bluuebunny/crossref_metadata_2025_split huggingface dataset:
An interlaboratory study of complex variant detection
Authors: Lincoln Stephen E , Zook Justin M , Chowdhury Shimul , Mahamdallie Shazia , Fellowes Andrew , Klee Eric W , Truty Rebecca , Huang Catherine , Tomson Farol L , Cleveland Megan H , Vallone Peter M , Ding Yan , Seal Sheila , DeSilva Wasanthi , Garlick Russell K , Salit Marc , Rahman Nazneen , Kingsmore Stephen F , Aradhya Swaroop , Nussbaum Robert L , Ferber Matthew J , Shirts Brian H 
Published: November 2017

ABSTRACTNext-generation sequencing (NGS) is widely used and cost-effective. Depending on the specific methods, NGS can have limitations detecting certain technically challenging variant types even though they are both prevalent in patients and medically important. These types are underrepresented in validation studies, hindering the uniform assessment of test methodologies by laboratory directors and clinicians. Specimens containing such variants can be difficult to obtain; thus, we evaluated a novel solution to this problem in which a diverse set of technically challenging variants was synthesized and introduced into a known genomic background. This specimen was sequenced by 7 laboratories using 10 different NGS workflows. The specimen was compatible with all 10 workflows and presented biochemical and bioinformatic challenges similar to those of patient specimens. Only 10 of 22 challenging variants were correctly identified by all 10 workflows, and only 3 workflows detected all 22. Many, but not all, of the sensitivity limitations were bioinformatic in nature. We conclude that Synthetic controls can provide an efficient and informative mechanism to augment studies with technically challenging variants that are difficult to obtain otherwise. Data from such specimens can facilitate inter-laboratory methodologic comparisons and can help establish standards that improve communication between clinicians and laboratories.
CaDrA: A computational framework for performing candidate driver analyses using binary genomic features
Authors: Kartha Vinay K. , Kern Joseph G. , Sebastiani Paola , Zhang Liye , Varelas Xaralabos , Monti Stefano 
Published: November 2017

AbstractIdentifying complementary genetic drivers of a given phenotypic outcome is a challenging task that is important to gaining new biological insight and discovering targets for disease therapy. Existing methods aimed at achieving this task lack analytical flexibility. We developed Candidate Driver Analysis or CaDrA, a framework to identify functionally-relevant subsets of binary genomic features that, together, are associated with a specific outcome of interest. We evaluate CaDrA’s sensitivity and specificity for typically-sized multi-omic datasets, and demonstrate CaDrA’s ability to identify both known and novel drivers of oncogenic activity in cancer cell lines and primary tumors.
Detecting past and ongoing natural selection among ethnically Tibetan women at high altitude in Nepal
Authors: Jeong Choongwon , Witonsky David B. , Basnyat Buddha , Neupane Maniraj , Beall Cynthia M. , Childs Geoff , Craig Sienna R. , Novembre John , Di Rienzo Anna 
Published: November 2017

AbstractAdaptive evolution in humans has rarely been characterized for its whole set of components, i.e. selective pressure, adaptive phenotype, beneficial alleles and realized fitness differential. We combined approaches for detecting selective sweeps and polygenic adaptations and for mapping the genetic bases of physiological and fertility phenotypes in approximately 1000 indigenous ethnically Tibetan women from Nepal, adapted to high altitude. We performed genome-wide association analysis and tests for polygenic adaptations which showed evidence of positive selection for alleles associated with more pregnancies and live births and evidence of negative selection for those associated with higher offspring mortality. Lower hemoglobin level did not show clear evidence for polygenic adaptation, despite its strong association with an EPAS1 haplotype carrying selective sweep signals.
The origin and remolding of genomic islands of differentiation in the European sea bass
Authors: Duranton Maud , Allal François , Fraïsse Christelle , Bierne Nicolas , Bonhomme François , Gagnaire Pierre-Alexandre 
Published: November 2017

AbstractSpeciation is a complex process that leads to the progressive establishment of reproductive isolation barriers between diverging populations. Genome-wide comparisons between closely related species have revealed the existence of heterogeneous divergence patterns, dominated by genomic islands of increased divergence supposed to contain reproductive isolation loci. However, this divergence landscape only provides a static picture of the dynamic process of speciation, during which confounding mechanisms unlinked to speciation can interfere. Here, we used haplotype-resolved whole-genome sequences to identify the mechanisms responsible for the formation of genomic islands between Atlantic and Mediterranean sea bass lineages. We show that genomic islands first emerged in allopatry through the effect of linked selection acting on a heterogeneous recombination landscape. Upon secondary contact, preexisting islands were strongly remolded by differential introgression, revealing variable fitness effects among regions involved in reproductive isolation. Interestingly, we found that divergent regions containing ancient polymorphisms conferred the strongest resistance to introgression.
Analysis of fMRI data using noise-diffusion network models: a new covariance-coding perspective
Authors: Gilson Matthieu 
Published: November 2017

