bluuebunny/crossref_metadata_2025_split huggingface dataset:
Kinematic analysis of cell lineage reveals coherent and robust mechanical deformation patterns in zebrafish gastrulation
Authors: Pastor-Escuredo David , Lombardot Benoît , Savy Thierry , Boyreau Adeline , Goicolea Jose M. , Santos Andrés , Bourgine Paul , del Álamo Juan C. , Peyriéras Nadine , Ledesma-Carbayo María J. 
Published: May 2016

AbstractDigital cell lineages reconstructed from 3D+time imaging data provide unique information to unveil mechanical cues and their role in morphogenetic processes. Our methodology based on a kinematic analysis of cell lineage data reveals deformation patterns and quantitative morphogenetic landmarks for a new type of developmental table. The characteristic spatial and temporal length scales of mechanical deformation patterns derived from a continuous approximation of cell displacements indicate a compressible fluid-like behavior of zebrafish gastrulating tissues. The instantaneous deformation rate at the mesoscopic level of the cell’s neighborhood is spatially and temporally heterogeneous. The robustness of mechanical patterns results from their cumulative history along cell trajectories. Unsupervised classification of mechanical descriptor profiles was used to assess the homogeneity of biomechanical cues in cell populations. Further clustering of cell trajectories according to their cumulative mesoscopic biomechanical history during gastrulation revealed ordered and coherent spatiotemporal patterns comparable to that of the embryonic fate map.
Population effect of influenza vaccination under co-circulation of non-vaccine variants and the case for a multi-strain A/H3N2 vaccine component
Authors: Worby Colin J , Wallinga Jacco , Lipsitch Marc , Goldstein Edward 
Published: May 2016

AbstractSome past epidemics of different influenza (sub)types (particularly A/H3N2) in the US saw co-circulation of vaccine-type and variant strains. There is evidence that natural infection with one influenza (sub)type offers short-term protection against infection with another influenza (sub)type (henceforth, cross-immunity). This suggests that such cross-immunity for strains within a (sub)type is expected to be strong. Therefore, while vaccination effective against one strain may reduce transmission of that strain, this may also lead to a reduction of the ability of the vaccine-type strain to suppress spread of a variant strain. It remains unclear what the joint effect of vaccination and cross-immunity is for co-circulating influenza strains, and what is the potential benefit of a bivalent vaccine that protects against both strains.We simulated co-circulation of vaccine-type and variant strains under a variety of scenarios. In each scenario, we considered the case when the vaccine efficacy against the variant strain is lower than the efficacy against the vaccine-type strain (monovalent vaccine), as well the case when vaccine is equally efficacious against both strains (bivalent vaccine).Administration of a bivalent vaccine results in a significant reduction in the overall incidence of infection compared to administration of a monovalent vaccine, even with lower coverage by the bivalent vaccine. Additionally, we found that the stronger is the degree of cross-immunity, the less beneficial is the increase in coverage levels for the monovalent vaccine, and the more beneficial is the introduction of the bivalent vaccine.Our work exhibits the limitations of influenza vaccines that have low efficacy against non-vaccine strains, and demonstrates the benefits of vaccines that offer good protection against multiple influenza strains. The results elucidate the need for guarding against the potential co-circulation of non-vaccine strains for an influenza (sub)type, at least during select seasons, possibly through inclusion of multiple strains within a (sub)type (particularly A/H3N2) in a vaccine.
Long shelf-life streptavidin support-films suitable for electron microscopy of biological macromolecules
Authors: Han Bong-Gyoon , Watson Zoe , Kang Hannah , Pulk Arto , Downing Kenneth H. , Cate Jamie , Glaeser Robert M. 
Published: May 2016

ABSTRACTWe describe a rapid and convenient method of growing streptavidin (SA) monolayer crystals directly on holey-carbon EM grids. As expected, these SA monolayer crystals retain their biotin-binding function and crystalline order through a cycle of embedding in trehalose and, later, its removal. This fact allows one to prepare, and store for later use, EM grids on which SA monolayer crystals serve as an affinity substrate for preparing specimens of biological macromolecules. In addition, we report that coating the lipid-tail side of trehalose-embedded monolayer crystals with evaporated carbon appears to improve the consistency with which well-ordered, single crystals are observed to span over entire, 2 μm holes of the support films. Randomly biotinylated 70 S ribosomes are used as a test specimen to show that these support films can be used to obtain a high-resolution cryo-EM structure.
Varying intolerance of gene pathways to mutational classes explain genetic convergence across neuropsychiatric disorders
Authors: Shohat Shahar , Ben-David Eyal , Shifman Sagiv 
Published: May 2016

