bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clustering gene expression time series data using an infinite Gaussian process mixture model
Authors: McDowell Ian C. , Manandhar Dinesh , Vockley Christopher M. , Schmid Amy K. , Reddy Timothy E. , Engelhardt Barbara E. 
Published: April 2017

AbstractTranscriptome-wide time series expression profiling is used to characterize the cellular response to environmental perturbations. The first step to analyzing transcriptional response data is often to cluster genes with similar responses. Here, we present a nonparametric model-based method, Dirichlet process Gaussian process mixture model (DPGP), which jointly models cluster number with a Dirichlet process and temporal dependencies with Gaussian processes. We demonstrate the accuracy of DPGP in comparison with state-of-the-art approaches using hundreds of simulated data sets. To further test our method, we apply DPGP to published microarray data from a microbial model organism exposed to stress and to novel RNA-seq data from a human cell line exposed to the glucocorticoid dexamethasone. We validate our clusters by examining local transcription factor binding and histone modifications. Our results demonstrate that jointly modeling cluster number and temporal dependencies can reveal novel regulatory mechanisms. DPGP software is freely available online athttps://github.com/PrincetonUniversity/DP_GP_cluster.
Cross-species complementation reveals conserved functions for EARLY FLOWERING 3 between monocots and dicots
Authors: Huang He , Gehan Malia A. , Huss Sarah E. , Alvarez Sophie , Lizarraga Cesar , Gruebbling Ellen L. , Gierer John , Naldrett Michael J. , Bindbeutel Rebecca K. , Evans Bradley S. , Mockler Todd C. , Nusinow Dmitri A. 
Published: April 2017

ABSTRACTPlant responses to the environment are shaped by external stimuli and internal signaling pathways. In both the model plantArabidopsis thalianaand crop species, circadian clock factors have been identified as critical for growth, flowering and circadian rhythms. Outside ofA. thaliana,however, little is known about the molecular function of clock genes. Therefore, we sought to compare the function ofBrachypodium distachyonandSeteria viridisorthologs ofEARLY FLOWERING3,a key clock gene inA. thaliana.To identify both cycling genes and putative ELF3 functional orthologs inS. viridis, a circadian RNA-seq dataset and online query tool (Diel Explorer) was generated as a community resource to explore expression profiles ofSetariagenes under constant conditions after photo- or thermo-entrainment. The function ofELF3orthologs fromA. thaliana, B. distachyon,andS. viridiswere tested for complementation of anelf3mutation inA. thaliana.Despite comparably low sequence identity versus AtELF3 (less than 37%), both monocot orthologs were capable of rescuing hypocotyl elongation, flowering time and arrhythmic clock phenotypes. Molecular analysis using affinity purification and mass spectrometry to compare physical interactions also found that BdELF3 and SvELF3 could be integrated into similar complexes and networks as AtELF3, including forming a composite evening complex. Thus, we find that, despite 180 million years of separation, BdELF3 and SvELF3 can functionally complement loss ofELF3at the molecular and physiological level.One Sentence SummaryOrthologs of a key circadian clock component ELF3 from grasses functionally complement the Arabidopsis counterpart at the molecular and physiological level, in spite of high sequence divergence.
The demographic history and mutational load of African hunter-gatherers and farmers
Authors: Lopez Marie , Kousathanas Athanasios , Quach Hélène , Harmant Christine , Mouguiama-Daouda Patrick , Hombert Jean-Marie , Froment Alain , Perry George H. , Barreiro Luis B. , Verdu Paul , Patin Etienne , Quintana-Murci Lluís 
Published: April 2017

