bluuebunny/crossref_metadata_2025_split huggingface dataset:
Three invariant Hi-C interaction patterns: applications to genome assembly
Authors: Oddes Sivan , Zelig Aviv , Kaplan Noam 
Published: April 2018

AbstractAssembly of reference-quality genomes from next-generation sequencing data is a key challenge in genomics. Recently, we and others have shown that Hi-C data can be used to address several outstanding challenges in the field of genome assembly. This principle has since been developed in academia and industry, and has been used in the assembly of several major genomes. In this paper, we explore the central principles underlying Hi-C-based assembly approaches, by quantitatively defining and characterizing three invariant Hi-C interaction patterns on which these approaches can build: Intrachromosomal interaction enrichment, distance-dependent interaction decay and local interaction smoothness. Specifically, we evaluate to what degree each invariant pattern holds on a single locus level in different species, cell types and Hi-C map resolutions. We find that these patterns are generally consistent across species and cell types but are affected by sequencing depth, and that matrix balancing improves consistency of loci with all three invariant patterns. Finally, we overview current Hi-C-based assembly approaches in light of these invariant patterns and demonstrate how local interaction smoothness can be used to easily detect scaffolding errors in extremely sparse Hi-C maps. We suggest that simultaneously considering all three invariant patterns may lead to better Hi-C-based genome assembly methods.
Transcription Factor Regulation of RNA polymerase’s Torsional Capacity
Authors: Ma Jie , Tan Chuang , Gao Xiang , Fulbright Robert M. , Roberts Jeffrey W. , Wang Michelle D. 
Published: April 2018

ABSTRACTDuring transcription, RNA polymerase (RNAP) supercoils DNA as it forsward-translocates. Accumulation of this torsional stress in DNA can become a roadblock for an elongating RNAP and thus should be subject to regulation during transcription. Here, we investigate whether, and how, a transcription factor may regulate the torque generation capacity of RNAP and torque-induced RNAP stalling. Using a real-time assay based on an angular optical trap, we found that under a resisting torque, RNAP was highly prone to extensive backtracking. However, the presence of GreB, a transcription factor that facilitates the cleavage of the 3’ end of the extruded RNA transcript, greatly suppressed backtracking and remarkably increased the torque that RNAP was able to generate by 65%, from 11.2 to 18.5 pN·nm. Analysis of the real-time trajectories of RNAP position at a stall revealed the kinetic parameters of backtracking and GreB rescue. These results demonstrate that backtracking is the primary mechanism that limits transcription against DNA supercoiling and the transcription factor GreB effectively enhances the torsional capacity of RNAP. These findings broaden the potential impact of transcription factors on RNAP functionality.
Evaluation of lung VEGF-A transduction during hyperoxia-induced injury in rats
Authors: Raoul William , Louzier Vanessa , Eddahibi Saadia , Adnot Serge , Maitre Bernard , Delclaux Christophe 
Published: April 2018

AbstractBackgroundSince Vascular Endothelial Growth Factor (VEGF) is a main factor for endothelial survival, we evaluated whether VEGF transduction could ameliorate hyperoxia induced injury, which is associated with predominant endothelial injury.Methods and ResultsTransduction (induced 48 hours before hyperoxic exposure) using adenoviral vector (Ad.) for VEGF (1010 viral particles [VP]) increased moderately survival under hyperoxia (fraction of inspired oxygen [FIO2] >95%) as compared with Ad.Null (1010 VP) transduction, whereas VEGF transduction with a lower dose (5.109 VP) had no effect. After 48 hours of hyperoxia, Ad.VEGF transduction increased lung VEGF concentration, prevented the diffuse loss of capillary bed and induced patchy areas of endothelial cell proliferation (CD31 immunostaining) with interstitial inflammatory cell recruitment as compared to Ad. Null transduction. Hyperoxia was associated with diffuse apoptosis that was inhibited only in patchy areas of endothelial proliferation under VEGF transduction. Hyperoxia-induced alveolar inflammation was similar with Ad.Null and Ad.VEGF. Under normoxia, the high dose of VEGF transduction induced diffuse alveolar inflammation whereas the low dose did not suggesting a pro-inflammatory effect of VEGF that may have participated to increased survival under hyperoxia.ConclusionsWe demonstrate that lung VEGF-A transduction despite inhibition of the loss of capillary bed has a marginal effect of on animal survival during hyperoxia-induced injury.
Transient Magnetothermal Neuronal Silencing using the Chloride Channel Anoctamin1 (TMEM16A)
Authors: Munshi Rahul , Qadri Shahnaz , Pralle Arnd 
Published: April 2018

