with medication adherence.

CONCLUSIONS

Antihypertensive drug class was not associated with electronically measured adherence after accounting for dosing frequency amongst patients with uncontrolled hypertension. Low adherence to beta-blockers may have been due to the common practice of prescribing multiple daily dosing. Providers may consider using once daily formulations to optimize adherence and should assess adherence among all treated patients with uncontrolled hypertension.
MP-GeneticSynth: inferring biological network regulations from time series
Authors: Castellini Alberto , Paltrinieri Daniele , Manca Vincenzo
Published: October 2014

Summary: MP-GeneticSynth is a Java tool for discovering the logic and regulation mechanisms responsible for observed biological dynamics in terms of finite difference recurrent equations. The software makes use of: (i) metabolic P systems as a modeling framework, (ii) an evolutionary approach to discover flux regulation functions as linear combinations of given primitive functions, (iii) a suitable reformulation of the least squares method to estimate function parameters considering simultaneously all the reactions involved in complex dynamics. The tool is available as a plugin for the virtual laboratory MetaPlab. It has graphical and interactive interfaces for data preparation, a priori knowledge integration, and flux regulator analysis.

Availability and implemention: Source code, binaries, documentation (including quick start guide and videos) and case studies are freely available at http://mplab.sci.univr.it/plugins/mpgs/index.html.

Contact:  castellini@mpimp-golm.mpg.de
iDoComp: a compression scheme for assembled genomes
Authors: Ochoa Idoia , Hernaez Mikel , Weissman Tsachy
Published: October 2014

Motivation: With the release of the latest next-generation sequencing (NGS) machine, the HiSeq X by Illumina, the cost of sequencing a Human has dropped to a mere $4000. Thus we are approaching a milestone in the sequencing history, known as the $1000 genome era, where the sequencing of individuals is affordable, opening the doors to effective personalized medicine. Massive generation of genomic data, including assembled genomes, is expected in the following years. There is crucial need for compression of genomes guaranteed of performing well simultaneously on different species, from simple bacteria to humans, which will ease their transmission, dissemination and analysis. Further, most of the new genomes to be compressed will correspond to individuals of a species from which a reference already exists on the database. Thus, it is natural to propose compression schemes that assume and exploit the availability of such references.

Results: We propose iDoComp, a compressor of assembled genomes presented in FASTA format that compresses an individual genome using a reference genome for both the compression and the decompression. In terms of compression efficiency, iDoComp outperforms previously proposed algorithms in most of the studied cases, with comparable or better running time. For example, we observe compression gains of up to 60% in several cases, including H.sapiens data, when comparing with the best compression performance among the previously proposed algorithms.

Availability: iDoComp is written in C and can be downloaded from: http://www.stanford.edu/~iochoa/iDoComp.html (We also provide a full explanation on how to run the program and an example with all the necessary files to run it.).

Contact:  iochoa@stanford.edu

Supplementary information: Supplementary Data are available at Bioinformatics online.
RETRACTED: LFQC: a lossless compression algorithm for FASTQ files
Authors: Pathak Sudipta , Rajasekaran Sanguthevar
Published: October 2014

Motivation

Next-generation sequencing (NGS) technologies have revolutionized genomic research by reducing the cost of whole-genome sequencing. One of the biggest challenges posed by modern sequencing technology is economic storage of NGS data. Storing raw data is infeasible because of its enormous size and high redundancy. In this article, we address the problem of storage and transmission of large Fastq files using innovative compression techniques.

Results

We introduce a new lossless non-reference-based fastq compression algorithm named lossless FastQ compressor. We have compared our algorithm with other state of the art big data compression algorithms namely gzip, bzip2, fastqz, fqzcomp, G-SQZ, SCALCE, Quip, DSRC, DSRC-LZ etc. This comparison reveals that our algorithm achieves better compression ratios. The improvement obtained is up to 225%. For example, on one of the datasets (SRR065390_1), the average improvement (over all the algorithms compared) is 74.62%.

Availability and implementation

The implementations are freely available for non-commercial purposes. They can be downloaded from http://engr.uconn.edu/∼rajasek/FastqPrograms.zip.
Semantic Body Browser: graphical exploration of an organism and spatially resolved expression data visualization
Authors: Lekschas Fritz , Stachelscheid Harald , Seltmann Stefanie , Kurtz Andreas
Published: October 2014

Summary: Advancing technologies generate large amounts of molecular and phenotypic data on cells, tissues and organisms, leading to an ever-growing detail and complexity while information retrieval and analysis becomes increasingly time-consuming. The Semantic Body Browser is a web application for intuitively exploring the body of an organism from the organ to the subcellular level and visualising expression profiles by means of semantically annotated anatomical illustrations. It is used to comprehend biological and medical data related to the different body structures while relying on the strong pattern recognition capabilities of human users.

