bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evocative gene–environment correlation in the mother–child relationship: A twin study of interpersonal processes
Authors: Klahr Ashlea M. , Thomas Katherine M. , Hopwood Christopher J. , Klump Kelly L. , Burt S. Alexandra 
Published: February 2013

AbstractThe behavior genetic literature suggests that genetically influenced characteristics of the child elicit specific behaviors from the parent. However, little is known about the processes by which genetically influenced child characteristics evoke parental responses. Interpersonal theory provides a useful framework for identifying reciprocal behavioral processes between children and mothers. The theory posits that, at any given moment, interpersonal behavior varies along the orthogonal dimensions of warmth and control and that the interpersonal behavior of one individual tends to elicit corresponding or contrasting behavior from the other (i.e., warmth elicits warmth, whereas control elicits submission). The current study thus examined these dimensions of interpersonal behavior as they relate to the parent–child relationship in 546 twin families. A computer joystick was used to rate videos of mother–child interactions in real time, yielding information on mother and child levels of warmth and control throughout the interaction. Analyses indicated that maternal control, but not maternal warmth, was influenced by evocative gene–environment correlational processes, such that genetic influences on maternal control and child control were largely overlapping. Moreover, these common genetic influences were present both cross-sectionally and over the course of the interaction. Such findings not only confirm the presence of evocative gene–environment correlational processes in the mother–child relationship but also illuminate at least one of the specific interpersonal behaviors that underlie this evocative process.
The promise of clinical interventions for hepatocellular carcinoma from the west to mainland China
Authors: Bai Mei , Reynolds Nancy R. , McCorkle Ruth 
Published: February 2013

AbstractObjective:Hepatocellular carcinoma (HCC) presents a major health problem with its steadily increasing incidence in Western countries, and persistent high fatality rates worldwide. The well-recognized complexity and toxicity of its treatment as well as inadequate care and limited resources in mainland China exacerbate the difficulty of maintaining quality of remaining life of patients living with this illness. The goal of this comprehensive literature review was to identify promising clinical interventions for improving quality of life (QOL) of people with advanced HCC in mainland China.Method:A comprehensive literature review was performed in China Academic Journals (CAJ), Cochrane, and PubMed databases. The review was confined to studies of randomized controlled trials (RCT) for adults, in Chinese and English, from 1980 to 2012.Results:A total of 676 studies in Chinese and 391 studies in English were identified. Eighteen RCTs were selected for the final review, among which three were conducted in mainland China.Significance of results:Nurse-led home-based comprehensive interventions using a collaborative care approach addressing multiple dimensions of QOL show promise for enhancing clinical outcomes for people with advanced HCC in mainland China. Education and psychosocial support combined with symptom management early in the illness trajectory and ongoing close attention to physical symptoms, emotional distress, as well as spiritual well-being are crucial for maintaining QOL of people with advanced HCC. Telephone monitoring appears to be a feasible way in rural as well as urban areas. Families are advised to be part of overall interventions. It is warranted that promising interventions aiming at improving QOL for advanced cancer patients reported in Western literature be further tested in mainland China.
Religion and Ethnic Minority Attitudes in Britain toward the War in Afghanistan
Authors: Clements Ben 
Published: February 2013

AbstractPublic opinion research has demonstrated that minority religious and ethnic groups hold distinctive preferences on foreign policy issues, including military interventions in the Cold War and post-Cold War eras. There has been little scholarly research in Britain into the attitudes of minority groups on foreign policy issues. This article uses a nationally-representative survey of the ethnic minority population in Britain to examine the sources of public opinion towards the war in Afghanistan. Using multivariate analysis, it finds strong effects for religious affiliation, religiosity and political alienation. There is also evidence of a “gender gap” and age-related differences. The paper contributes to the literature on the impact of religion on public opinion and foreign policy and to analysis of the political attitudes of minority groups in Britain.
RNA-eXpress annotates novel transcript features in RNA-seq data
Authors: Forster Samuel C. , Finkel Alexander M. , Gould Jodee A. , Hertzog Paul J. 
Published: February 2013