AbstractThe importance of specific neurons to a network’s function is best studied by precisely timed, reversible silencing of these neurons. Previously, we showed that alternating magnetic field mediated heating of magnetic nanoparticles bound to neurons expressing temperature-sensitive cation channels TRPV1, stimulates these neurons to fire and affects animal behavior in vivo (Munshi et al., 2017). Here, we demonstrate how to apply magnetic nanoparticle mediated heating to silence target neurons. Rat hippocampal neuron cultures are transfected to express the temperature gated chloride Anoctamin1 (TMEM16A) channels. Within seconds the heating of the membrane opens the Anoctamin1 (TMEM16A) channels, suppressing action potential firing. Five seconds of magnetic field application leads to about 12 seconds of silencing, with a latency of about 2 seconds and an average suppression ratio of more than 80%. The method provides a promising avenue for tether free, remote, transient neuronal silencing in vivo for both scientific and therapeutic applications.
Analytical strategies to include the X-chromosome in variance heterogeneity analyses: evidence for trait-specific polygenic variance structure
Authors: Deng Wei Q. , Mao Shihong , Kalnapenkis Anette , Esko Tõnu , Mägi Reedik , Paré Guillaume , Sun Lei 
Published: April 2018

AbstractGenotype-stratified variance of a quantitative trait could differ in the presence of gene-gene or gene-environment interactions. Genetic markers associated with phenotypic variance are thus considered promising candidates for follow-up interaction or joint location-scale analyses. However, as in studies of main effects, the X-chromosome is routinely excluded from ‘whole-genome’ scans due to analytical challenges. Specifically, as males carry only one copy of the X-chromosome, the inherent sex-genotype dependency could bias the trait-genotype association, through sexual dimorphism in quantitative traits with sex-specific means or variances. Here we investigate phenotypic variance heterogeneity associated with X-chromosome SNPs and propose valid and powerful strategies. Among those, a generalized Levene’s test has adequate power and remains robust to sexual dimorphism. An alternative approach is sex-stratified analysis but at the cost of slightly reduced power and modeling flexibility. We applied both methods to an Estonian study of gene expression quantitative trait loci (eQTL; n=841), and two complex trait studies of height, hip and waist circumferences, and body mass index from multi-ethnic study of atherosclerosis (MESA; n=2,073) and UK Biobank (UKB; n=327,393). Consistent with previous eQTL findings on mean, we found some but no conclusive evidence for cis regulators being enriched for variance association. SNP rs2681646 is associated with variance of waist circumference (p=9.5E-07) at X-chromosome-wide significance in UKB, with a suggestive female-specific effect in MESA (p=0.048). Collectively, an enrichment analysis using permutated UKB (p<1/10) and MESA (p<1/100) datasets, suggests a possible polygenic structure for the variance of human height.
Physical and functional cell-matrix uncoupling in a developing tissue under tension
Authors: Proag Amsha , Monier Bruno , Suzanne Magali 
Published: April 2018