AbstractThe distribution of deleterious genetic variation across human populations is a key issue in evolutionary biology and medical genetics. However, the impact of different modes of subsistence on recent changes in population size, patterns of gene flow, and deleterious mutational load remains unclear. Here, we report high-coverage exome sequencing data from various populations of rainforest hunter-gatherers and farmers from central Africa. We find that the recent demographic histories of hunter-gatherers and farmers differed considerably, with population collapses for hunter-gatherers and expansions for farmers, accompanied by increased gene flow. We show that purifying selection against deleterious alleles is of similar efficiency across African populations, in contrast with Europeans where we detect weaker purifying selection. Furthermore, the per-individual mutation load of rainforest hunter-gatherers is similar to that of farmers, under both additive and recessive models. Our results indicate that differences in the cultural practices and demographic regimes of African populations have not resulted in large differences in mutational burden, and highlight the beneficial role of gene flow in reshaping the distribution of deleterious genetic variation across human populations.
VCF2CNA: A tool for efficiently detecting copy-number alterations in VCF genotype data
Authors: Putnam Daniel K. , Xiaotu Ma , Rice Stephen V. , Liu Yu , Zhang Jinghui , Chen Xiang 
Published: April 2017

AbstractVCF2CNA is a web interface tool for copy-number alteration (CNA) analysis of VCF and other variant file formats. We applied it to 46 adult glioblastoma and 146 pediatric neuroblastoma samples sequenced by Illumina and Complete Genomics (CGI) platforms respectively. VCF2CNA was highly consistent with a state-of-the-art algorithm using raw sequencing data (mean F1-score=0.994) in high-quality glioblastoma samples and was robust to uneven coverage introduced by library artifacts. In the neuroblastoma set, VCF2CNA identified MYCN high-level amplifications in 31 of 32 clinically validated samples compared to 15 found by CGI’s HMM-based CNA model. The findings suggest that VCF2CNA is an accurate, efficient and platform-independent tool for CNA analyses without accessing raw sequence data.
Alternative cleavage of a bone morphogenetic protein (BMP) produces ligands with distinct developmental functions and receptor preference
Authors: Anderson Edward N. , Wharton Kristi A. 
Published: April 2017

ABSTRACTTGF-β and Bone Morphogenetic Protein (BMP) family proteins are made as proprotein dimers, which are cleaved by proprotein convertases to release the active C-terminal ligand dimer. Multiple proteolytic processing sites in Glass bottom boat (Gbb), theDrosophilaBMP7 ortholog, can produce distinct forms of active ligand. Cleavage at the S1 or atypical S0 site produces Gbb15, the conventional small BMP ligand, while cleavage at the NS site produces the larger Gbb38 ligand (1, 2). Here, we found that blocking NS cleavage increased association of the full length prodomain with Gbb15 resulting in a concomitant decrease in signaling activity. NS cleavage is requiredin vivofor Gbb-Decapentaplegic (Dpp) heterodimer-mediated wing vein patterning but not in cell culture to enable Gbb15-Dpp het-erodimer activity. Gbb NS cleavage is also requiredin vivofor the regulation of pupal ecdysis and viability that is dependent on the type II receptor Wishful thinking (Wit). We found that the ability of Gbb38 to signal requires the expression of either Wit or the type I receptor, Saxophone (Sax). Finally, we discovered that the production of Gbb38 in 3rd instar larvae results when processing at the S1/S0 site is blocked by O-linked glycosylation. Our findings demonstrate that BMP prodomain cleavage can ensure that the mature ligand is not inhibited by the prodomain. Furthermore, alternative processing of BMP proproteins produces ligand types that signal preferentially through different receptors and exhibit specific developmental functions.
Structure-based analysis of CysZ-mediated cellular uptake of sulfate
Authors: Sanghai Zahra Assur , Liu Qun , Clarke Oliver B. , Pinto Edgar Leal , Kloss Brian , Tabuso Shantelle , Love James , Punta Marco , Banerjee Surajit , Rajashankar Kanagalaghatta R. , Rost Burkhard , Logothetis Diomedes , Quick Matthias , Hendrickson Wayne A. , Mancia Filippo 
Published: April 2017