Abstract
Summary: Next-generation sequencing is rapidly becoming the approach of choice for transcriptional analysis experiments. Substantial advances have been achieved in computational approaches to support these technologies. These approaches typically rely on existing transcript annotations, introducing a bias towards known genes, require specific experimental design and computational resources, or focus only on identification of splice variants (ignoring other biologically relevant transcribed features contained within the data that may be important for downstream analysis). Biologically relevant transcribed features also include large and small non-coding RNA, new transcription start sites, alternative promoters, RNA editing and processing of coding transcripts. Also, many existing solutions lack accessible interfaces required for wide scale adoption. We present a user-friendly, rapid and computation-efficient feature annotation framework (RNA-eXpress) that enables identification of transcripts and other genomic and transcriptional features independently of current annotations. RNA-eXpress accepts mapped reads in the standard binary alignment (BAM) format and produces a study-specific feature annotation in GTF format, comparison statistics, sequence extraction and feature counts. The framework is designed to be easily accessible while allowing advanced users to integrate new feature-identification algorithms through simple class extension, thus facilitating expansion to novel feature types or identification of study-specific feature types.
Availability and implementation: RNA-eXpress software, source code, user manuals, supporting tutorials, developer guides and example data are available at http://www.rnaexpress.org.
Contact: paul.hertzog@monash.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Oxfold: kinetic folding of RNA using stochastic context-free grammars and evolutionary information
Authors: Anderson James W. J. , Haas Pierre A. , Mathieson Leigh-Anne , Volynkin Vladimir , Lyngsø Rune , Tataru Paula , Hein Jotun 
Published: February 2013

Abstract
Motivation: Many computational methods for RNA secondary structure prediction, and, in particular, for the prediction of a consensus structure of an alignment of RNA sequences, have been developed. Most methods, however, ignore biophysical factors, such as the kinetics of RNA folding; no current implementation considers both evolutionary information and folding kinetics, thus losing information that, when considered, might lead to better predictions.
Results: We present an iterative algorithm, Oxfold, in the framework of stochastic context-free grammars, that emulates the kinetics of RNA folding in a simplified way, in combination with a molecular evolution model. This method improves considerably on existing grammatical models that do not consider folding kinetics. Additionally, the model compares favourably to non-kinetic thermodynamic models.
Availability: http://www.stats.ox.ac.uk/∼anderson.
Contact: anderson@stats.ox.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Quantifying spatial relationships from whole retinal images
Authors: Ruttenberg Brian E. , Luna Gabriel , Lewis Geoffrey P. , Fisher Steven K. , Singh Ambuj K. 
Published: February 2013

Abstract
Motivation: Microscopy advances have enabled the acquisition of large-scale biological images that capture whole tissues in situ. This in turn has fostered the study of spatial relationships between cells and various biological structures, which has proved enormously beneficial toward understanding organ and organism function. However, the unique nature of biological images and tissues precludes the application of many existing spatial mining and quantification methods necessary to make inferences about the data. Especially difficult is attempting to quantify the spatial correlation between heterogeneous structures and point objects, which often occurs in many biological tissues.
Results: We develop a method to quantify the spatial correlation between a continuous structure and point data in large (17 500 × 17 500 pixel) biological images. We use this method to study the spatial relationship between the vasculature and a type of cell in the retina called astrocytes. We use a geodesic feature space based on vascular structures and embed astrocytes into the space by spatial sampling. We then propose a quantification method in this feature space that enables us to empirically demonstrate that the spatial distribution of astrocytes is often correlated with vascular structure. Additionally, these patterns are conserved in the retina after injury. These results prove the long-assumed patterns of astrocyte spatial distribution and provide a novel methodology for conducting other spatial studies of similar tissue and structures.
Availability: The Matlab code for the method described in this article can be found at http://www.cs.ucsb.edu/∼dbl/software.php.
Contact: bruttenberg@cra.com or ambuj@cs.ucsb.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
aCSM: noise-free graph-based signatures to large-scale receptor-based ligand prediction
Authors: Pires Douglas E. V. , de Melo-Minardi Raquel C. , da Silveira Carlos H. , Campos Frederico F. , Meira Wagner 
Published: February 2013

Abstract
Motivation: Receptor-ligand interactions are a central phenomenon in most biological systems. They are characterized by molecular recognition, a complex process mainly driven by physicochemical and structural properties of both receptor and ligand. Understanding and predicting these interactions are major steps towards protein ligand prediction, target identification, lead discovery and drug design.
Results: We propose a novel graph-based–binding pocket signature called aCSM, which proved to be efficient and effective in handling large-scale protein ligand prediction tasks. We compare our results with those described in the literature and demonstrate that our algorithm overcomes the competitor’s techniques. Finally, we predict novel ligands for proteins from Trypanosoma cruzi, the parasite responsible for Chagas disease, and validate them in silico via a docking protocol, showing the applicability of the method in suggesting ligands for pockets in a real-world scenario.
Availability and implementation: Datasets and the source code are available at http://www.dcc.ufmg.br/∼dpires/acsm.
Contact: dpires@dcc.ufmg.br or raquelcm@dcc.ufmg.br
Supplementary information: Supplementary data are available at Bioinformatics online.
displayHTS: a R package for displaying data and results from high-throughput screening experiments
Authors: Zhang Xiaohua Douglas , Zhang Zhaozhi 
Published: February 2013

