bluuebunny/crossref_metadata_2025_split huggingface dataset:
Host traits drive viral life histories across phytoplankton viruses
Authors: Edwards Kyle F. , Steward Grieg F. 
Published: April 2017

AbstractViruses are integral to ecological and evolutionary processes, but we have a poor understanding of what drives variation in key traits across diverse viruses. For lytic viruses, burst size, latent period, and genome size are primary characteristics controlling host-virus dynamics. Burst size and latent period are analogous to organismal traits of fecundity and generation time, and genome size affects the size of the virion as well as viral control of host metabolism. Here we synthesize data on these traits for 75 strains of phytoplankton viruses, which play an important role in global biogeochemistry. We find that primary traits of the host (genome size, growth rate) are major ecological drivers, explaining 40-50% of variation in burst size and latent period. We analyze an eco-evolutionary model to explore mechanisms underlying these patterns. We find that burst size may be set by the host genomic resources available for viral construction, while latent period evolves to permit this maximal burst size, modulated by host metabolic rate. These results suggest that general mechanisms may underlie the evolution of diverse viruses, which will facilitate our understanding of viral community processes, ecosystem impacts, and coevolutionary dynamics.
Cortical Representations of Speech in a Multi-talker Auditory Scene
Authors: Puvvada Krishna C. , Simon Jonathan Z. 
Published: April 2017

AbstractThe ability to parse a complex auditory scene into perceptual objects is facilitated by a hierarchical auditory system. Successive stages in the hierarchy transform an auditory scene of multiple overlapping sources, from peripheral tonotopically-based representations in the auditory nerve, into perceptually distinct auditory-objects based representation in auditory cortex. Here, using magnetoencephalography (MEG) recordings from human subjects, both men and women, we investigate how a complex acoustic scene consisting of multiple speech sources is represented in distinct hierarchical stages of auditory cortex. Using systems-theoretic methods of stimulus reconstruction, we show that the primary-like areas in auditory cortex contain dominantly spectro-temporal based representations of the entire auditory scene. Here, both attended and ignored speech streams are represented with almost equal fidelity, and a global representation of the full auditory scene with all its streams is a better candidate neural representation than that of individual streams being represented separately. In contrast, we also show that higher order auditory cortical areas represent the attended stream separately, and with significantly higher fidelity, than unattended streams. Furthermore, the unattended background streams are more faithfully represented as a single unsegregated background object rather than as separated objects. Taken together, these findings demonstrate the progression of the representations and processing of a complex acoustic scene up through the hierarchy of human auditory cortex.Significance StatementUsing magnetoencephalography (MEG) recordings from human listeners in a simulated cocktail party environment, we investigate how a complex acoustic scene consisting of multiple speech sources is represented in separate hierarchical stages of auditory cortex. We show that the primary-like areas in auditory cortex use a dominantly spectro-temporal based representation of the entire auditory scene, with both attended and ignored speech streams represented with almost equal fidelity. In contrast, we show that higher order auditory cortical areas represent an attended speech stream separately from, and with significantly higher fidelity than, unattended speech streams. Furthermore, the unattended background streams are represented as a single undivided background object rather than as distinct background objects.
Accounting for cell lineage and sex effects in the identification of cell-specific DNA methylation using a Bayesian model selection algorithm
Authors: White Nicole M. , Benton Miles C. , Kennedy Daniel W. , Fox Andrew , Griffiths Lyn R. , Lea Rodney A. , Mengersen Kerrie L. 
Published: April 2017

AbstractCell- and sex-specific differences in DNA methylation are major sources of epigenetic variation in whole blood. Failure to account for these confounders may lead to substantial bias in the identification of differentially methylated CpGs and predicted levels of differential methylation. Previous studies have provided evidence of cell-specific methylation, but all of these have been restricted to the detection of differential methylation in a single cell type. We developed a Bayesian model selection algorithm for the identification of cell-specific methylation profiles that incorporates knowledge of shared cell lineage, to accommodate differential methylation in one or more cell types. Under the proposed methodology, sex-specific differences in methylation by cell type are also assessed. Using publicly available cell-sorted methylation data, we show that 51.3% of female CpG markers and 61.4% of male CpG markers identified were associated with differential methylation in more than one cell type. The impact of cell lineage on differential methylation was also highlighted. An evaluation of sex-specific differences revealed marked differences in CD56+NK methylation, within both single and multi-cell dependent methylation patterns. Our findings demonstrate the need to account for cell lineage in studies of differential methylation and associated sex effects.
Insight and Inference for DVARS
Authors: Afyouni Soroosh , Nichols Thomas E. 
Published: April 2017

