bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling of DNA methylation in cis reveals principles of chromatin folding in vivo in the absence of crosslinking and ligation
Authors: Redolfi Josef , Zhan Yinxiu , Valdes Christian , Kryzhanovska Mariya , Guerreiro Isabel Misteli , Iesmantavicius Vytautas , Tiana Guido , Pollex Tim , Kind Jop , Smallwood Sebastien , Laat Wouter de , Giorgetti Luca 
Published: September 2018

AbstractMammalian chromosomes are folded into an intricate hierarchy of structural domains, within which topologically associating domains (TADs) and CTCF-associated loops partition the physical interactions between regulatory sequences. Current understanding of chromosome folding largely relies on chromosome conformation capture (3C)-based experiments, where chromosomal interactions are detected as ligation products after crosslinking of chromatin. To measure chromosome structure in vivo, quantitatively and without relying on crosslinking and ligation, we have implemented a new method named damC. DamC combines DNA-methylation based detection of chromosomal interactions with next-generation sequencing and a biophysical model of methylation kinetics. DamC performed in mouse embryonic stem cells provides the first in vivo validation of the existence of TADs and CTCF loops, confirms 3C-based measurements of the scaling of contact probabilities within TADs, and provides evidence that mammalian chromatin in vivo is essentially rigid below 5 kilobases. Combining damC with transposon-mediated genomic engineering shows that new loops can be formed between ectopically introduced and endogenous CTCF sites, which alters the partitioning of physical interactions within TADs. This establishes damC as a crosslinking-and ligation-free framework to measure and modify chromosome interactions combined with a solid theoretical background for rigorous data interpretation. This orthogonal approach to 3C validates the existence of key structural features of mammalian chromosomes and provides novel insights into how chromosome structure within TADs can be manipulated.
A role for Gic1 and Gic2 in Cdc42 polarization
Authors: Daniels Christine N. , Zyla Trevin R. , Lew Daniel J. 
Published: September 2018

AbstractThe conserved Rho-family GTPase Cdc42 is a master regulator of polarity establishment in many cell types. Cdc42 becomes activated and concentrated in a region of the cell cortex, and recruits a variety of effector proteins to that site. In turn, many effectors participate in regulation of cytoskeletal elements in order to remodel the cytoskeleton in a polarized manner. The budding yeast Saccharomyces cerevisiae has served as a tractable model system for studies of cell polarity. In yeast cells, Cdc42 polarization involves a positive feedback loop in which effectors called p21-activated kinases (PAKs) act to recruit a Cdc42-directed guanine nucleotide exchange factor (GEF), generating more GTP-Cdc42 in areas that already have GTP-Cdc42. The GTPase-interacting components (GICs) Gic1 and Gic2 are also Cdc42 effectors, and have been implicated in regulation of the actin and septin cytoskeleton. However, we report that cells lacking GICs are primarily defective in polarizing Cdc42 itself, suggesting that they act upstream as well as downstream of Cdc42 in yeast. Our findings suggest that feedback pathways involving GTPase effectors may be more prevalent than had been appreciated.
Assessing the pathogenicity, penetrance and expressivity of putative disease-causing variants in a population setting
Authors: Wright Caroline F. , West Ben , Tuke Marcus , Jones Samuel E. , Patel Kashyap , Laver Thomas W. , Beaumont R. N. , Tyrrell Jessica , Wood Andrew R. , Frayling Timothy M. , Hattersley Andrew T. , Weedon Michael N. 
Published: September 2018