Availability and implementation: The Semantic Body Browser is a JavaScript web application that is freely available at http://sbb.cellfinder.org. The source code is provided on https://github.com/flekschas/sbb.

Contact:  sbb@cellfinder.org
A novel representation of genomic sequences for taxonomic clustering and visualization by means of self-organizing maps
Authors: Delgado Soledad , Morán Federico , Mora Antonio , Merelo Juan Julián , Briones Carlos
Published: October 2014

Motivation: Self-organizing maps (SOMs) are readily available bioinformatics methods for clustering and visualizing high-dimensional data, provided that such biological information is previously transformed to fixed-size, metric-based vectors. To increase the usefulness of SOM-based approaches for the analysis of genomic sequence data, novel representation methods are required that automatically and bijectively transform aligned nucleotide sequences into numeric vectors, dealing with both nucleotide ambiguity and gaps derived from sequence alignment.

Results: Six different codification variants based on Euclidean space, just like SOM processing, have been tested using two SOM models: the classical Kohonen’s SOM and growing cell structures. They have been applied to two different sets of sequences: 32 sequences of small sub-unit ribosomal RNA from organisms belonging to the three domains of life, and 44 sequences of the reverse transcriptase region of the pol gene of human immunodeficiency virus type 1 belonging to different groups and sub-types. Our results show that the most important factor affecting the accuracy of sequence clustering is the assignment of an extra weight to the presence of alignment-derived gaps. Although each of the codification variants shows a different level of taxonomic consistency, the results are in agreement with sequence-based phylogenetic reconstructions and anticipate a broad applicability of this codification method.

Contact:  sole@eui.upm.es

Supplementary information:  Supplementary Data are available at Bioinformatics online.
A coalescent-based method for population tree inference with haplotypes
Authors: Wu Yufeng
Published: October 2014

Motivation: Population trees represent past population divergence histories. The inference of population trees can be useful for the study of population evolution. With the size of data increases in large-scale population genetic projects, such as the 1000 Genomes Project, there are new computational challenges for ancestral population inference, including population tree inference. Existing methods for population tree inference are mainly designed for unlinked genetic variants (e.g. single nucleotide polymorphisms or SNPs). There is a potential loss of information by not considering the haplotypes.

Results: In this article, we propose a new population tree inference method (called STELLSH) based on coalescent likelihood. The likelihood is for haplotypes over multiple SNPs within a non-recombining region, not unlinked variants. Unlike many existing ancestral inference methods, STELLSH does not use Monte Carlo approaches when computing the likelihood. For efficient computation, the likelihood model is approximated but still retains much information about population divergence history. STELLSH can find the maximum likelihood population tree based on the approximate likelihood. We show through simulation data and the 1000 Genomes Project data that STELLSH gives reasonably accurate inference results. STELLSH is reasonably efficient for data of current interest and can scale to handle whole-genome data.

Availability and implementation: The population tree inference method STELLSH has been implemented as part of the STELLS program: http://www.engr.uconn.edu/∼ywu/STELLS.html.

Contact:  ywu@engr.uconn.edu

Supplementary information:  Supplementary Data are available at Bioinformatics online.
Hepatitis E Vaccine to Prevent Morbidity and Mortality During Epidemics
Authors: Nelson Kenrad E. , Shih James W. K. , Zhang Jun , Zhao Qinjian , Xia Ningshao , Ticehurst John R. , Labrique Alain B.
Published: October 2014

Recurrent, large, waterborne epidemics of hepatitis E virus (HEV) occur regularly after monsoon rains contaminate water supplies in Asia or during humanitarian crises in Africa. These epidemics commonly affect thousands of persons, and it has a high mortality in pregnant women who become infected. Although a subunit HEV vaccine has been developed by Chinese investigators and was found to be highly effective and safe in a large clinical trial, this vaccine is only available in China. Until it is prequalified by the World Health Organization, the vaccine may not be available for use outside of China in low-income countries that lack national vaccine regulatory agencies. In this manuscript, we explore possible strategies for providing access to this potentially important vaccine for international use in responding to epidemics of HEV in low-resource countries.
Urinary Tract Infections in Male Veterans With Human Immunodeficiency Virus
Authors: Eccles-Radtke Caitlin , Rector Thomas S. , Cutting Andrea , Drekonja Dimitri M.
Published: October 2014