AbstractTissue mechanics play a crucial role in organ development. It relies on cells and extracellular matrix (ECM) mechanical properties, but also on their reciprocal interaction. The relative physical contribution of cells and ECM to morphogenesis is poorly understood. Here, we dissected the mechanics of the envelope of theDrosophiladeveloping leg, an epithelium submitted to a number of mechanical stresses: first stretched, it is then torn apart and withdrawn to free the leg. During stretching, we found that mechanical tension is entirely borne by the ECM at first, then by the cellular monolayer as soon as they detach themselves from one another. Then, each envelope layer is removed by an independent mechanism: while ECM withdraws following local proteolysis, cellular monolayer withdrawal is independent of ECM degradation and driven by an autonomous myosin-II-dependent contraction. These results reveal a physical and functional cell-matrix uncoupling that could timely control tissue dynamics during development.
Pay gap, inventor promotion and corporate technology innovation
Authors: Zhao Qifeng , Wang Yongzhong 
Published: April 2018

PurposeThe purpose of this paper is to investigate how the pay gap between the management and ordinary employees influence corporate technology innovation.Design/methodology/approachThis study built a tournament model based on inventor innovation and career promotion. In addition, the authors use IV-GMM estimation method to address the possible endogeneity issue in the regressions.FindingsBased on the unbalanced panel data of patents and pay gap in 1,501 Chinese listed manufacturing firms during 2001-2015, this paper finds that the pay gap could lead inventor innovation and improve technology innovation. The pay gap could encourage corporate innovation significantly: 1 percent increase in pay gap may increase the number of patents by 2 percent in the next year. The pay gap between the management and ordinary employees facilitates corporate innovation via two possible channels. First, inventor innovation and career promotion. Inventors are selected into the management mainly based on their innovation output. The larger the pay gap, the more innovation incentives and patents would gain. Second, investment increase in technology innovation. The pay gap and more patents that inventors gain would increase the ratio of inventors promoted to the management, who tend to pour more resources into R&D activities and absorb more inventors to the management due to their sectionalism and R&D preference. The above two channels constitute a positive feedback mechanism among technology innovation, inventor promotion and increase in R&D investment.Research limitations/implicationsThis paper highlights that pay gap between the management and ordinary employees is an important issue that could encourage corporate innovation. The conclusions imply that pay gap could encourage inventors to work hard and produce more patents, which could help them to enter into the management such as executives or directors.Originality/valueThis study contributes to the current literature by implying that pay gap could have positive effects on innovation through theoretical and empirical analysis. Also, this study finds that inventor promotion due to the pay gap is a critical channel to stimulate corporate technology innovation.
Customer satisfaction/delight and behavioural intentions of cell phone network customers – an emerging market perspective
Authors: Roberts-Lombard Mornay , Petzer Daniël Johannes 
Published: April 2018

PurposeThis study aims to investigate the extent to which the satisfaction/delight experienced by customers of cell phone network service providers is influenced by their perceptions of the networks’ employee service delivery skills and the value that the customers derive from the networks’ offerings. In turn, the influence of the extent of their satisfaction/delight on future behavioural intention (BI) is determined.Design/methodology/approachA descripto-explanatory research design is followed and data are collected from satisfied/delighted cell phone network service provider customers using self-administered questionnaires. A total of 593 responses were suitable for analysis. An exploratory factor analysis is used to uncover the interrelationships between the items measuring the study’s constructs. Furthermore, the measurement and structural models are assessed.FindingsPerceived employee service delivery skills (PESDS) and value significantly and positively influence customer satisfaction/delight experiences, whereas customer satisfaction/delight experiences significantly and positively influence their BIs.Research limitations/implicationsThe model tested confirms the hypothesised relationships between PESDS, perceived value, customer satisfaction/delight experiences and BIs of cell phone network customers. Customer satisfaction/delight experiences are linked to their two antecedents (PESDS and value) and their outcome, BI.Practical implicationsThe findings assist cell phone network service providers in understanding how PESDS and value can foster customer delight, ultimately leading to positive BIs from customers.Originality/valueThis study focuses only on satisfied customers and determines the interrelationships of the extent to which they encounter customer satisfaction/delight experiences and related constructs. Few research studies, however, have examined how customer satisfaction/delight experiences relate to its antecedents and outcome.
Keggfarms Pvt. Ltd: a social enterprise and a way of life
Authors: Rizvi Saima , Teckchandany Shivani 
Published: April 2018

Subject area
Entrepreneurship, Design thinking and innovation, Strategy, Social entrepreneurship and rural markets, Business at the base of pyramid, Sustainability and leadership.