AbstractGenetic susceptibility to Intellectual disability (ID), autism spectrum disorder (ASD) and schizophrenia (SCZ) often arises from mutations in the same genes, suggesting that they share common mechanisms. We studied genes withde novomutations in the three disorders and genes implicated by SCZ genome-wide association study (GWAS). Using biological annotations and brain gene expression, we show that mutation class explains enrichment patterns more than specific disorder. Genes with loss of function mutations and genes with missense mutations were enriched with different pathways, shared with genes intolerant to mutations. Specific gene expression patterns were found for each disorder. ID genes were preferentially expressed in fetal cortex, ASD genes also in fetal cerebellum and striatum, and genes associated with SCZ were most significantly enriched in adolescent cortex. Our study suggests that convergence across neuropsychiatric disorders stems from vulnerable pathways to genetic variations, but spatiotemporal activity of genes contributes to specific phenotypes.
A better design for stratified medicine based on genomic prediction
Authors: Lee S. Hong , Weerasinghe W.M. Shalanee P. , Wray Naomi R. , Goddard Michael E. , Van der Werf Julius H.J. 
Published: May 2016

ABSTRACTGenomic prediction shows promise for personalised medicine in which diagnosis and treatment are tailored to individuals based on their genetic profiles. Genomic prediction is arguably the greatest need for complex diseases and disorders for which both genetic and non-genetic factors contribute to risk. However, we have no adequate insight of the accuracy of such predictions, and how accuracy may vary between individuals or between populations. In this study, we present a theoretical framework to demonstrate that prediction accuracy can be maximised by targeting more informative individuals in a discovery set with closer relationships with the subjects, making prediction more similar to those in populations with small effective size (Ne). Increase of prediction accuracy from closer relationships is achieved under an additive model and does not rely on any interaction effects (gene × gene, gene × environment or gene × family). Using theory, simulations and real data analyses, we show that the predictive accuracy or the area under the receiver operating characteristic curve (AUC) increased exponentially with decreasingNe. For example, with a set of realistic parameters (the sample size of discovery set N=3000 and heritability h2=0.5), AUC value approached to 0.9(Ne=100) from 0.6(Ne=10000), and the top percentile of the estimated genetic profile scores had 23 times higher proportion of cases than the general population (withNe=100), which increased from 2 times higher proportion of cases (withNe=10000). This suggests that different interventions in the top percentile risk groups maybe justified (i.e. stratified medicine). In conclusion, it is argued that there is considerable room to increase prediction accuracy for polygenic traits by using an efficient design of a smallerNe(e.g. a design consisting of closer relationships) so that genomic prediction can be more beneficial in clinical applications in the near future.
A metric on phylogenetic tree shapes
Authors: Colijn C. , Plazzotta G. 
Published: May 2016

AbstractThe shapes of evolutionary trees are influenced by the nature of the evolutionary process, but comparisons of trees from different processes are hindered by the challenge of completely describing tree shape. We present a full characterization of the shapes of rooted branching trees in a form that lends itself to natural tree comparisons. The resulting metric distinguishes trees from random models known to produce different tree shapes. It separates trees derived from tropical vs USA influenza A sequences, which reflect the differing epidemiology of tropical and seasonal flu. We extend the shape metric to incorporate summary features such as asymmetry, or statistics on branch lengths. Our approach allows us to construct addition and multiplication on trees, and to create a convex metric on tree shapes which formally allows computation of average trees.
Tellurium: A Python Based Modeling and Reproducibility Platform for Systems Biology
Authors: Choi Kiri , Medley J. Kyle , Cannistra Caroline , König Matthias , Smith Lucian , Stocking Kaylene , Sauro Herbert M. 
Published: May 2016

AbstractIn this article, we present Tellurium, a powerful Python-based integrated environment designed for model building, analysis, simulation and reproducibility in systems and synthetic biology. Tellurium is a modular, cross-platform, and open-source integrated development environment (IDE) composed of multiple libraries, plugins, and specialized modules and methods. Tellurium ensures exchangeability and reproducibility of computational models by supporting SBML (Systems Biology Markup Language), SED-ML (Simulation Experiment Description Markup Language), the COMBINE archive, and SBOL (Synthetic Biology Open Language). Tellurium is a self-contained modeling platform which comes with a fully configured Python distribution independent of other local Python installations on the target machine. The main interface is based on the Spyder IDE which has a highly accessible user interface akin to MATLAB (https://www.mathworks.com/). Tellurium uses libRoadRunner as the default SBML simulation engine due to its superior performance, scalability and ease of integration. libRoadRunner supports deterministic simulations, stochastic simulations and steady state analyses. Tellurium also includes Antimony, a human-readable model definition language which can be converted to and from SBML. Other standard Python scientific libraries such as NumPy, SciPy, and matplotlib are included by default. Additionally, we include several user-friendly plugins and advanced modules for a wide-variety of applications, ranging from visualization tools to complex algorithms for bifurcation analysis and multi-dimensional parameter scanning. By combining multiple libraries, plugins, and modules into a single package, Tellurium provides a unified but extensible solution for biological modeling and simulation.
MPAthic: Quantitative Modeling of Sequence-Function Relationships for massively parallel assays
Authors: Ireland William T. , Kinney Justin B. 
Published: May 2016