Treatment duration for men with urinary tract infection (UTI) and human immunodeficiency virus (HIV) infection is unknown. Fiscal year 2009 Veterans Affairs administrative data were used to compare men with HIV and UTI with non-HIV men with UTI. Antimicrobial selection and duration were similar. Shorter treatment (≤7 days) did not affect recurrence, suggesting that treatment beyond 7 days may be unnecessary.
Point-of-Use Mixing of Influenza H5N1 Vaccine and MF59 Adjuvant for Pandemic Vaccination Preparedness: Antibody Responses and Safety. A Phase 1 Clinical Trial
Authors: Mulligan Mark J. , Bernstein David I. , Frey Sharon , Winokur Patricia , Rouphael Nadine , Dickey Michelle , Edupuganti Srilatha , Spearman Paul , Anderson Edwin , Graham Irene , Noah Diana L. , Mangal Brian , Kim Sonnie , Hill Heather , Whitaker Jenifer , Emery William , Beck Allison , Stephens Kathy , Hartwell Brooke , Ogilvie Melinda , Rimann Nayoka , Osinski Eileen , Destefano Ellen , Gajadhar Theda , Strudwick Amanda , Pierce Karen , Lai Lilin , Yue Ling , Wang Dongli , Ying Carl , Cline Amy , Foltz Tara , Wagner Nancy , Dull Geraldine , Pacatte Thomas , Taggart Barbara , Johnson Valerie , Haller Logan , Looney Candi , Li Shixiong , May Megan , Myers Bridgette , May Rachel , Parker Lawanda , Cochran Nertaissa , Bowen Donna , Bell Michelle , Scoggins Jeffery , Burns Angela , Stablein Claire , Wolff Mark , Jolles Bernadette , Leung Brenda , Lambert Linda , Shorer Shy , Buchanan Wendy , Murray Suzanne , Chang Soju , Gorman Richard
Published: October 2014

Background.  Avian influenza A/H5N1 has threatened human health for nearly 2 decades. Avian influenza A vaccine without adjuvant is poorly immunogenic. A flexible rapid tactic for mass vaccination will be needed if a pandemic occurs.

Methods.  A multicenter, randomized, blinded phase 1 clinical trial evaluated safety and antibody responses after point-of-use mixing of influenza A/Indonesia/05/2005 (H5N1) vaccine with MF59 adjuvant. Field-site pharmacies mixed 3.75, 7.5, or 15 mcg of antigen with or without MF59 adjuvant just prior to intramuscular administration on days 0 and 21 of healthy adults aged 18–49 years.

Results.  Two hundred and seventy subjects were enrolled. After vaccination, titers of hemagglutination inhibition antibody ≥1:40 were achieved in 80% of subjects receiving 3.75 mcg + MF59 vs only 14% receiving 15 mcg without adjuvant (P < .0001). Peak hemagglutination inhibition antibody geometric mean titers for vaccine + MF59 were ∼65 regardless of antigen dose, and neutralizing titers were 2- to 3-fold higher. Vaccine + MF59 produced cross-reactive antibody responses against 4 heterologous H5N1 viruses. Excellent safety and tolerability were demonstrated.

Conclusions.  Point-of-use mixing of H5N1 antigen and MF59 adjuvant achieved target antibody titers in a high percentage of subjects and was safe. The feasibility of the point-of-use mixing should be studied further.
Interplay of TGFb superfamily members governs optic fissure closure
Authors: Heermann Stephan , Eckert Priska , Mateo Juan L. , Roussa Eleni , Rahhal Belal , Zuniga Aimee , Krieglstein Kerstin , Wittbrodt Jochim
Published: October 2014

The optic fissure is a gap in the developing vertebrate eye and must be closed as development proceeds. A persisting optic fissure is referred to as coloboma, a major cause for blindness in children. Multiple factors have been linked to coloboma formation, however, the actual process of fissure closure is only poorly understood.

Based on our findings we propose an important role of TGFb signaling for optic fissure closure. We show active TGFb signaling in the fissure margins, analyzed by a new TGFb signaling reporter zebrafish. We found BMP antagonists regulated by TGFb. These antagonists we also found expressed in the fissure margins. Finally we show a coloboma phenotype in a TGFb KO mouse. Microarray data analysis indicates intense TGFb dependent remodeling of the extracellular matrix (ECM) during optic fissure closure.

