bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting precision grip grasp locations on three-dimensional objects
Authors: Klein Lina K. , Maiello Guido , Paulun Vivian C. , Fleming Roland W. 
Published: November 2018

AbstractWe rarely experience difficulty picking up objects, yet of all potential contact points on the surface, only a small proportion yield effective grasps. Here, we present extensive behavioral data alongside a normative model that correctly predicts human precision grasping of unfamiliar 3D objects. We tracked participants’ forefinger and thumb as they picked up objects of 10 wood and brass cubes configured to tease apart effects of shape, weight, orientation, and mass distribution. Grasps were highly systematic and consistent across repetitions and participants. We employed these data to construct a model which combines five cost functions related to force closure, torque, natural grasp axis, grasp aperture, and visibility. Even without free parameters, the model predicts individual grasps almost as well as different individuals predict one another’s, but fitting weights reveals the relative importance of the different constraints. The model also accurately predicts human grasps on novel 3D-printed objects with more naturalistic geometries and is robust to perturbations in its key parameters. Together, the findings provide a unified account of how we successfully grasp objects of different 3D shape, orientation, mass, and mass distribution.Author SummaryA model based on extensive behavioral data unifies the varied and fragmented literature on human grasp selection by correctly predicting human grasps across a wide variety of conditions.
Isolation and characterization of extracellular vesicles from Caenorhabditis elegans for multi-omic analysis
Authors: Russell Joshua C. , Merrihew Gennifer E. , Robbins Julia E. , Postupna Nadia , Kim Tyek-Kyun , Golubeva Alexandra , Noori Ayush , Wang Kai , Keene C. Dirk , MacCoss Michael J. , Kaeberlein Matt 
Published: November 2018

AbstractCells from bacteria to human release vesicles into their extracellular environment. These extracellular vesicles (EVs) contain multiple classesof molecules, including nucleic acids, proteins, and lipids. The isolation and analysis of EV cargos from mammalian cell culture and liquid biopsysamples has become a powerful approach for uncovering the messages that are packaged into these organelles. However, this approach has not been tenable in invertebrate model systems due to lack of sufficient amounts of pure EVs. Here we report a robust and reproducible procedure to isolateEVs from Caenorhabditis elegans with yields similar to those obtained from human cell culture. Through nanoparticle tracking, transmission electron microscopy, flow cytometry, mass spectrometry, RNAseq, and immunoaffinity analysis we provide the first ever detailed characterization of C. elegans EV composition and demonstrate that C. elegans EVs share fundamentally similar properties with their mammalian counterparts. These include vesicle size, enrichment for lipid rafts, and similar types of RNA and protein cargos. This ability of isolate pure EVs on ascale amenable to multiple types of downstream analyses permits, multi-omics characterization of EV cargos in an invertebrate model system.
Pipeliner: A Nextflow-based framework for the definition of sequencing data processing pipelines
Authors: Federico Anthony , Karagiannis Tanya , Karri Kritika , Kishore Dileep , Koga Yusuke , Campbell Joshua D. , Monti Stefano 
Published: November 2018

AbstractThe advent of high-throughput sequencing technologies has led to the need for flexible and user-friendly data pre-processing platforms. The Pipeliner framework provides an out-of-the-box solution for processing various types of sequencing data. It combines the Nextflow scripting language and Anaconda package manager to generate modular computational workflows. We have used Pipeliner to create several pipelines for sequencing data processing including bulk RNA-seq, single-cell RNA-seq (scRNA-seq), as well as Digital Gene Expression (DGE) data. This report highlights the design methodology behind Pipeliner which enables the development of highly flexible and reproducible pipelines that are easy to extend and maintain on multiple computing environments. We also provide a quick start user guide demonstrating how to setup and execute available pipelines with toy datasets.
Analysis of Single Nucleotide Polymorphisms in human Voltage-Gated Ion Channels
Authors: Nastou Katerina C. , Batskinis Michail A. , Litou Zoi I. , Hamodrakas Stavros J. , Iconomidou Vassiliki A. 
Published: November 2018