AbstractMassively parallel assays (MPAs) are being rapidly adopted for studying a wide range of DNA, RNA, and protein sequence-function relationships. However, the software available for quantitatively modeling these relationships is severely limited. Here we describe MPAthic, a software package that enables the rapid inference of such models from a variety of MPA datasets. Using both simulated and previously published data, we show that the modeling capabilities of MPAthic greatly improve on those of existing software. In particular, only MPAthic can accurately quantify the strength of epistatic interactions. These capabilities address a major need in the analysis of MPA data.
Improved methods for multi-trait fine mapping of pleiotropic risk loci
Authors: Kichaev Gleb , Roytman Megan , Johnson Ruth , Eskin Eleazar , Lindstroem Sara , Kraft Peter , Pasaniuc Bogdan 
Published: May 2016

AbstractGenome-wide association studies (GWAS) have identified thousands of regions in the genome that contain genetic variants that increase risk for complex traits and diseases. However, the variants uncovered in GWAS are typically not biologicaly causal, but rather, correlated to the true causal variant through linkage disequilibrium (LD). To discern the true causal variant(s), a variety of statistical fine-mapping methods have been proposed to prioritize variants for functional validation. In this work we introduce a new approach, fastPAINTOR, that leverages evidence across correlated traits, as well as functional annotation data, to improve fine-mapping accuracy at pleiotropic risk loci. To improve computational efficiency, we describe an new importance sampling scheme to perform model inference. First, we demonstrate in simulations that by leveraging functional annotation data, fastPAINTOR increases fine-mapping resolution relative to existing methods. Next, we show that jointly modeling pleiotropic risk regions improves fine-mapping resolution relative to standard single trait and pleiotropic fine mapping strategies. We report a reduction in the number of SNPs required for follow-up in order to capture 90% of the causal variants from 23 SNPs per locus using a single trait to 12 SNPs when fine-mapping two traits simultaneously. Finally, we analyze summary association data from a large-scale GWAS of lipids and show that these improvements are largely sustained in real data.
Scaffolding and Completing Genome Assemblies in Real-time with Nanopore Sequencing
Authors: Cao Minh Duc , Nguyen Son Hoang , Ganesamoorthy Devika , Elliott Alysha G. , Cooper Matthew , Coin Lachlan J.M. 
Published: May 2016

AbstractGenome assemblies obtained from short read sequencing technologies are often fragmented into many contigs because of the abundance of repetitive sequences. Long read sequencing technologies allow the generation of reads spanning most repeat sequences, providing the opportunity to complete these genome assemblies. However, substantial amounts of sequence data and computational resources are required to overcome the high per-base error rate inherent to these technologies. Furthermore, most existing methods only assemble the genomes after sequencing has completed which could result in either generation of more sequence data at greater cost than required or a low-quality assembly if insufficient data are generated. Here we present the first computational method which utilises real-time nanopore sequencing to scaffold and complete short-read assemblies while the long read sequence data is being generated. The method reports the progress of completing the assembly in real-time so users can terminate the sequencing once an assembly of sufficient quality and completeness is obtained. We use our method to complete four bacterial genomes and one eukaryotic genome, and show that it is able to construct more complete and more accurate assemblies, and at the same time, requires less sequencing data and computational resources than existing pipelines. We also demonstrate that the method can facilitate real-time analyses of positional information such as identification of bacterial genes encoded in plasmids and pathogenicity islands.
Practice transfer in MNCs: a process of tension and contestation
Authors: Bjerregaard Toke , Linneberg Mai S. , Lauring Jakob 
Published: May 2016