Study level/applicability
Undergraduate and Post Graduate Students

Case overview
Keggfarms Private Ltd was a private company started by Mr Vinod Kapur, a social entrepreneur who wanted to create a scalable social impact with his endeavor, which was the first of its kind outside the developed world. Keggfarms was established in 1967 with the aim of creating a business model which could benefit the rural sector by generating income and also enabling nutritional self-sufficiency. The case study aims to explore the sustainable model which had survived for 48 years without a push strategy and without a sole focus on profit. The business had spread to around 19 states in India, and the enterprise had decided to replicate a similar business model in the African continent. The social enterprise had aimed to touch the lives of millions of people in poverty by providing them with a low cost chicken – Kuroiler, which could survive the harsh weather and environmental conditions of rural India.

Expected learning outcomes
The study will help students to understand how social enterprises are born and built from the vision of the founder; how social capital is generated in the economy and how a blue ocean strategy was applied in this case to build a sustainable and financially viable social entrepreneurship model.

Supplementary materials
Teaching Notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes.

Subject code
CSS 3: Entrepreneurship
Experiences with a universal mindfulness and well-being programme at a UK medical school
Authors: Stewart-Brown Sarah , Cader Mizaya , Walker Thomas , Janjua Sabah , Hanson Emma , Chilton Anne-Marie 
Published: April 2018

Purpose
The purpose of this paper is to examine the evaluation of a universal, mental well-being and mindfulness programme in a UK graduate entry medical school.

Design/methodology/approach
Mixed methods used in the paper were the measurement of mental well-being and mindfulness in two cohorts at three time points over 15 months; descriptive, regression and repeated measures analysis with post hoc pairwise comparisons; qualitative interviews with purposive sample of 13 students after one year analysed thematically; and spontaneous anonymous feedback on the course.

Findings
The course was a surprise to students, and reactions were mixed. Respect for its contents grew over the first year. Most students had actively implemented a well-being strategy by the end of the course, and an estimated quarter was practicing some mindful activity. In the context of an overall decline in well-being and limited engagement with mindfulness practice, increases in mindfulness were protective against this decline in both cohorts (p<001). A small minority of students thought that the course was a waste of time. Their attitudes influenced engagement by their peers. The mindfulness and well-being practices of the facilitators were evident to students and influenced perceived effects.

Research limitations/implications
The uncontrolled nature of this observational study and low response rates to the survey limit conclusions. Further research in other medical education settings is needed.

Practical implications
Results are encouraging, suggesting modest benefit in terms of changing attitudes and practices and a modest protective effect on the well-being of students who engaged.

Originality/value
This is the first study of a universal well-being and mindfulness programme in a UK medical school. Universal programmes are rare and evaluation studies are scarce.
Randomized controlled trial of educational intervention to increase consumption of vegetables by Japanese university students
Authors: Ohtsuki Makoto , Shibata Katsumi , Fukuwatari Tutomu , Sasaki Yuko , Nakai Kunihiko 
Published: April 2018

Purpose
The purpose of this paper is to evaluate the effect of an educational intervention to increase vegetable consumption by university students.

Design/methodology/approach
This study is an open, parallel randomized controlled trial for 25 weeks. University students aged 18-24 years were divided into an intervention group (n=52) and a control group (n=52). Vegetable intake was assessed using a questionnaire.