AbstractVoltage-Gated Ion Channels (VGICs) are one of the largest groups of transmembrane proteins. Due to their major role in the generation and propagation of electrical signals, VGICs are considered important from a medical viewpoint and their dysfunction is often associated with a group of diseases known as “Channelopathies”. We identified disease associated mutations and polymorphisms in these proteins through mapping missense Single Nucleotide Polymorphisms (SNPs) from the UniProt and ClinVar databases on their amino acid sequence, taking into consideration their special topological and functional characteristics. Statistical analysis revealed that disease associated SNPs are mostly found in the Voltage Sensor Domain – and especially at its fourth transmembrane segment (S4) – and in the Pore Loop. Both these regions are extremely important for the activation and ion conductivity of VGICs. Moreover, amongst the most frequently observed mutations are those of arginine to glutamine, to histidine or to cysteine, which can probably be attributed to the extremely important role of arginine residues in the regulation of membrane potential in these proteins. We suggest that topological information in combination with genetic variation data can contribute towards a better evaluation of the effect of currently unclassified mutations in VGICs. It is hoped that potential associations with certain disease phenotypes will be revealed in the future, with the use of similar approaches.
Genotyping-by-sequencing and SNP-arrays are complementary for detecting quantitative trait loci by tagging different haplotypes in association studies
Authors: Negro Sandra Silvia , Millet Emilie , Madur Delphine , Bauland Cyril , Combes Valérie , Welcker Claude , Tardieu François , Charcosset Alain , Nicolas Stéphane Dimitri 
Published: November 2018

AbstractBackgroundSingle Nucleotide Polymorphism (SNP) array and re-sequencing technologies have different properties (e.g.calling rate, minor allele frequency profile) and drawbacks (e.g.ascertainment bias). This lead us to study their complementarity and the consequences of using them separately or combined in diversity analyses and Genome-Wide Association Studies (GWAS). We performed GWAS on three traits (grain yield, plant height and male flowering time) measured in 22 environments on a panel of 247 F1 hybrids obtained by crossing 247 diverse dent maize inbred lines with a same flint line. The 247 lines were genotyped using three genotyping technologies (Genotyping-By-Sequencing, Illumina Infinium 50K and Affymetrix Axiom 600K arrays).ResultsThe effects of ascertainment bias of the 50K and 600K arrays were negligible for deciphering global genetic trends of diversity and for estimating relatedness in this panel. We developed an original approach based on linkage disequilibrium (LD) extent in order to determine whether SNPs significantly associated with a trait and that are physically linked should be considered as a single Quantitative Trait Locus (QTL) or several independent QTLs. Using this approach, we showed that the combination of the three technologies, which have different SNP distributions and densities, allowed us to detect more QTLs (gain in power) and potentially refine the localization of the causal polymorphisms (gain in resolution).ConclusionsConceptually different technologies are complementary for detecting QTLs by tagging different haplotypes in association studies. Considering LD, marker density and the combination of different technologies (SNP-arrays and re-sequencing), the genotypic data available were most likely enough to well represent polymorphisms in the centromeric regions, whereas using more markers would be beneficial for telomeric regions.
Comparative assessment of long-read error-correction software applied to RNA-sequencing data
Authors: Lima Leandro , Marchet Camille , Caboche Ségolène , Da Silva Corinne , Istace Benjamin , Aury Jean-Marc , Touzet Hélène , Chikhi Rayan 
Published: November 2018