We propose that TGFb is driving optic fissure closure by ECM remodeling. As previously shown, inhibition of BMP signaling is important for such TGFb dependent ECM remodeling. We show that this is achieved by the regulation of BMP antagonists, expressed in the optic fissure margins.
TRF1 negotiates TTAGGG repeat-associated replication problems by recruiting the BLM helicase and the TPP1/POT1 repressor of ATR signaling
Authors: Zimmermann Michal , Kibe Tatsuya , Kabir Shaheen , de Lange Titia
Published: October 2014

The semiconservative replication of telomeres is facilitated by the shelterin component TRF1. Without TRF1, replication forks stall in the telomeric repeats, leading to ATR kinase signaling upon S-phase progression, fragile metaphase telomeres that resemble the common fragile sites (CFSs), and the association of sister telomeres. In contrast, TRF1 does not contribute significantly to the end protection functions of shelterin. We addressed the mechanism of TRF1 action using mouse conditional knockouts of BLM, TRF1, TPP1, and Rap1 in combination with expression of TRF1 and TIN2 mutants. The data establish that TRF1 binds BLM to facilitate lagging but not leading strand telomeric DNA synthesis. As the template for lagging strand telomeric DNA synthesis is the TTAGGG repeat strand, TRF1-bound BLM is likely required to remove secondary structures formed by these sequences. In addition, the data establish that TRF1 deploys TIN2 and the TPP1/POT1 heterodimers in shelterin to prevent ATR during telomere replication and repress the accompanying sister telomere associations. Thus, TRF1 uses two distinct mechanisms to promote replication of telomeric DNA and circumvent the consequences of replication stress. These data are relevant to the expression of CFSs and provide insights into TIN2, which is compromised in dyskeratosis congenita (DC) and related disorders.
An Optical Clearing Technique for Plant Tissues Allowing Deep Imaging and Compatible with Fluorescence Microscopy
Authors: Warner Cherish A. , Biedrzycki Meredith L. , Jacobs Samuel S. , Wisser Randall J. , Caplan Jeffrey L. , Sherrier D. Janine
Published: October 2014

We report on a nondestructive clearing technique that enhances transmission of light through specimens from diverse plant species, opening unique opportunities for microscope-enabled plant research. After clearing, plant organs and thick tissue sections are amenable to deep imaging. The clearing method is compatible with immunocytochemistry techniques and can be used in concert with common fluorescent probes, including widely adopted protein tags such as GFP, which has fluorescence that is preserved during the clearing process.
The human herpesvirus 6 U21–U24 gene cluster is dispensable for virus growth
Authors: Jasirwan Chyntia , Tang Huamin , Kawabata Akiko , Mori Yasuko
Published: October 2014

Human herpesvirus 6 (HHV‐6) is a T‐lymphotrophic virus belongs to the genus Roseolovirus within the beta herpesvirus subfamily. The U20–U24 gene cluster is unique to Roseoloviruses; however, both their function and whether they are essential for virus growth is unknown. Recently, bacterial artificial chromosome (BAC) techniques have been used to investigate HHV‐6A. This study describes generation of a virus genome lacking U21–U24 (HHV‐6ABACΔU21–24) and shows that infectious virus particles can be reconstituted from this BAC DNA. Our data indicate that the HHV‐6 U21–U24 gene cluster is dispensable for virus propagation.
Molecular characterization of dengue and chikungunya virus strains circulating in New Delhi, India
Authors: Afreen Nazia , Deeba Farah , Khan Wajihul H. , Haider Shakir H. , Kazim Syed Naqui , Ishrat Romana , Naqvi Irshad Hussain , Shareef Mohammad Y. , Broor Shobha , Ahmed Anwar , Parveen Shama
Published: October 2014