AbstractEstimates of functional connectivity using resting state functional Magnetic Resonance Imaging (rs-fMRI) are acutely sensitive to artifacts and large scale nuisance variation. As a result much effort is dedicated to preprocessing rs-fMRI data and using diagnostic measures to identify bad scans. One such diagnostic measure is DVARS, the spatial standard deviation of the data after temporal differencing. A limitation of DVARS however is the lack of concrete interpretation of the absolute values of DVARS, and finding a threshold to distinguish bad scans from good. In this work we describe a variance decomposition of the entire 4D dataset that shows DVARS to be just one of three sources of variation we refer to asD-var (closely linked to DVARS),S-var andE-var.D-var andS-var partition the variance at adjacent time points, whileE-var accounts for edge effects; each can be used to make spatial and temporal summary diagnostic measures. Extending the partitioning to global (and non-global) signal leads to a rs-fMRI DSE ANOVA table, which decomposes the total and global variability into fast (D-var), slow (S-var) and edge (E-var) components. We find expected values for each component under nominal models, showing howD-var (and thus DVARS) scales with overall variability and is diminished by temporal autocorrelation. Finally we propose a null sampling distribution for DVARS-squared and robust methods to estimate this null model, allowing computation of DVARS p-values. We propose that these diagnostic time series, images, p-values and ANOVA table will provide a succinct summary of the quality of a rs-fMRI dataset that will support comparisons of datasets over preprocessing steps and between subjects.
FiloQuant reveals increased filopodia density during DCIS progression
Authors: Jacquemet Guillaume , Paatero Ilkka , Carisey Alexandre F. , Padzik Artur , Orange Jordan S. , Hamidi Hellyeh , Ivaska Johanna 
Published: April 2017

AbstractFilopodia are commonly observed cellular protrusions in vitro and in vivo. Defective filopodia formation is linked to several pathologies including cancer, wherein actively protruding filopodia, at the invasive front, and filopodia-mediated probing of the microenvironment accompanies cancer cell dissemination. Despite wide biological significance, delineating the function of these finger-like protrusions in more complex systems remains technically challenging, particularly hindered by lack of compatible methods to quantify filopodia properties. Here, we present FiloQuant, a freely available ImageJ plugin, to detect filopodia and filopodia-like protrusions in both fixed and live-cell microscopy data. We demonstrate that FiloQuant can extract quantifiable information including protrusion dynamics, density and length from multiple cell types and in a range of microenvironments, such as during collective or single cancer cell migration in 2D and 3D, in fixed neuronal cultures, in activated natural killer cells and in sprouting endothelial cells in vivo. In cellular models of breast ductal carcinoma in situ (DCIS) we reveal a link between filopodia formation at the cell-matrix interface, during collective invasion and in 3D tumour spheroids, with the previously reported local invasive potential of these breast cancer models in vivo. Finally, using intravital microscopy, we observed that tumour spheroids display prominent filopodia in vivo, supporting a potential role for these protrusions during tumorigenesis.
Burst activation of dopamine neurons produces prolonged post-burst availability of actively released dopamine
Authors: Lohani Sweyta , Martig Adria K. , Underhill Suzanne M. , DeFrancesco Alicia , Roberts Melanie J. , Rinaman Linda , Amara Susan , Moghaddam Bita 
Published: April 2017

SummaryBoth phasic and tonic modes of neurotransmission are implicated in critical functions assigned to dopamine. In learning, for example, sub-second phasic responses of ventral tegmental area (VTA) dopamine neurons to salient events serve as teaching signals, but learning is also interrupted by dopamine antagonists administered minutes after training. Our findings bridge the multiple timescales of dopamine neurotransmission by demonstrating that burst stimulation of VTA dopamine neurons produces a prolonged post-burst increase (> 20 min) of extracellular dopamine in nucleus accumbens and prefrontal cortex. This elevation is not due to spillover from the stimulation surge but depends on impulse flow-mediated dopamine release. We identified Rho-mediated internalization of dopamine transporter as a mechanism responsible for prolonged availability of actively released dopamine. These results demonstrate that phasic and tonic dopamine neurotransmission can be a continuum and may explain why both modes of signaling are critical for motivational and cognitive functions associated with dopamine.
Post-transcriptional regulation of adult CNS axonal regeneration by Cpeb1
Authors: Pak-Kin Lou Wilson , Mateos Alvaro , Koch Marta , Klussman Stefan , Yang Chao , Lu Na , Limpert Stefanie , Göpferich Manuel , Zschaetzsch Marlen , Maillo Carlos , Senis Elena , Grimm Dirk , Mendez Raul , Liu Kai , Hassan Bassem A. , Martin-Villalba Ana 
Published: April 2017