Findings
On investigation, the results indicated that the vegetable intake of the intervention group was well maintained at the end of the study, whereas that of the control group was significantly decreased by the seasonal change. This research showed that using three educational projects could significantly improve the vegetable consumption of university students.

Research limitations/implications
These results suggest that the educational approach is a promising method to improve the vegetable consumption status, particularly the consumption of green and yellow vegetables, by university students.

Originality/value
This parallel randomized controlled study investigated intervention via educational approaches, including a lecture on the nutritional significance of vegetable intake, a tour of an agricultural farm, and learning of cooking skills, focusing on increasing the consumption of vegetables by university students. Although there have been many intervention studies aimed at improving intake of vegetables in the world, there have been no intervention studies on the vegetable intake of young adults in Japan.
Stern review on the economics of climate change: implications for Bangladesh
Authors: Roy Apurba , Haider Mohammed Ziaul 
Published: April 2018

Purpose
The purpose of this study is to investigate the impact of climate change on economic development in Bangladesh. More specifically, the research aims to figure out the influence of climate change on gross domestic product (GDP) growth rate related to different sectors such as agriculture, forest, water, health and infrastructure. It also attempts to explore the effect of climate change on the coastal economy of Bangladesh.

Design/methodology/approach
A set of statistical and econometric techniques, including descriptive and correlation analysis and time series regression model, was applied to address the objective of the research. Sector-wise time series economic data were collected from the World Bank for the period between 1971 and 2013. Climate data were received from the Bangladesh Agricultural Research Council online database for the period between 1948 and 2013.

Findings
The results from the statistical analysis show that climate variables such as temperature and rainfall have changed between 1948 and 2013 in the context of Bangladesh. The econometric regression analysis demonstrates that an increase by 1°C of annual mean temperature leads to a decrease in the GDP growth rate by 0.44 per cent on average, which is statistically significant at the 5 per cent level. On the other hand, the estimated coefficients of agriculture, industry, services, urbanization and export are positively associated with GDP growth rate, and these are statistically significant at the 1 per cent level. Sector-wise correlation analysis provides statistical evidence that climate change is negatively associated with various sectors, such as agriculture, forest, human health and arable land. In contrast, it has a positive relation to water access and electricity consumption. Analysis of coastal regions shows that climate change negatively affects the local economic sectors of the coastal zone of the country.

Originality/value
Although this study has received significant insight from the world-renowned research publication “The Economics of Climate Change: The Stern Review”, there is a dearth of research on the economic impact of climate change in the context of Bangladesh. The findings of the paper provide deep insight into and comprehensive views of policy makers on the impact of climate change on economic growth and various sectors in Bangladesh.
The potential of strategic environmental assessment to reduce disaster risks through climate change adaptation in the coastal zone of Bangladesh
Authors: Islam Md. Suzaul , Zhang Yanrong 
Published: April 2018

Purpose
The purpose of this paper is to analyze the potential of strategic environmental assessment (SEA) to mainstream consideration of climate change adaptation (CCA) in Bangladesh, particularly for the coastal zone, to improve disaster risk reduction (DRR) strategies in this region. Continuing climate risks require adaptation at all levels of society. The densely populated and resource-rich coastal zone of Bangladesh is at risk to the impacts of climate change.

Design/methodology/approach
This research is based on secondary sources (gray and published literature) of information on climate change impacts on the coastal zone of Bangladesh. The sources include research reports, online publications, governmental reports, scientific journals, international reports, books, journal articles and other academic resources on SEA, climate change adaptation and mitigation, and DRR. In addition to examining SEA in Bangladesh, this paper investigates SEA cases in different countries to obtain insights from the successful application of SEA for CCA.

Findings
The paper draws on several cases from different countries demonstrating that SEA has a significant potential to coordinate CCA objectives. The findings reveal that the appropriate use of SEA can enable DRR through CCA.

Originality/value
This study argues that SEA has a potential role in supporting CCA.