ABSTRACTSulfur, most abundantly found in the environment as sulfate (SO42-), is an essential element in metabolites required by all living cells, including amino acids, co-factors and vitamins. Current understanding of the cellular delivery of SO42-at the molecular level is limited however. CysZ has been described as a SO42-permease, but its sequence family is without known structural precedent. Based on crystallographic structure information, SO42-binding and uptake experiments in cells and proteoliposomes, and single-channel conductance measurements, we provide insight into the molecular mechanism of CysZ-mediated translocation of SO42-across membranes. CysZ properties differ markedly from those of known transporters and ion channels. The structures display a hitherto unknown fold with dual topology, assembling in CysZ fromPseudomonas denitrificansas a trimer of antiparallel dimers in the membrane. CysZ structures from two other species recapitulate dimers from this assembly. Mutational studies highlight the functional relevance of conserved CysZ residues.
Playing the game: explaining how Luxembourg has responded to the Networked Readiness Index
Authors: Binsfeld Nico , Whalley Jason , Pugalis Lee 
Published: April 2017

Purpose
Over the past decade or so, successive Luxembourgish governments have sought to develop the country’s information and communication technologies (ICT) sector. In this paper, the authors will aim to examine how Luxembourg’s relative position in the “Networked Readiness Index” (NRI), a key international benchmarking exercise published by the World Economic Forum, has evolved over time as these ambitions have been achieved. The paper also explores what policy initiatives could be implemented to further improve Luxembourg’s ranking in the NRI.

Design/methodology/approach
A longitudinal case study-based approach, drawing on secondary data and the annual publication of the NRI between 2003 and 2016, was adopted.

Findings
Luxembourg’s position in the NRI has improved from 27th in 2003, so that it now ranks among the top ten countries in the world. In particular, Luxembourg has substantially improved its position with regards to “infrastructure” and “international connectivity”. However, there are also areas, mainly linked to education, the provision of human resources and policies that allow for and stimulate entrepreneurship where further improvements appear possible.

Social implications
The paper highlights the need for an overall, holistic, ICT development strategy. Such a strategy would cover not only cover infrastructural and technical aspects but also educational, social, regulatory and economic issues as well.

Originality/value
The paper charts the evolution over time of Luxembourg’s position in an important international ICT index and identifies its current strengths and weaknesses in terms of the different elements that constitute the NRI. This paper represents the first attempt to investigate the position of a small country, which are often overlooked in the literature, in terms of its changing position and the policies developed and enacted by a national government.
National origin as a means of customer segmentation – an analysis of mobile communications users in a GCC country
Authors: Gerpott Torsten J. , May Sebastian , Nas Gokhan 
Published: April 2017

Purpose
In the field of mobile communications services (MCS), it is of importance to segment MCS users to support operators in better tailoring their offers to the needs of specific customer groups. This paper analyzes the suitability of national origin of MCS subscribers to segment residential customers into groups with significantly diverging usage behaviors in a sample living in one of the Gulf Cooperation Council (GCC) member states with a large share of expatriates in its population, particularly from South Asian countries. If MCS use patterns vary considerably between nationals, South Asian migrants and other foreign nationalities, it makes much sense to segment customers at least into these three groups.

Design/methodology/approach
The investigation applies discriminant and regression analysis on a sample of 4,892 residential postpaid MCS customers in a GCC country. The sample comprises individual usage data of 2,446 national citizens and an equal number of non-nationals between July 2014 and July 2015, living in the focal country. The data set was extracted from the billing and customer management systems of a collaborating mobile network operator (MNO).

Findings
The results imply that national origin is a highly significant predictor of individual MCS usage. Nationals and all expatriates primarily differ in international voice and SMS usage but not in established national MCS and mobile internet use intensity. Among expatriates, South Asians consume more national and international voice minutes than migrants originating from other foreign nations.

Research limitations
The analysis is based on objective MCS usage data retrieved from an MNO’s data warehouse. It lacks information on customer perceptions of the utility of various MNO service categories and on other individual characteristics, such as the customers’ level of education or language proficiency. To overcome this limitation, empirical research is needed that incorporates additional objective customer descriptors as well as subjective perceptual constructs.

Practical implications
MNOs are well advised to develop service bundles and tariff portfolios specifically designed for nationals and for different groups of expatriates.