Abstract
Summary: The R package displayHTS implements recently developed methods and figures for displaying data and hit selection results in high-throughput screening (HTS) experiments. It generates not only certain useful distinctive graphics such as the plate-well series plot, plate image and dual-flashlight plot but also other commonly used figures such as volcano plot and plate correlation plot. These figures are critical for visualizing the data and displaying important features of HTS data and hit selection results.
Availability and implementation: The package is freely available from CRAN: http://cran.r-project.org/mirrors.html, being distributed under the GNU General Public License.
Contact: xiaohua_zhang@merck.com
Supplementary information: Supplementary data are available at Bioinformatics online.
MODexplorer: an integrated tool for exploring protein sequence, structure and function relationships
Authors: Kosinski Jan , Barbato Alessandro , Tramontano Anna 
Published: February 2013

Abstract
Summary: MODexplorer is an integrated tool aimed at exploring the sequence, structural and functional diversity in protein families useful in homology modeling and in analyzing protein families in general. It takes as input either the sequence or the structure of a protein and provides alignments with its homologs along with a variety of structural and functional annotations through an interactive interface. The annotations include sequence conservation, similarity scores, ligand-, DNA- and RNA-binding sites, secondary structure, disorder, crystallographic structure resolution and quality scores of models implied by the alignments to the homologs of known structure.
MODexplorer can be used to analyze sequence and structural conservation among the structures of similar proteins, to find structures of homologs solved in different conformational state or with different ligands and to transfer functional annotations. Furthermore, if the structure of the query is not known, MODexplorer can be used to select the modeling templates taking all this information into account and to build a comparative model.
Availability and implementation: Freely available on the web at http://modorama.biocomputing.it/modexplorer. Website implemented in HTML and JavaScript with all major browsers supported.
Contact: anna.tramontano@uniroma1.it
Supplementary information: Supplementary data are available at Bioinformatics online
Phylogenomic clustering for selecting non-redundant genomes for comparative genomics
Authors: Moreno-Hagelsieb Gabriel , Wang Zilin , Walsh Stephanie , ElSherbiny Aisha 
Published: February 2013

Abstract
Motivation: Analyses in comparative genomics often require non-redundant genome datasets. Eliminating redundancy is not as simple as keeping one strain for each named species because genomes might be redundant at a higher taxonomic level than that of species for some analyses; some strains with different species names can be as similar as most strains sharing a species name, whereas some strains sharing a species name can be so different that they should be put into different groups; and some genomes lack a species name.
Results: We have implemented a method and Web server that clusters a genome dataset into groups of redundant genomes at different thresholds based on a few phylogenomic distance measures.
Availability: The Web interface, similarity and distance data and R-scripts can be accessed at http://microbiome.wlu.ca/research/redundancy/.
Contact: gmoreno@wlu.ca
The acoustic multifrequency classification of two sympatric euphausiid species (Meganyctiphanes norvegica and Thysanoessa raschii), with empirical and SDWBA model validation
Authors: McQuinn Ian H. , Dion Maxime , St. Pierre Jean-François 
Published: February 2013

AbstractMcQuinn, I. H., Dion, M., and St. Pierre, J.-F. 2013. The acoustic multifrequency classification of two sympatric euphausiid species (Meganyctiphanes norvegica and Thysanoessa raschii), with empirical and SDWBA model validation. – ICES Journal of Marine Science, 70: 636–649. The ecosystem approach to fishery management requires monitoring capabilities at all trophic levels, including pelagic organisms. However, the usefulness of active acoustics for ecosystem monitoring has been limited by ambiguities in the identification of scattering layers. Increasingly, multifrequency acoustic methods are being developed for the classification of scattering layers into species or species groups. We describe a method for distinguishing between sympatric northern and Arctic krill (Meganyctiphanes norvegica and Thysanoessa raschii) using sv amplitude ratios from 38, 120, and 200 kHz data which were pre-processed through a self-noise removal algorithm. Acoustic frequency responses of both euphausiid species were predicted from species-specific parameterizations of a SDWBA physical model using specific body forms (shape, volume, and length) for Arctic and northern krill. Classification and model validation were achieved using macrozooplankton samples collected from multiple-sampler (BIONESS) and ringnet (JackNet) hauls, both equipped with a strobe light to reduce avoidance by euphausiids. SDWBA frequency responses were calculated for a range of orientations (± 45°) and compared with observed frequency responses, solving for orientation by least squares. A tilt angle distribution of N[9°,4°] and N[12°,6°] for T. raschii and M. norvegica, respectively resulted in best fits. The models also provided species-specific TS–length relationships.
Spatial and temporal scales of environmental forcing of Acartia populations (Copepoda: Calanoida) in the Canal de Mira (Ria de Aveiro, Portugal)†
Authors: Leandro Sérgio Miguel , Tiselius Peter , Queiroga Henrique 
Published: February 2013