AbstractMotivationLong-read sequencing technologies offer promising alternatives to high-throughput short read sequencing, especially in the context of RNA-sequencing. However these technologies are currently hindered by high error rates in the output data that affect analyses such as the identification of isoforms, exon boundaries, open reading frames, and the creation of gene catalogues. Due to the novelty of such data, computational methods are still actively being developed and options for the error-correction of RNA-sequencing long reads remain limited.ResultsIn this article, we evaluate the extent to which existing long-read DNA error correction methods are capable of correcting cDNA Nanopore reads. We provide an automatic and extensive benchmark tool that not only reports classical error-correction metrics but also the effect of correction on gene families, isoform diversity, bias towards the major isoform, and splice site detection. We find that long read error-correction tools that were originally developed for DNA are also suitable for the correction of RNA-sequencing data, especially in terms of increasing base-pair accuracy. Yet investigators should be warned that the correction process perturbs gene family sizes and isoform diversity. This work provides guidelines on which (or whether) error-correction tools should be used, depending on the application type.Benchmarking softwarehttps://gitlab.com/leoisl/LR_EC_analyser
The autism and schizophrenia-associated protein CYFIP1 regulates bilateral brain connectivity
Authors: Domínguez-Iturza Nuria , Shah Disha , Vannelli Anna , Lo Adrian C. , Armendáriz Marcelo , Li Ka Wan , Mercaldo Valentina , Trusel Massimo , Gastaldo Denise , Mameli Manuel , Linden Annemie Van der , Smit August B. , Achsel Tilmann , Bagni Claudia 
Published: November 2018

SUMMARYCopy-number variants of theCYFIP1gene in humans have been linked to Autism and Schizophrenia, two neuropsychiatric disorders characterized by defects in brain connectivity. CYFIP1 regulates molecular events underlying post-synaptic functions. Here, we show that CYFIP1 plays an important role in brain functional connectivity and callosal functions. In particular, we find thatCyfip1heterozygous mice have reduced brain functional connectivity and defects in white matter architecture, typically relating to phenotypes found in patients with Autism, Schizophrenia and other neuropsychiatric disorders. In addition,Cyfip1deficient mice present deficits in the callosal axons, namely reduced myelination, altered pre-synaptic function, and impaired bilateral-connectivity related behavior. Altogether, our results show thatCyfip1haploinsufficiency compromises brain connectivity and function, which might explain its genetic association to neuropsychiatric disorders.
Does a meaningful relationship exist between copper prices and economic growth in Zambia?
Authors: Chikalipah Sydney 
Published: November 2018

PurposeThe purpose of this paper is to examine the causal relationship between the copper price dynamics and economic growth in Zambia over the period from 1995 to 2015.Design/methodology/approachThe study uses a data set assembled from five difference sources: the heritage foundation; the London metal exchange index; the Penn World Tables version 9.0; the total economy database; and the World Bank Development Indicators. The paper employs the Bayesian Model Averaging (BMA) approach as the estimation technique.FindingsThe estimates demonstrate that there exists a positive and significant relationship between movements in copper prices and economic growth in Zambia. The study draws policy implications from these findings.Research limitations/implicationsThis study is limited to the period from 1995 to 2015, this is due to lack of data on the country’s institutional indicators, trade openness and the real exchange rate.Practical implicationsThere have been calls to diversify the economy of Zambia due to the recurring chaotic events, which are often induced by over-dependence on copper exports. Thus, the study findings will be useful to academia, policy makers and stakeholders with vested interest in the economy of Zambia.Originality/valueTo the best of the author’s knowledge, this is the first empirical study to investigate the causal relationship that exists between copper prices and economic growth in Zambia. The existing empirical studies in the domain have devoted their attention on establishing the relationship between commodity price movements and exchange rates in Zambia.
Discrete differential operators for periodic and two-periodic time functions
Authors: Sobczyk Tadeusz , Radzik Michał , Radwan-Pragłowska Natalia 
Published: November 2018

Purpose
To identify the properties of novel discrete differential operators of the first- and the second-order for periodic and two-periodic time functions.

Design/methodology/approach
The development of relations between the values of first and second derivatives of periodic and two-periodic functions, as well as the values of the functions themselves for a set of time instants. Numerical tests of discrete operators for selected periodic and two-periodic functions.

Findings
Novel discrete differential operators for periodic and two-periodic time functions determining their first and the second derivatives at very high accuracy basing on relatively low number of points per highest harmonic.

Research limitations/implications
Reduce the complexity of creation difference equations for ordinary non-linear differential equations used to find periodic or two-periodic solutions, when they exist.