AbstractSince the middle of the 1990s, studies of resting-state fMRI/BOLD data have explored the correlation patterns of activity across the whole brain, which is referred to as functional connectivity (FC). Among the many methods that have been developed to interpret FC, a recently proposed model-based approach describes the propagation of fluctuating BOLD activity within the recurrently connected brain network by inferring the effective connectivity (EC). In this model, EC quantifies the strengths of directional interactions between brain regions, viewed from the proxy of BOLD activity. In addition, the tuning procedure for the model provides estimates for the local variability (input variances) to explain how the observed FC is generated. Generalizing, the network dynamics can be studied in the context of an input-output mapping - determined by EC - for the second-order statistics of fluctuating nodal activities. The present paper focuses on the following detection paradigm: observing output covariances, how discriminative is the (estimated) network model with respect to various input covariance patterns? An application with the model fitted to experimental fMRI data - movie viewing versus resting state - illustrates that changes in excitability and changes in brain coordination go hand in hand.
Habitat complexity and benthic predator-prey interactions in Chesapeake Bay
Authors: Glaspie Cassandra N. , Seitz Rochelle D. 
Published: November 2017

ABSTRACTIn Chesapeake Bay, the soft-shell clamMya arenaria(thin-shelled, deep-burrowing) exhibits population declines when predators are active and persists at low densities. In contrast, the hard clamMercenaria mercenaria(thick-shelled, shallow-burrowing) has a stable population and age distribution. We examined the potential for habitat and predators to control densities and distributions of bivalves in a field caging experiment (Myaonly) and laboratory mesocosm experiments (both species). In the field, clams exposed to predators experienced 76.3% greater mortality as compared to caged individuals, and blue crabs were likely responsible for most of the mortality of juvenileMya. In mesocosm experiments,Myahad lower survival in sand and seagrass than in shell hash or oyster shell habitats. However, crabs often missed one or more prey in seagrass, shell, and oyster shell habitats. Predator search times and encounter rates declined when prey were at low densities, likely due to the added cost of inefficient foraging; however, this effect was more pronounced forMyathan forMercenaria.Mercenariahad higher survival thanMyain mesocosm experiments, likely because predators feeding onMercenariaspent less time foraging than those feeding onMya.Myamay retain a low-density refuge from predation even with the loss of structurally complex habitats, though a loss of habitat refuge may result in clam densities that are not sustainable. A better understanding of density-dependent predator-prey interactions is necessary to prevent loss of food-web integrity and to conserve marine resources.
Differences across farm typologies in capital investment during 1996-2013
Authors: Stutzman Sarah Anne 
Published: November 2017

Purpose
The purpose of this paper is to examine the impact of changes in farm economic conditions and macroeconomic trends on US farm capital expenditures between 1996 and 2013.

Design/methodology/approach
A synthetic panel is constructed from Agricultural Resource Management Survey (ARMS) data. A dynamic system GMM regression model is estimated for farms as a whole and separately within farm typology categories. The use of farm typologies allows for comparison of the relative magnitudes of these estimates across farms by farm sales level and the operator’s primary occupation.

Findings
Changes in gross farm income levels, tax depreciation rates, and interest rates have a significant impact on crop farm investment, while changes in output prices, net cash farm income levels, tax depreciation rates, and farm specialization levels have significant impacts on livestock farm capital investment. The relative significance and magnitudes of these impacts differ within farm typologies. Significant differences include a greater responsiveness to change in tax policy variables for residential crop farms, greater responsiveness to changes in output prices and debt to asset ratios for intermediate livestock farms, and larger changes in commercial crop and livestock farm investment given equivalent changes in farm sales or the returns to investment.

Research limitations/implications
These findings are of interest to agricultural economists when constructing farm investment models and employing pseudo panel methods, to those in the agricultural equipment and manufacturing sector when constructing models to manage inventories and plan for production needs across regions and over time, to those involved in drafting tax policy and evaluating the potential impacts of tax changes on agricultural investment, and for those in the agricultural lending sector when designing and executing agricultural capital lending programs.