Abstract
Zooplankton and hydrological data were collected from August 2000 and June 2002 at six stations distributed throughout Canal de Mira (Ria de Aveiro, Portugal). The abundance of Acartia clausi and Acartia tonsa adults and juveniles of Acartia spp. for each station and month were combined in a three-way data matrix, which was decomposed into three two-way matrices corresponding to different modes: biological, time, and space. Cluster analysis applied on the space mode revealed the existence of three different zones as a consequence of zooplankton composition. At each mode, principal component analysis showed strong seasonal variations in zones 1 and 2. A different spatial pattern was found between the periods November 2000–April 2001 and November 2001–April 2002, with the displacement of the highest abundance levels from the middle estuary to near the mouth. The congeneric populations were segregated in space: the A. clausi population was restricted to downstream stations (zone 1), whereas the A. tonsa population dominated the middle estuary. Significant correlations between hydrological parameters and copepod abundance were found to differ from zone to zone. The statistical methodology was a valuable tool to (i) discriminate spatial and seasonal distribution patterns, (ii) define estuarine sections based on the faunistic composition, and (iii) evaluate delayed effects of phytoplankton.
Growth and planning strategies within women‐led SMEs
Authors: Mitchelmore Siwan , Rowley Jennifer 
Published: February 2013

PurposeThis paper aims to explore the planning strategies of female entrepreneurs who have indicated a desire to grow their businesses, the time horizons of planning strategies and the relationship between planning horizons and number of employees and annual sales as measures of business performance.Design/methodology/approachIn order to gather data for this exploratory study, a questionnaire was sent by e‐mail to members of networks of female entrepreneurs across England and Wales. Questionnaires were selected for analysis on the basis of an indication from the respondent that they wished to grow their business. Data were entered into SPSS to generate descriptive statistics, and conduct hypothesis testing.FindingsThe most preferred business growth strategies were: improving existing products or services and expanding advertising and promotion. Planning horizons are very short (often under three months), although the planning horizons associated with new products and entry into new markets were in some instances a little longer. Such short planning horizons could have serious consequences for business performance and growth. The planning horizons for cashflow, and investment in infrastructure showed a correlation with number of employees, whilst the planning horizons for cashflow, new product development, and expenditure showed a correlation with annual sales.Practical implicationsFemale entrepreneurs need to be encouraged to extend their planning horizons, especially in terms of financial indicators such as expenditure, cash flow, and investment.Originality/valueThis research contributes to the growing literature on female entrepreneurs and their business, by providing further insight into their growth strategies and planning horizons.
Building and sustaining a culture of assessment: best practices for change leadership
Authors: Gorran Farkas Meredith 
Published: February 2013

PurposeThe purpose of this paper is to explore the idea of using Kotter's eight‐step model for change leadership to create a culture of assessment that is embedded in the organizational culture of an academic library.Design/methodology/approachThis is a conceptual paper that examines the potential application of a business change model to an academic library change context. Each step of Kotter's model is described within the context of building a culture of assessment, supported by examples and suggestions from the literature of libraries, higher education, organizational behavior and change leadership.FindingsWhile building a culture of assessment is critical for libraries in the current environment, it is a difficult and complex process that requires grassroots initiative, top‐down support and strong leadership. Kotter's model for change management provides a pragmatic structure for culture change through behavioral change and change leadership regardless of positional authority.Practical implicationsThis paper includes best practices for facilitating a culture of assessment, including necessary resources and possible approaches.Originality/valueWhile the literature contains articles about building a culture of assessment, no studies have applied models of change leadership from the management literature to this unique cultural process. This is the first paper that suggests concrete steps for libraries towards building a culture of assessment, even in the absence of an ideal organizational culture. The focus is also on enabling change leadership regardless of whether the change agents have positional authority.