Dengue and chikungunya are acute viral infections with overlapping clinical symptoms. Both diseases are transmitted by common mosquito vectors resulting in their co‐circulation in a region. Molecular and serological tests specific for both dengue and chikungunya infections were performed on 87 acute phase blood samples collected from patients with suspected dengue/chikungunya infections in Delhi from September to December, 2011. RT‐PCR and IgM ELISA were performed to detect dengue virus (DENV) and chikungunya virus (CHIKV). NS1 and IgG ELISA were also performed to detect DENV specific antigen and secondary DENV infection. DENV infection was detected in 49%, CHIKV infection in 29% and co‐infection with DENV and CHIKV in 10% of the samples by RT‐PCR. DENV serotypes 1, 2 and 3 were detected in this study. Nine DENV‐1 strains, six DENV‐2 strains and 20 CHIKV strains were characterized by DNA sequencing and phylogenetic analysis of their respective envelope protein genes. DENV‐1 strains grouped in the American African genotype, DENV‐2 strains in the Cosmopolitan genotype and CHIKV strains in the East Central South African genotype by phylogenetic analysis. This is one of the few studies reporting the phylogeny of two dengue virus serotypes (DENV‐1 and DENV‐2) and CHIKV. Surveillance and monitoring of DENV and CHIKV strains are important for design of strategies to control impending epidemics.
Herbivore effect traits and their impact on plant community biomass: an experimental test using grasshoppers
Authors: Deraison Hélène , Badenhausser Isabelle , Börger Luca , Gross Nicolas
Published: October 2014

Using trait‐based approaches to study trophic interactions may represent one of the most promising approaches to evaluate the impact of trophic interactions on ecosystem functioning. To achieve this goal, it is necessary to clearly identify which traits determine the impact of one trophic level on another.

Using functionally contrasting grasshopper species, we tested the ability of multiple traits (morphological, chemical and biomechanical) to predict herbivore impact on the biomass of a diverse plant community. We set‐up a cage experiment in an old species rich grassland field and evaluated how multiple candidate grasshopper effect traits mediated herbivore impact on plant biomass.

Grasshoppers had different impact on plant community biomass (consuming up to 60% of plant community biomass). Grasshopper impact was positively correlated with their incisive strength while body size or grasshopper C:N ratio exhibited low predictive ability. Importantly, the strong relationship between the incisive strength and the impact was mediated by the grasshopper feeding niche, which was well predicted in our study by two simple plant traits (leaf dry matter content, leaf C:N ratio). Feeding niche differences between grasshoppers were explained by differences in incisive strength, highlighting the fundamental linkage between grasshopper effect traits and their niche.

Our study contributes to the development of the trait‐based approach in the study of trophic interactions by providing a first experimental test of the relationship between herbivore effect traits, their impact on plant community biomass, and in a larger extent on ecosystem functioning. By comparing the relative importance of multiple interacting grasshopper traits, our study showed that incisive strength was a key effect trait which determined grasshopper feeding niche and its relative impact on plant community biomass.
Bringing animal personality research into the food web arena
Authors: Kalinkat Gregor
Published: October 2014

The consumption rate of the crab Panopeus herbstii feeding on the mussel Brachidontes exustus depends on predator and prey body size as well as the predator individual activity level. Photo credit: Kathryn Levasseur.

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The consumption rate of the crab Panopeus herbstii feeding on the mussel Brachidontes exustus depends on predator and prey body size as well as the predator individual activity level. Photo credit: Kathryn Levasseur.

Toscano, B.J. & Griffen,B.D. (2014) . Journal of Animal Ecology, 83, 1469–1477.

While the concept of consistent behavioural differences among individuals of the same population has gained a lot of scientific attention over the last decade, its implementation into a community context with a focus on species‐level interactions is still in its infancy. In their study on the effects of animal personalities on predator–prey functional responses of mussel‐eating crabs, Toscano & Griffen (2014) introduce a promising avenue for future research synthesizing concepts and ideas from animal behaviour and food web ecology. More precisely, by showing that the interplay of animal personalities and predator and prey body sizes significantly alters the outcome of predator–prey interactions, this study provides important evidence that the concept of animal personalities needs greater consideration if we want to refine and improve current models of predator–prey interactions and the impact of individual‐level variation on quantitative food‐web dynamics.
Personality and Political Tolerance: Evidence from India and Pakistan
Authors: Oskarsson Sven , Widmalm Sten
Published: October 2014

Inspired by recent studies on personality and political attitudes and behaviour we use the Big Five approach to assess the influence of a comprehensive set of personality traits on political tolerance. Our study is based on surveys in Bhopal in India and Lahore in Pakistan. We find that all Big Five traits – openness, conscientiousness, extraversion, agreeableness and neuroticism – are significantly related to individuals’ willingness to grant political rights to groups they dislike in one or both countries. As one of only a few studies examining the relationship between the Big Five traits and political attitudes and behaviour outside a Western context, these findings demonstrate the importance of also paying attention to personality traits when studying contexts where situational factors such as political violence, poverty, and severe inequalities might be expected to be the main influence on individuals’ behavioural choices.