Originality/value
This study uniquely identifies differences in the level of investment and the magnitude of investment responsiveness to changes in farm economic conditions and macroeconomic trends given differences in income levels and primary operator occupation. In addition, this study is one of the few which utilizes ARMS data to study farm capital investment. Utilizing ARMS data provides a rich panel data set, covering producers across many different crop production types and regions. Finally, employing pseudo panel construction methods contributes to efforts to effectively employ cross-sectional data and dynamic models to study farm behavior across time.
Food waste reduction practices in German food retail
Authors: Hermsdorf David , Rombach Meike , Bitsch Vera 
Published: November 2017

Purpose
The purpose of this paper is to investigate food retailers food waste reduction practices in Germany. The focus is on selling and redistributing agricultural produce with visual impairments and other surplus food items. In addition, drivers and barriers regarding the implementation of both waste reduction practices are explored.

Design/methodology/approach
In total, 12 in-depth interviews with managerial actors in the food retail sector and a food bank spokesperson were recorded, transcribed and analyzed through a qualitative content analysis.

Findings
In contrast to organic retailers, conventional retailers were reluctant to include agricultural produce with visual impairments in their product assortments, due to fears of negative consumer reactions. Another obstacle was EU marketing standards for specific produce. All retailers interviewed engaged in redistribution of surplus food. Logistics and the regulatory framework were the main barriers to food redistribution.

Originality/value
The present study adds to the existing body of literature on food waste reduction practices as it explores selling produce with visual impairments and elaborates on the legal background of food redistribution in German retail. The results are the foundation for providing recommendations to policy makers and charitable food organizations.
Measuring and explaining multi-directional inefficiency in the Malaysian dairy industry
Authors: Mohd Suhaimi Nurul Aisyah Binti , de Mey Yann , Oude Lansink Alfons 
Published: November 2017

Purpose
The purpose of this paper is to measure the technical inefficiency of dairy farms and subsequently investigate the factors affecting technical inefficiency in the Malaysian dairy industry.

Design/methodology/approach
This study uses multi-directional efficiency analysis to measure the technical inefficiency scores on a sample of 200 farm observations and single-bootstrap truncated regression model to define factors affecting technical inefficiency.

Findings
Managerial and program inefficiency scores are presented for intensive and semi-intensive production systems. The results reveal marked differences in the inefficiency scores across inputs and between production systems.

Practical implications
Intensive systems generally have lowest managerial and program inefficiency scores in the Malaysian dairy farming sector. Policy makers could use this information to advise dairy farmers to convert their farming system to the intensive system.

Social implications
The results suggest that the Malaysian Government should redefine its policy for providing farm finance and should target young farmers when designing training and extension programs in order to improve the performance of the dairy sector.

Originality/value
The existing literature on Southeast Asian dairy farming has neither focused on investigating input-specific efficiency nor on comparing managerial and program efficiency. This paper aims to fill this gap.
The development dynamics of business networks
Authors: Wegner Douglas , Silva Susana C. , De Rossi Greice 
Published: November 2017

PurposeThe purpose of this paper is to compare the development dynamics of two business networks initially created to promote the internationalization of its members. Wines of Brasil – a Brazilian wineries network – was established in 2002 and remains active, while Vitrocristal (VtC) – a Portuguese network of glass producers – was established in 1994 and is already closed.Design/methodology/approachData were collected from 14 interviews, with network managers and representatives of companies with different sizes and participation times. Information obtained was compared with the life cycle model of Wegneret al.(2015) and enabled the authors to understand the dynamic development of each network and its current stage in the life cycle.FindingsThe results allowed the authors to describe the development pattern of both business networks, showing that the Brazilian network is in the consolidation stage while the Portuguese one finished its activities in 2007 after a period of financial constraints due to the end of governmental support.Practical implicationsThe comparison of the two cases shows that the experience of the Portuguese business network may be useful for networks in emerging markets, as it displays several difficulties that the management of such networks may face during their life cycle.Originality/valueThis study provides a more comprehensive and nuanced understanding of the dynamics of change in business networks. The cases confirm the life cycle stages proposed by Wegneret al.(2015) and shed more light on the development process of business networks, by describing how exogenous variables such as public support may affect cooperation.
Modelling the influence of velocity on wet friction-element friction in clutches
Authors: Wang Yanzhong , Guo Chao , Li Yuan , Li Guoxing 
Published: November 2017

Purpose
This study aims to establish a friction coefficient model relative to the rotation speed of a wet clutch engagement, which can predict friction coefficient under different stages of slipping velocity and different load pressures. In particular, the model has been improved by accounting the speed effect for the perdition of wet friction-element boundary friction, which is significant for understanding the friction mechanisms and for supporting the development of more efficient and related products.