PurposeThe purpose of this paper is to further the understanding of how the transfer and adoption of headquarters (HQ)-mandated work practices are shaped by ongoing struggles among the multiple actors of a subsidiary. This paper suggests an alternative perspective for theorizing and researching the management practices and structures that emerge in the face of HQ demands for divergent practice change in subsidiaries, namely, a theory of practice approach.Design/methodology/approachThe paper reports the findings of an ethnographic field study in a UK subsidiary of a multinational corporation based in Denmark.FindingsThe study provides a relevant contribution by demonstrating how the degree of adoption of alternative, HQ-mandated work systems undergoes dramatic changes over time due to socially dynamic negotiations and struggles between interest groups in a subsidiary.Research limitations/implicationsA practice theoretical approach unveils the underlying social micro-dynamics that shape the degree to which employees in subsidiaries “internalize”, actively sustain or disrupt divergent practices representing a given contextual rationale.Originality/valueThe practice perspective provides a way for understanding how the practices and rationales that emerge locally in response to HQ-demands are under ongoing (re)reconstruction. It responds to calls for research on why and how contextual rationales, institutional or cultural features, actively are made salient, polarized or convergent, in conflictual practice transfer processes due to local contingencies.
Lost overseas?
Authors: Yang Inju 
Published: May 2016

PurposeThis conceptual paper aims to explore the leadership of Korean middle managers in a cross-cultural context.Design/methodology/approachThis paper presents three propositions in relation to perceived charisma, individualized consideration and inspirational communication of Korean transformational leadership at home and overseas, especially in comparison with Anglo-Saxon countries such as North America and the UK.FindingsFollowing the notion of implicit theory of leadership, this paper argues that the effectiveness of Korean leadership may depend on cultural dimensions such as collectivism/individualism and power distance.Research limitations/implicationsIn this paper, the perspective of transformational leadership with its universal appeal to various cultures in examining the effectiveness of Korean leadership at home and overseas has been adapted.Practical implicationsThis illustration of the Korean leadership in a cross-cultural context sheds light on the challenges facing the Korean management in global contexts.Originality/valueDespite significant ongoing investment abroad by Korean conglomerates, relatively little has been written on Korean leadership in cross-cultural contexts. This paper could stimulate further studies in this area.
The impact of environmental management awards and certifications in property management on property price
Authors: Hui Eddie Chi-man , Yu Ka-hung , Tse Cheuk-kin 
Published: May 2016

PurposeAs the awareness of environmental preservation and of sustainable development have become increasingly pronounced among various stakeholders, such as governments and communities, many businesses, in response, commence to introduce environmental-friendly measures and/or implement an environmental management system (EMS) in their daily operations. Even a service-oriented industry such as property management is no exception. To showcase their commitment to this cause, property management companies tend to obtain different environmental certifications. This study aims to investigate the effect of green property management, through environmental certifications, on property price.Design/methodology/approachThe hedonic price model is used to determine the impacts of different environmental certifications on prices of selected residential properties in Hong Kong. Three districts from different parts of Hong Kong, including 16 private residential developments, are covered in this study.FindingsThe results show that ISO 14001 certification itself is not statistically significant in explaining property price. It is only when a property management company has obtained other local environmental management awards/certificates that varying levels of (positive) property price premiums are found. Nonetheless, the authors also find that controlling for other housing attributes, obtaining as many environmental certifications as possible does not necessarily result in the highest property price premium.Research limitations/implicationsNonetheless, the data sample has its limitations, such as its relatively small size and the unavailability of housing attribute(s) such as orientations.Practical implicationsFor the implications, the value of environmental management awards/certificates, from the perspective of the end-users of property management services, is based on the scopes of these environmental certifications; the promotional effort on the part of organizations behind these awards/certificates; the disclosure of information about the EMS itself and the assessment criteria; and the public’s perceptions as to the companies’ rationale behind such certifications.Originality/valueThe study has provided some insights regarding the effect of various management standard certifications in property management, from the perspective of the end-users of the service (i.e. homeowners and potential homebuyers). This serves as a reference for developers, property managers, buyers and users alike.
Typologies for co-working spaces in Finland – what and how?
Authors: Kojo Inka , Nenonen Suvi 
Published: May 2016

Purpose
This paper aims to categorize the typologies of co-working spaces and describe their main characteristics.

Design/methodology/approach
The aim is reached by means of analyzing 15 co-working spaces located in the capital area of Finland. The data used consist of interviews, websites, event presentations and brochures.

Findings
As a result, six co-working space typologies were identified: public offices, third places, collaboration hubs, co-working hotels, incubators and shared studios. The categorization was made by using two axes: business model (for profit and non-profit) and level of user access (public, semi-private and private).

Research limitations/implications
The results provide a viewpoint on how co-working spaces can be categorized.

Practical implications
In practise, the results can be applied by all stakeholders who are working with alternative workplace solutions to respond to the needs of new ways of working, especially via workplace services for multi-locational and flexible working, including facilities managers, corporate real estate executives and designers.

Originality/value
This research builds on the previous academic literature on co-working spaces by making the phenomena more explicit for researchers and practitioners who are facing the challenges of developing new alternative workplace offerings.