Practical implications
Application to steady-state analysis of non-linear dynamic systems for solutions predicted as periodic or two-periodic in time.

Originality/value
Identify novel discrete differential operators for periodic and two-periodic time functions engaging a large set of time instants that determine the first and second derivatives with very high accuracy.
The effects of goodwill and competence trust on strategic information sharing in buyer–supplier relationships
Authors: Newell William James , Ellegaard Chris , Esbjerg Lars 
Published: November 2018

PurposeThe purpose of this paper is to explore how the choice of buying managers to share or limit the sharing of strategic information with their suppliers relates to the presence or absence of goodwill and competence trust in the buyer–supplier relationship.Design/methodology/approachAn interpretive single case study of a mid-sized retailer was used. In total, 17 semi-structured interviews examining information sharing events were conducted with buying managers, along with the analysis of company documents.FindingsGoodwill and competence trust have a positive effect on strategic information sharing, yet this study reveals several tactics used by buying managers in the presence of competence trust only. With a lack of established trust, or earlier trust breaches, little to no information sharing occurs.Research limitations/implicationsThis study featured cross-sectional data of a single case from the buyer’s perspective. This limits its generalizability, yet provides opportunities to test the findings through longitudinal studies, potentially gathering data from both buyers and suppliers.Practical implicationsRelating which types of information being shared for different forms of trust guides managers’ expectations on which type of trust they wish to build for each of their buyer–supplier relationships.Originality/valueThis study examines the trust and information sharing relationship in more detail, linking different types of trust to categories of strategic information. It also distinguishes between the different concepts of encouraging information sharing and deliberately limiting strategic information sharing.
Collaboration in a distributed research program
Authors: Haman Magdalena , Hertzum Morten 
Published: November 2018

PurposeResearchers need to collaborate to address grand challenges such as climate change, poverty and sustainable food production. The purpose of this paper is to investigate how the researchers in a globally distributed research program interact to move their research forward.Design/methodology/approachThe authors interviewed 14 participants in the research program.FindingsIn spite of the spatial distribution of the researchers the output from the research program is predominantly collaborative; as much as 79 percent of the publications are co-authored by researchers from multiple countries. However, the researchers mostly work alone on their contributions to their joint work and spend minimal time interacting. This strategy of minimal interaction is punctuated by islands of intense interaction when they occasionally meet in person. Interaction feels natural, productive and satisfying to them when they are co-located but less so when they are distributed, probably because they experience technology-mediated interaction over a distance as somewhat impoverished. The interviewees mention that the minimal-interaction strategy incurs the risks of cracks in common ground and of misconstruing minimal interaction as lack of commitment. But the strategy is generally well-liked.Research limitations/implicationsThe experience of technology-mediated interaction as impoverished points to an explanation for the finding of less interaction in distributed than co-located research. It should be noted that the study is restricted to one research program.Originality/valueBy questioning widely touted recommendations for ongoing, regular and sustained interaction this study provides a fresh look at scientific collaboration.
When do women reach the top spot? A multilevel study of female CEOs in emerging markets
Authors: Elango B. 
Published: November 2018

PurposeThe purpose of this paper is to link country factors which impact the selection of women as CEOs of firms in emerging markets.Design/methodology/approachUsing a multilevel model, this study investigates the factors driving the selection of a woman as CEO using a sample of 30,015 firms from 20 emerging markets during the years 2008 to 2016.FindingsBased on analysis of nested multilevel logistic models, study findings indicate that country wealth, gender egalitarianism and humane orientation increase the likelihood that a firm would be led by a female CEO. Findings also indicate a greater opportunity for women to secure the top role in service industries relative to manufacturing industries.Originality/valueIn spite of the magnitude of emerging markets and their varied social, economic and cultural contexts, there is scant research focusing on female CEOs in these countries. This topic is of considerable importance to gender empowerment, equity, fairness and social welfare and this paper contributes to the knowledge in this area by incorporating a multilevel model focusing on the factors driving the choice of female CEOs. Study findings serve as an important starting point on the opportunity for managerial women from emerging nations.
Hydrothermal investigation of a stratified system in enclosure with jagged surface for application in lead-acid batteries
Authors: Salari Mahmoud , Malekshah Emad Hasani , Sarlak Mohammad Reza , Hasani Malekshah Masoud , Pilfoush Mohammad 
Published: November 2018

Purpose
The purpose of this paper is to investigate the three-dimensional natural convection and entropy generation in a cuboid enclosure filled with two immiscible fluids of nanofluid and air.