ABSTRACTAdult mammalian CNS neurons are unable to regenerate following axonal injury, leading to permanent functional impairments. Yet, the reasons underlying this regeneration failure are not fully understood. Here, we study the transcriptome and proteome shortly after spinal cord injury. Profiling of the total and ribosome-bound RNA in injured and naïve spinal cords identify a substantial post-transcriptional regulation of gene expression. In particular, transcripts associated with nervous system development were downregulated in the total RNA-fraction while remaining stably loaded onto ribosomes. Interestingly, motif association analysis of post-transcriptionally regulated transcripts identified the cytoplasmic polyadenylation element (CPE) as enriched in a subset of these transcripts that was more resistant to injury-induced reduction at transcriptome level. Modulation of these transcripts by overexpression of the CPE binding protein, Cpeb1, in mouse and Drosophila CNS neurons promoted axonal regeneration following injury. Our study uncovers a global conserved post-transcriptional mechanism enhancing regeneration of injured CNS axons.
ZINB-WaVE: A general and flexible method for signal extraction from single-cell RNA-seq data
Authors: Risso Davide , Perraudeau Fanny , Gribkova Svetlana , Dudoit Sandrine , Vert Jean-Philippe 
Published: April 2017

AbstractSingle-cell RNA sequencing (scRNA-seq) is a powerful high-throughput technique that enables researchers to measure genome-wide transcription levels at the resolution of single cells. Because of the low amount of RNA present in a single cell, some genes may fail to be detected even though they are expressed; these genes are usually referred to as dropouts. Here, we present a general and flexible zero-inflated negative binomial model (ZINB-WaVE), which leads to low-dimensional representations of the data that account for zero inflation (dropouts), over-dispersion, and the count nature of the data. We demonstrate, with simulated and real data, that the model and its associated estimation procedure are able to give a more stable and accurate low-dimensional representation of the data than principal component analysis (PCA) and zero-inflated factor analysis (ZIFA), without the need for a preliminary normalization step.
Comprehensive statistical inference of the clonal structure of cancer from multiple biopsies
Authors: Liu Jie , Halloran John T. , Bilmes Jeffrey A. , Daza Riza M. , Lee Choli , Mahen Elisabeth M. , Prunkard Donna , Song Chaozhong , Blau Sibel , Dorschner Michael O. , Gadi Vijayakrishna K. , Shendure Jay , Blau C. Anthony , Noble William S. 
Published: April 2017

AbstractA comprehensive characterization of tumor genetic heterogeneity is critical for understanding how cancers evolve and escape treatment. Although many algorithms have been developed for capturing tumor heterogeneity, they are designed for analyzing either a single type of genomic aberration or individual biopsies. Here we present THEMIS (Tumor Heterogeneity Extensible Modeling via an Integrative System), which allows for the joint analysis of different types of genomic aberrations from multiple biopsies taken from the same patient, using a dynamic graphical model. Simulation experiments demonstrate higher accuracy of THEMIS over its ancestor, TITAN. The heterogeneity analysis results from THEMIS are validated with single cell DNA sequencing from a clinical tumor biopsy. When THEMIS is used to analyze tumor heterogeneity among multiple biopsies from the same patient, it helps to reveal the mutation accumulation history, track cancer progression, and identify the mutations related to treatment resistance. We implement our model via an extensible modeling platform, which makes our approach open, reproducible, and easy for others to extend.
Radiography registration for mosaic tomography
Authors: Vescovi R. F. C. , Cardoso M. B. , Miqueles E. X. 
Published: April 2017

A hybrid method of stitching X-ray computed tomography (CT) datasets is proposed and the feasibility to apply the scheme in a synchrotron tomography beamline with micrometre resolution is shown. The proposed method enables the field of view of the system to be extended while spatial resolution and experimental setup remain unchanged. The approach relies on taking full tomographic datasets at different positions in a mosaic array and registering the frames using Fourier phase correlation and a residue-based correlation. To ensure correlation correctness, the limits for the shifts are determined from the experimental motor position readouts. The masked correlation image is then minimized to obtain the correct shift. The partial datasets are blended in the sinogram space to be compatible with common CT reconstructors. The feasibility to use the algorithm to blend the partial datasets in projection space is also shown, creating a new single dataset, and standard reconstruction algorithms are used to restore high-resolution slices even with a small number of projections.
From K-Pop to K-Preparedness: Korea confronts disaster reduction
Authors: Oliver Kasdan David , Kim Kyehyun 
Published: April 2017

Purpose
The purpose of this paper is to describe a recent effort by the South Korean Government to stimulate a domestic disaster risk reduction (DRR) technology industry for the export market. The project is a novel form of public-private partnership (PPP) that simultaneously fulfills the mandates of the Sendai Framework for Disaster Risk Reduction while promoting Korea’s economic development agenda.

Design/methodology/approach
The research is primarily a review study of the Global DRR Technology project as it is situated in the literature of PPP research from both the public administration and disaster management disciplines.