ABSTRACTOver 100,000 genetic variants are classified as disease-causing in public databases. However, the true penetrance of many of these rare alleles is uncertain and may be over-estimated by clinical ascertainment. As more people undergo genome sequencing there is an increasing need to assess the true penetrance of alleles. Until recently, this was not possible in a population-based setting. Here, we use data from 388,714 UK Biobank (UKB) participants of European ancestry to assess the pathogenicity and penetrance of putatively clinically important rare variants.Although rare variants are harder to genotype accurately than common variants, we were able to classify 1,244 of 4,585 (27%) putatively clinically relevant rare variants genotyped on the UKB microarray as high-quality. We defined “rare” as variants with a minor allele frequency of <0.01, and “clinically relevant” as variants that were either classified as pathogenic/likely pathogenic in ClinVar or are in genes known to cause two specific monogenic diseases in which we have some expertise: Maturity-Onset Diabetes of the Young (MODY) and severe developmental disorders (DD). We assessed the penetrance and pathogenicity of these high-quality variants by testing their association with 401 clinically-relevant traits available in UKB.We identified 27 putatively clinically relevant rare variants associated with a UKB trait but that exhibited reduced penetrance or variable expressivity compared with their associated disease. For example, the P415APER3variant that has been reported to cause familial advanced sleep phase syndrome is present at 0.5% frequency in the population and associated with an odds ratio of 1.38 for being a morning person (P=2×10-18). We also observed novel associations with relevant traits for heterozygous carriers of some rare recessive conditions, e.g. heterozygous carriers of the R799WERCC4variant that causes Xeroderma pigmentosum were more susceptible to sunburn (one extra sunburn episode reported,P=2×10-8). Within our two disease subsets, we were able to refine the penetrance estimate for the R114WHNF4Avariant in diabetes (only ~10% by age 40yrs) and refute the previous disease-association ofRNF135in developmental disorders.In conclusion, this study shows that very large population-based studies will help refine the penetrance estimates of rare variants. This information will be important for anyone receiving information about their health based on putatively pathogenic variants.
Integration of Molecular Interactome and Targeted Interaction Analysis to Identify a COPD Disease Network Module
Authors: Sharma Amitabh , Kitsak Maksim , Cho Michael H. , Ameli Asher , Zhou Xiaobo , Jiang Zhiqiang , Crapo James D. , Beaty Terri H. , Menche Joerg , Bakke Per S. , Santolini Marc , Silverman Edwin K. 
Published: September 2018

AbstractThe polygenic nature of complex diseases offers potential opportunities to utilize network-based approaches that leverage the comprehensive set of protein-protein interactions (the human interactome) to identify new genes of interest and relevant biological pathways. However, the incompleteness of the current human interactome prevents it from reaching its full potential to extract network-based knowledge from gene discovery efforts, such as genome-wide association studies, for complex diseases like chronic obstructive pulmonary disease (COPD). Here, we provide a framework that integrates the existing human interactome information with new experimental protein-protein interaction data for FAM13A, one of the most highly associated genetic loci to COPD, to find a more comprehensive disease network module. We identified an initial disease network neighborhood by applying a random-walk method. Next, we developed a network-based closeness approach (CAB) that revealed 9 out of 96 FAM13A interacting partners identified by affinity purification assays were significantly close to the initial network neighborhood. Moreover, compared to a similar method (local radiality), the CAB approach predicts low-degree genes as potential candidates. The candidates identified by the network-based closeness approach were combined with the initial network neighborhood to build a comprehensive disease network module (163 genes) that was enriched with genes differentially expressed between controls and COPD subjects in alveolar macrophages, lung tissue, sputum, blood, and bronchial brushing datasets. Overall, we demonstrate an approach to find disease-related network components using new laboratory data to overcome incompleteness of the current interactome.
Entrepreneurial capability (EC) environment in ASEAN-05 emerging economies
Authors: Afzal Munshi Naser Ibne , Mansur Kasim , Manni Umme Humayara 
Published: September 2018