Design/methodology/approach
One surface of the enclosure is jagged and another one is smooth. The finite volume approach is applied for computation. There are two partially side heaters. Furthermore, the Navier–Stokes equations and entropy generation formulation are solved in the 3D form.

Findings
The effects of different governing parameters, such as the jagged surface (JR=0, 0.02, 0.04, 0.08, 0.12 and 0.16), Rayleigh number (103⩽Ra⩽106) and solid volume fraction of nanofluid (φ=1, 1.5, 2 vol%), on the fluid flow, temperature field, Nusselt number, volumetric entropy generation and Bejan number are presented, comprehensively. The results indicate that the average Nusselt number increases with the increase in the Rayleigh number and solid volume fraction of nanofluid. Moreover, the flow structure is significantly affected by the jagged surface.

Originality/value
The originality of this work is to analyze the natural-convection fluid flow and heat transfer under the influence of jagged surfaces of electrodes in high-current lead–acid batteries.
Inclined magnetic field effects on unsteady nanofluid flow and heat transfer in a finite thin film with non-uniform heat source/sink
Authors: Giri Shib Sankar , Das Kalidas , Kundu Prabir Kumar 
Published: November 2018

PurposeThe purpose of this paper is to discuss the flow and heat transference of unsteady nanofluid thin film flow due to linear stretching velocity over a horizontally placed stretching sheet in corporation of aligned magnetic field and non-uniform heat source/sink.Design/methodology/approachLeading equations of the course have been normalized via similarity approach and unraveled the resulting non-linear equations numerically by consuming RK-4 shooting practice to execute flow analysis.FindingsA close agreement of two sets (for two different base fluids – polyvinyl alcohol and water) of result is perceived. The authors find that inclined magnetic field and nanoparticles concentration curbed velocity distribution which, in turn, causes enrichment of system of temperature distribution.Originality/valueThe paper acquires realistic numerical explanations in form of rapidly convergent series. The influence of emergent flow parameters on specific flow are made appropriately via graphs and charts. An unbiased result scrutiny of the existing section with formerly conveyed result is provided.
Effects of thermal radiation and magnetohydrodynamics on Ree-Eyring fluid flows through porous medium with slip boundary conditions
Authors: Ramesh K. , Eytoo Sartaj Ahmad 
Published: November 2018

PurposeThe purpose of this paper is to investigate the three fundamental flows (namely, both the plates moving in opposite directions, the lower plate is moving and other is at rest, and both the plates moving in the direction of flow) of the Ree-Eyring fluid between infinitely parallel plates with the effects of magnetic field, porous medium, heat transfer, radiation and slip boundary conditions. Moreover, the intention of the study is to examine the effect of different physical parameters on the fluid flow.Design/methodology/approachThe mathematical modeling is performed on the basis of law of conservation of mass, momentum and energy equation. The modeling of the present problem is considered in Cartesian coordinate system. The governing equations are non-dimensionalized using appropriate dimensionless quantities in all the mentioned cases. The closed-form solutions are presented for the velocity and temperature profiles.FindingsThe graphical results are presented for the velocity and temperature distributions with the pertinent parameters of interest. It is observed from the present results that the velocity is a decreasing function of Hartmann number. Temperature increases with the increase of Ree-Eyring fluid parameter, radiation parameter and temperature slip parameter.Originality/valueFirst time in the literature, the authors obtained closed-form solutions for the fundamental flows of Ree-Erying fluid between infinitely parallel plates with the effects of magnetic field, porous medium, heat transfer, radiation and slip boundary conditions. Moreover, the results of this paper are new and original.