Findings
Korea’s approach to address DRR through a PPP targeting the needs of East Asian countries is unique. The overall effectiveness of the effort will take time to assess, but the model is an interesting and potentially fruitful mean of advancing DRR technology dissemination.

Practical implications
Korea may position itself as a global leader of DRR technology through this effort in terms of both market share and support of the Sendai Framework’s objectives. If successful, the PPP approach may be adopted as a viable means of improving DRR for other countries.

Social implications
Using PPPs for various aspects of DRR can be win-win situation for economic development and disaster management outcomes.

Originality/value
This paper presents a distinct application of the PPP model for DRR that other countries may appreciate and/or adopt for their own DRR needs.
Developing best practice in psychologically informed environments
Authors: Westaway Coral , Nolte Lizette , Brown Rachel 
Published: April 2017

PurposeThe purpose of this paper is to extend our understanding of the issues facing those who experience multiple moves around homelessness projects. It considers these issues and how they relate to best practice, informing the delivery of psychologically informed environments (PIEs).Design/methodology/approachA qualitative design was employed, with interviews undertaken with men currently residing in hostels for those with additional needs. These men had already experienced multiple moves within the hostel system. Interpretative phenomenological analysis was used to analyse the data.FindingsMain themes consider issues and challenges associated with hope and moving forward; help and the conditional or temporal nature of this; identity and stigma; and intimacy and relationships. Clinical implications of these findings are discussed.Research limitations/implicationsImplications include best practice for future planning with service users, the relational nature of hope, how best to manage endings and practical guidance for service developments in these settings.Originality/valueThese findings further the understanding of the challenges faced by service users with complex needs and how best to address them. They build on PIE guidance, offering tangible advice for practice.
Factors affecting the success of women’s entrepreneurship: a review of literature
Authors: Cabrera Ezilda María , Mauricio David 
Published: April 2017

Purpose
Women entrepreneurship has grown significantly all over the world, and it is widely established that entrepreneurship is important for economic growth and wealth. Despite those facts, women’s participation in entrepreneurship is lower than men’s in almost all societies. Those phenomena get the attention of scholars from diverse disciplines, all of them interested in the behaviour and profile of female entrepreneurs and their business success rates. Several isolated factors were studied, with positive and negative effects on each stage of the entrepreneur process, for women entrepreneurs, so the purpose of this research is identify, classify by their impact and organise those factors in relation to the stages of the entrepreneur process.

Design/methodology/approach
The literature on factors affecting female entrepreneurship produced since January 2010 until October 2015 is analysed to define entrepreneurial success, identify factors affecting success at each stage of the entrepreneurial process and propose and organise those factors at individual and environment levels.

Findings
Several factors affecting female entrepreneurial success at each stage of the entrepreneurship process were found and organised at the internal (individual), micro, meso and macro environment level. In the literature reviewed, the most considered factors are: at the internal level, human capital, education and experience, with effects on the opportunity identification stage of the entrepreneurial process, and at the micro environment level, access to resources with effects on the opportunity recognition, acquiring resources and entrepreneurial performance stages, both with influence on quantitative and qualitative indicators of success.

Originality/value
This paper proposes an integrated classification and an array for all those factors that have an influence on women’s entrepreneurship and its success, relating those to the entrepreneurship process.
Promotional support: a formative scale development
Authors: R.M. Harindranath , Jacob Jayanth 
Published: April 2017

PurposeIn pharmaceutical marketing, salespeople require promotional instruments to satisfy and retain their customers (physicians), but companies ignore the need because of the costs involved. It appears that the importance of promotional support is understood differently by managers and sales representatives. This study aims at developing a new construct called “promotional support”, as a resource support provided to salespeople to help them satisfy customer needs and achieve sales goals.Design/methodology/approachA detailed review of literature is followed by in-depth interviews to create items for the construct “promotional support”. Substantive validity is performed for identification of items measuring the construct. To initially validate the measures, a vignette study is performed. Formative index development procedure is followed. Data from a sample of 124 pharmaceutical sales representatives are collected and analyzed.FindingsA formative construct is developed which possesses convergent (redundancy analysis) and nomological validity. The results of post hoc validation tests like confirmatory tetrad analysis and inter-item correlation are satisfactory and confirm the authors’ conceptualization.Research limitations/implicationsThe scale requires external validation by testing it with different samples such as managers of pharmaceutical firms.Practical implicationsThis study will help managers of pharmaceutical firms gain insights into the role and importance of promotional inputs given to their sales representatives.Originality/valueThis study uses the formative scale development procedure to develop promotional support. This construct can be used to understand the effect of promotional support given to pharmaceutical sales representatives on other constructs, which in turn helps in theory-building.