PurposeThe entrepreneurial capability (EC) environment refers to the general social and economic settings of a given local/regional entrepreneurship environment. The primary purpose of this study is to uncover key indicators of the EC milieu and test these components empirically within the context of the Association of South East Asian Nations (ASEAN)-5 economies to elucidate the current state of their EC environments, at the regional and national levels. To this end, the aim of this study is twofold. First, this work endeavors to explicate the determinants of EC, with aims of elucidating its association to commercial opportunities in (ASEAN)-5 economies, namely, Indonesia, Malaysia, the Philippines, Singapore and Thailand. Next, this study applies the developed theory, including the identified determinants of EC to empirically test the efficiency and imperative coefficients of variables that have an impact on perceived entrepreneurial capabilities within a given environment.Design/methodology/approachThis research applies two frontier models, namely, the consistent estimation of fixed-effects and linear transformation stochastic frontier models, to assess the coefficients of significant EC variables for the panel sample. Data corresponding to the assessed variables were retrieved from the databases of the Global Entrepreneurship Monitor (GEM) – 2016 and the World Competitiveness Yearbook (WCY) – 2016, for the period, 2010-2016.FindingsThe attained results suggest that factors corresponding to the variables “Entrepreneurship as a good career choice” and “perceived opportunities” have played a significantly positive role on the EC environment of ASEAN 05, although findings suggest both factors may still be improved upon. Conversely, the “fear of failure rate” factor was shown to have exerted a negative impact on the efficiency of the EC environment of ASEAN 05. Other important variables – such as intellectual property rights, university education and knowledge transfer rate – were shown to generate a positive impact on the EC environment of these economies.Originality/valueThis study makes an important contribution to the entrepreneurship literature and can stimulate policymakers to rethink the EC settings of ASEAN-05 in their pursuit of an innovation-driven region.
Entrepreneurial orientation, entrepreneurial education and performance
Authors: Cho Yun Hee , Lee Joo-Heon 
Published: September 2018

PurposeKorean economy is demanding to change from an industrial society to an entrepreneurial society. It is asking for a generational change from the preexisting paradigms of such as labor consciousness, the concept of work and company management. Entrepreneurship is one of the key elements that will lead to a successful business performance under highly uncertain business conditions. The purpose of this paper is to examine the relationship between entrepreneurial orientation and business performance. Also, the authors look for the role of entrepreneurship education in the influence of entrepreneurial orientation on financial and nonfinancial business performance.Design/methodology/approachTo accomplish the purpose of this study, the authors carried out a survey targeting nascent entrepreneurs and total early-stage entrepreneurs with less than seven years of experience. Based on the Miller’s (1983) definition, a group of questions for entrepreneurial orientation, similar to Covin and Slevin (1989), were developed.FindingsFirst, among the subfactors of entrepreneurial orientation, it was clear that innovative progressiveness affected nonfinancial business performance. Second, risk-taking propensity did not influence both financial business performance and nonfinancial business performance. Third, entrepreneurship education had no connection with entrepreneurial orientation or business performance.Practical implicationsNonfinancial business performances are related with long-term goals and growth potential. Innovative proactiveness affects nonfinancial business performance. Thus, entrepreneurs should look for ways to promote their innovative proactiveness. Entrepreneurship education for experienced entrepreneurs is not as effective as that for students.Originality/valueIn the authors’ study, survey questionnaires were sent to 200 nascent and total early-stage entrepreneurs searching for business angel investments or entrepreneurship consultants in Korea. A total of 180 entrepreneurs answered the survey questions online. There are not so many valid studies examining the effect of entrepreneurship education for nascent and total early-stage entrepreneurs in Korea.
Overflow oscillation-free realization of digital filters with saturation
Authors: Agarwal Neha , Kar Haranath 
Published: September 2018

Purpose
The purpose of this paper is to establish a criterion for the global asymptotic stability of fixed-point state–space digital filters using saturation overflow arithmetic.

Design/methodology/approach
The method of stability analysis used in this paper is the second method of Lyapunov. The approach in this paper makes use of a precise upper bound of the state vector of the system and a novel passivity property associated with the saturation nonlinearities.

Findings
The presented criterion leads to an enhanced stability region in the parameter-space as compared to several existing criteria.