Originality/value
The paper extends the literature on MCS usage behavior in Arab states in general and on customer MCS usage segmentation based on individuals’ national citizenship in particular.
Large-deformation finite element analysis of the interaction between concrete cut-off walls and high-plasticity clay in an earth core dam
Authors: Yu Xiang , Zou Degao , Kong Xianjing , Yu Long 
Published: April 2017

PurposeA large, uneven settlement that is unfavourable to dam safety can occur between a concrete cut-off wall and the high-plasticity clay of earth core dam built on alluviums. This issue has been often studied using the small-strain finite element (FE) method in previous research. This paper aims to research the interaction behaviour between a concrete cut-off wall and high-plasticity clay using large-deformation FE analyses.Design/methodology/approachThe re-meshing and interpolation technique with a small-strain (RITSS) method was performed using an independently developed program and adopted for large-deformation FE analyses, and a suitable element size for the high-plasticity clay region was suggested. The layered construction process of an earth core dam built on thick alluviums was simulated using the RITSS method incorporating a hyperbolic model for soil.FindingsThe RITSS method is an effective technique for simulating the soil–structure interaction during dam construction. The RITSS analysis predicted a higher maximum principle stress of the concrete cut-off wall and higher stress levels in the high-plasticity clay region than small-strain FE analysis.Originality/valueA practical method for large-deformation FE analysis was advised and was used for the first time to study the interaction between a concrete cut-off wall and high-plasticity clay in dam engineering. Large deformation in the high-plasticity clay was handled using the RITSS method. Moreover, the penetration process of the concrete cut-off wall into the high-plasticity clay was captured using a favourable element shape and mesh density.
Computationally efficient algorithm for vision-based simultaneous localization and mapping of mobile robots
Authors: Hsu Chen-Chien , Yang Cheng-Kai , Chien Yi-Hsing , Wang Yin-Tien , Wang Wei-Yen , Chien Chiang-Heng 
Published: April 2017

PurposeFastSLAM is a popular method to solve the problem of simultaneous localization and mapping (SLAM). However, when the number of landmarks present in real environments increases, there are excessive comparisons of the measurement with all the existing landmarks in each particle. As a result, the execution speed will be too slow to achieve the objective of real-time navigation. Thus, this paper aims to improve the computational efficiency and estimation accuracy of conventional SLAM algorithms.Design/methodology/approachAs an attempt to solve this problem, this paper presents a computationally efficient SLAM (CESLAM) algorithm, where odometer information is considered for updating the robot’s pose in particles. When a measurement has a maximum likelihood with the known landmark in the particle, the particle state is updated before updating the landmark estimates.FindingsSimulation results show that the proposed CESLAM can overcome the problem of heavy computational burden while improving the accuracy of localization and mapping building. To practically evaluate the performance of the proposed method, a Pioneer 3-DX robot with a Kinect sensor is used to develop an RGB-D-based computationally efficient visual SLAM (CEVSLAM) based on Speeded-Up Robust Features (SURF). Experimental results confirm that the proposed CEVSLAM system is capable of successfully estimating the robot pose and building the map with satisfactory accuracy.Originality/valueThe proposed CESLAM algorithm overcomes the problem of the time-consuming process because of unnecessary comparisons in existing FastSLAM algorithms. Simulations show that accuracy of robot pose and landmark estimation is greatly improved by the CESLAM. Combining CESLAM and SURF, the authors establish a CEVSLAM to significantly improve the estimation accuracy and computational efficiency. Practical experiments by using a Kinect visual sensor show that the variance and average error by using the proposed CEVSLAM are smaller than those by using the other visual SLAM algorithms.
Numerical simulations for the fluid-thermal-structural interaction lubrication in a tilting pad thrust bearing
Authors: Zhai Liming , Luo Yongyao , Liu Xin , Chen Funan , Xiao Yexiang , Wang Zhengwei 
Published: April 2017

Purpose
The purpose of this paper is to analyze lubrication characteristics of a tilting pad thrust bearing considering the effect of the thermal elastic deformation of the pad and collar.