Design/methodology/approach
This research investigated the mechanism of wet friction in a wet clutch engagement. A mixed friction model is established based on the asperity model and Newton’s law of viscosity. To obtain a friction coefficient computed by the model, the normal load shared by both asperities and lubrication fluid needs to be determined. Therefore, rough surface contact mechanism is analysed; a surface topography model is established; and surface parameters are obtained by means of surface topography measurement and reconstruction. Finally, verification of the mixed friction model is achieved.

Findings
Friction will be generated by both the asperity contact and the lubrication film shear relative to the rotation speed. And, the higher the relative speed, the larger the shearing power of lubrication film. It is caused by decrease in contact area of asperity. Surface morphology of a sintered bronze friction disk was obtained by a Laser-Micro-Test. The predicted results by the established model show that the total friction coefficient slightly reduced and then increased suddenly with speed. The surface topography model is responsible for the nonlinear behaviour of the asperity friction. Results of the simulation model are in agreement with those of the wet clutch engagement experiments.

Originality/value
This research is original and it is supported by the national defence project. The wet friction element which is applied on tracked vehicles is analysed for the first time. Through the model, the trend of the friction coefficient can be more accurately predicted. The problem of the wet friction plate modelling difficult is solved by using the mixed friction model.
A numerical study on the contact fatigue life of a coated gear pair under EHL
Authors: Zhou Ye , Zhu Caichao , Liu Huaiju , Song Chaosheng , Li Zufeng 
Published: November 2017

Purpose
Coatings are widely used in gears to keep interface from wearing excessively. The purpose of this paper is to study the effect of coating properties and working conditions on the pressure, the shear traction, stresses as well as the fatigue life of spur gear.

Design/methodology/approach
A numerical contact fatigue life model of a coated spur gear pair under elastohydrodynamic lubrication (EHL) is developed based on the characteristics of gear geometry and kinematics, lubrication conditions and material properties. Frequency response functions and the discrete convolute and fast Fourier transform (DC-FFT) algorithm are applied to obtain elastic deformation and stress. Mutil-axial fatigue criteria are used to evaluate the contact fatigue life based upon the predicted time-varying stress fields of coated bodies.

Findings
The maximum Mises stress decreases while the fatigue life increases as the coating modulus decreases. A thinner coating leads to a longer life and a smaller maximum Mises stress for hard coatings. The load has more significant effect on the contact fatigue life of soft coatings.

Originality/value
The developed model can be used to evaluate the contact fatigue life of coated gear under EHL and help designers analyze the effect of coating elastic modulus and thickness on the contact pressure, film thickness and stress.
A fast computing approach concerning recess pressure
Authors: Liang Peng , Lu Changhou , Yang Fazhan 
Published: November 2017

Purpose
This paper aims to provide a new method for fast calculation of the recess pressure for hydrostatic bearing compensated by orifice restrictor.

Design/methodology/approach
Three methods (new method, old method and finite difference method) are used to calculate recess pressure for hydrostatic bearing at different eccentricity ratios and radial clearances, and the results with the three methods are compared.

Findings
From the results, the conclusion is that the new method has a simple calculation process and a quick calculation speed.

Originality/value
The new method can be used to calculate the recess pressure of hydrostatic bearing with high precision and simple computing process.
A multi-platform collaboration innovation ecosystem: the case of China
Authors: Su Yu-Shan , Zheng Zong-Xi , Chen Jin 
Published: November 2017

Purpose
Innovation ecosystem is an emerging and popular concept in both academic and industrial circles. It offers a new perspective for enterprise strategy positioning. A business can create more value through a healthy innovation ecosystem. The paper aims to discuss these issues.

Design/methodology/approach
In this paper, the authors utilize a new triple-layer core-periphery framework to analyze Insigma Group’s multi-platform collaboration innovation ecosystem, in order to explore the architecture and heterogeneous functions inside an innovation ecosystem.

Findings
The authors illustrate the components and working mechanisms of the four platforms, which function as ideation, entrepreneurship, financing and investment, and innovation, inside Insigma’s innovation ecosystem in detail, and explain how they interact and collaborate toward a shared aim of the whole innovation ecosystem.

Research limitations/implications
The innovation ecosystem is an emerging concept. In this study, the authors combined two existing analytical frameworks of innovation ecosystem, and proposed a triple-layer core-periphery framework, which enable us to analyze the heterogeneity inside an innovation ecosystem.

Practical implications
The authors discussed the role of government and its policies in shaping the innovation ecosystem at the enterprise level.

Originality/value
The authors believe that this paper provides a holistic study of Insigma’s innovation ecosystem. The triple-layer core-periphery framework can be used to study other enterprise innovation ecosystem in the future.