Practical implications
When dealing with the design of fixed-point state–space digital filters, it is desirable to have a criterion for selecting the filter coefficients so that the designed filter becomes free of overflow oscillations. The criterion presented in this paper provides enhanced saturation overflow stability region and therefore facilitates the designer greater flexibility in selecting filter parameters for overflow oscillation-free realization of digital filters.

Originality/value
The approach uses the structural properties of the saturation nonlinearities in a greater detail. The exploitation of upper bound of the system state vector together with a new passivity property of saturation nonlinearities is a unique feature of the present approach. The presented approach may lead to results not covered by several existing approaches.
Numerical simulation of pressure drop for three-dimensional rectangular microchannels
Authors: Duan Zhipeng , Liang Peng , Ma Hao , Ma Niya , He Boshu 
Published: September 2018

Purpose
The purpose of this paper is to numerically investigate the flow characteristics and extend the data of friction factor and Reynolds number product of hydrodynamically developing laminar flow in three-dimensional rectangular microchannels with different aspect ratios.

Design/methodology/approach
Using a finite-volume approach, the friction factor characteristics of Newtonian fluid in three-dimensional rectangular ducts with aspect ratios from 0.1 to 1 are conducted numerically under no-slip boundary conditions. A simple model that approximately predicts the apparent friction factor and Reynolds number product fappRe is referenced as a semi-theoretical fundamental analysis for numerical simulations.

Findings
The accurate and reliable results of fappRe are obtained, which are compared with classic numerical data and experimental data, and the simple semi-theoretical model used and all comparisons show good agreement. Among them, the maximum relative error with the classic numerical data is less than 3.9 per cent. The data of fappRe are significantly extended to other different aspect ratios and the novel values of fappRe are presented in the tables. The characteristics of fappRe are analyzed as a function of a non-dimensional axial distance and the aspect ratios. A more effective and accurate fourth-order fitting equation for the Hagenbach's factor of rectangular channels is proposed.

Originality/value
From the reliable data, it is shown that the values of fappRe and the model can be references of pressure drop and friction factor for developing laminar flow in rectangular channels for researchers and engineering applications.
Future of the discrete element method in the modelling of grinding wheels
Authors: Osa Juan Luis , Ortega Naiara , Vidal Gorka , Fernandez-Gauna Borja , Carballo Asier , Tolosa Ibon 
Published: September 2018

Purpose
The granular structure of a grinding wheel determines its performance remarkably when grinding. Nowadays, grinding wheels are man-made porous conglomerates of hard abrasive grains bonded with a binder. As an engineered material, it would be interesting to foresee the behaviour of the wheel, but it is hindered under its complex heterogeneous nature. Recently, some models based on the discrete element method (DEM) have been presented to model the grinding wheel. This paper aims to identify and propose a framework that must comply with such models and to identify new applications for DEM models in grinding.

Design/methodology/approach
First, the characteristics of the grinding wheel are described. In this way, the framework of DEM models of a grinding wheel material is developed, reproducing both the granular morphology and stiffness.

Findings
The paper asserts a promising future that provides the DEM in the modelling of grinding.

Originality/value
The potential of DEM in grinding is analysed, proposing new applications. It can be used as topography model, which can also model the stiffness. In addition, DEM opens a new interesting research line: the modelling of the grit breakout. It draws up the development of essential dressing and wear models.
Information security behaviour of smartphone users
Authors: Nowrin Shohana , Bawden David 
Published: September 2018

Purpose
The purpose of this study is to understand the information security behaviour of the students of the University of Dhaka, Bangladesh in the use of smartphones. Bangladesh is well-known as one of the largest and fastest growing mobile phone market of the world, and the University of Dhaka is also the largest student’s assembly in the country in terms of using smartphones. Besides, the rising use of smartphones is also likely to be typical of other sub-continent countries.

Design/methodology/approach
To gain an understanding of the information security behaviours of the students of University of Dhaka, Bangladesh, a quantitative survey method was deployed in revealing the approaches of the students towards avoidance of various security risks. A total of 356 students participated in the study, although eight of the participants did not carry out the full survey because they do not use smartphones. The collected data were analysed with suitable statistical methods.