Design/methodology/approach
This study used the fluid–solid interaction (FSI) technique to investigate the lubrication characteristics of a tilting pad thrust bearing for several typical operating conditions. The influences of the rotational speed, the thrust load and the oil supply temperature on the lubrication characteristics were analyzed.

Findings
The three-dimensional (3D) film model clearly shows that there is no pressure gradient but large temperature gradients across the film thickness. The wall heat transfer coefficients on the pad surfaces distribute in a very complex way and change within a large range. The rotational speed, the thrust load and the oil supply temperature have great but different influences on the lubrication characteristics.

Originality/value
This paper has preliminarily revealed the lubrication mechanism of the tilting-pad thrust bearings. The 3D FSI method is suggested to evaluate the thermal-elastic-hydrodynamic deformations of thrust bearings instead of the conventional method which iteratively solves the Reynolds equation, the energy equation, the heat conduction equation and the elastic equilibrium equation. Using FSI method, the heat transfer coefficients on the pad surfaces can be evaluated better.
Fatigue crack growth prediction of 7075 aluminum alloy based on the GMSVR model optimized by the artificial bee colony algorithm
Authors: Yang Dalian , Liu Yilun , Li Songbai , Tao Jie , Liu Chi , Yi Jiuhuo 
Published: April 2017

Purpose
The aim of this paper is to solve the problem of low accuracy of traditional fatigue crack growth (FCG) prediction methods.

Design/methodology/approach
The GMSVR model was proposed by combining the grey modeling (GM) and the support vector regression (SVR). Meanwhile, the GMSVR model parameter optimal selection method based on the artificial bee colony (ABC) algorithm was presented. The FCG prediction of 7075 aluminum alloy under different conditions were taken as the study objects, and the performance of the genetic algorithm, the particle swarm optimization algorithm, the n-fold cross validation and the ABC algorithm were compared and analyzed.

Findings
The results show that the speed of the ABC algorithm is the fastest and the accuracy of the ABC algorithm is the highest too. The prediction performances of the GM (1, 1) model, the SVR model and the GMSVR model were compared, the results show that the GMSVR model has the best prediction ability, it can improve the FCG prediction accuracy of 7075 aluminum alloy greatly.

Originality/value
A new prediction model is proposed for FCG combined the non-equidistant grey model and the SVR model. Aiming at the problem of the model parameters are difficult to select, the GMSVR model parameter optimization method based on the ABC algorithm was presented. the results show that the GMSVR model has better prediction ability, which increase the FCG prediction accuracy of 7075 aluminum alloy greatly.
Factors in an end user security expertise instrument
Authors: Rajivan Prashanth , Moriano Pablo , Kelley Timothy , Camp L. Jean 
Published: April 2017

Purpose
The purpose of this study is to identify factors that determine computer and security expertise in end users. They can be significant determinants of human behaviour and interactions in the security and privacy context. Standardized, externally valid instruments for measuring end-user security expertise are non-existent.

Design/methodology/approach
A questionnaire encompassing skills and knowledge-based questions was developed to identify critical factors that constitute expertise in end users. Exploratory factor analysis was applied on the results from 898 participants from a wide range of populations. Cluster analysis was applied to characterize the relationship between computer and security expertise. Ordered logistic regression models were applied to measure efficacy of the proposed security and computing factors in predicting user comprehension of security concepts: phishing and certificates.

Findings
There are levels to peoples’ computer and security expertise that could be reasonably measured and operationalized. Four factors that constitute computer security-related skills and knowledge are, namely, basic computer skills, advanced computer skills, security knowledge and advanced security skills, and these are identified as determinants of computer expertise.

Practical implications
Findings from this work can be used to guide the design of security interfaces such that it caters to people with different expertise levels and does not force users to exercise more cognitive processes than required.

Originality/value
This work identified four factors that constitute security expertise in end users. Findings from this work were integrated to propose a framework called Security SRK for guiding further research on security expertise. This work posits that security expertise instrument for end user should measure three cognitive dimensions: security skills, rules and knowledge.