Findings
The findings of the study reveal that students of University of Dhaka possess a moderately secure behaviour in terms of avoiding harmful behaviours, using useful phone settings and add-on utilities and disaster recovery. This study also shows that the students do not behave securely in all aspects of using different security features in the same way, and it also varies somewhat according to gender, and between faculties and institutions. The university library is recommended as the focus for instruction and guidance on the best practice in smartphone use by students.

Research limitations/implications
The study does not include any other universities of Bangladesh except University of Dhaka due to the shortage of time. A further study can be conducted to gain an understanding in a greater extent by including students of the other universities and perhaps also other countries.

Originality/value
This is the first paper in Bangladesh related to the study of information security behaviour regarding the use of smartphone among the student of University of Dhaka. This study will help to raise information security awareness among the students and encourage the authorities to adopt appropriate strategies and policies to resolve information security risks in the use of smartphones. Specially, the university library can take some initiatives in this case, such as providing advice, seminars, workshops and lectures to make the students aware about security issues.
Participating by activity or by week in MOOCs
Authors: Baikadi Alok , Demmans Epp Carrie , Schunn Christian D. 
Published: September 2018

Purpose
The purpose of this study was to provide a new characterization of the extent to which learners complete learning activities in massive open online courses (MOOCs), a central challenge in these contexts. Prior explorations of learner interactions with MOOC materials have often described these interactions through stereotypes, which accounts for neither the full spectrum of potential learner activities nor the ways those patterns differ across course designs.

Design/methodology/approach
To overcome these shortcomings, the authors apply confirmatory and exploratory factor analysis to learner activities within three MOOCs to test different models of participation across courses and populations found within those courses.

Findings
Courses varied in the extent to which participation was driven by learning activities vs time/topic or a mixture of both, but this was stable across offerings of the same course.

Research limitations/implications
The results call for a reconceptualization of how different learning activities within a MOOC are designed to work together, to better allow strong learning outcomes even within one activity form or more strongly encourage participation across activities.

Originality/value
The authors validate new continuous-patterns rather than a discrete-pattern participation model for MOOC learning.
The Moderating Effect of Criminal Thinking on Certainty of Apprehension in Decisions to Engage in Antisocial Behavior: Replication and Extension
Authors: Walters Glenn D. , Morgan Robert D. , Scanlon Faith 
Published: September 2018

AbstractThis study explored whether the rational (certainty of punishment) and nonrational (criminal thinking) aspects of antisocial decision‐making interact. A convenience sample of 319 undergraduates (106 men, 213 women) completed a measure of criminal thinking and responded to three fictional vignettes (i.e., cheating on a final examination in a class they were in jeopardy of failing, stealing $50 off a table in a dorm room, and selling marijuana for a friend) at three different levels of risk or certainty of apprehension (50%, 10%, and 1%). Results indicated that participants reported that they would be more likely to engage in antisocial behavior when the certainty of getting caught was low and the level of proactive (P) or reactive (R) criminal thinking was high. An interaction between certainty and criminal thinking was also observed in which the gap between lower and higher criminal thinking respondents grew as the probability of getting caught fell.
Value of labeling credence attributes—common structures and individual preferences
Authors: Dahlhausen Johanna Lena , Rungie Cam , Roosen Jutta 
Published: September 2018

AbstractThis article analyzes the common preference structure underlying purchase intentions for food products labeled with credence attributes. In three consecutive, hypothetical discrete choice experiments, consumers selected pork, eggs, and pasta containing egg based on the attributes organic, local, animal welfare, certified “free of antibiotics,” and price. The data were analyzed using structural choice modeling, a factor‐analytic approach modeling latent sources of preference heterogeneity. The results of this analysis show that preference heterogeneity is stable across products and can be explained best by common characteristics in credence attributes. The article gives guidance as to how to use factors in the analysis of multiple discrete choice experiments.