bluuebunny/crossref_metadata_2025_split huggingface dataset:
Actin cytoskeleton self-organization in single epithelial cells and fibroblasts under isotropic confinement
Authors: Jalal Salma , Huang Ruby Yun-Ju , Viasnoff Virgile , Tee Yee Han , Bershadsky Alexander 
Published: May 2018

AbstractWe systematically investigated the principles of actin cytoskeleton self-organization in two cell types, fibroblasts and epitheliocytes, by confining isolated cells on isotropic adhesive islands of varying size. In fibroblasts, we previously described that an initially circular pattern of circumferential actin dynamically evolves into a radial pattern of actin bundles that spontaneously transforms into a chiral pattern, before finally producing parallel linear stress fibres. We now show that progression from circular to chiral actin patterns depends on cell projected area and rarely occurs on small islands. Epitheliocytes however, did not exhibit succession through all the actin patterns described above even on large islands. Upon confinement, the actin cytoskeleton in non-keratinocyte epitheliocytes is arrested at the circular stage, while in keratinocytes it can progress as far as the radial pattern but still cannot break symmetry. Epithelial-mesenchymal transition pushed actin cytoskeleton development from circular towards radial patterns but remains insufficient to cause chirality. Surprisingly, small doses of G-actin sequestering drug, latrunculin A, induced chiral swirling in keratinocytes. During this swirling, keratin filaments follow actin and also demonstrate chiral swirling movement. Elimination of the keratin network by genetic silencing of Type II keratins, however, did not affect the self-organization of the actin cytoskeleton.
Family-Based Haplotype Estimation and Allele Dosage Correction for Polyploids Using Short Sequence Reads
Authors: Motazedi Ehsan , Finkers Richard , Maliepaard Chris , de Ridder Dick 
Published: May 2018

AbstractDNA sequence reads contain information about the genomic variants located on a single chromosome. By extracting and extending this information (using the overlaps of the reads), the haplotypes of an individual can be obtained. Adding parent-offspring relationships to the read information in a population can considerably improve the quality of the haplotypes obtained from short reads, as pedigree information can compensate for spurious overlaps (due to sequencing errors) and insufficient overlaps (due to shallow coverage). This improvement is especially beneficial for polyploid organisms, which have more than two copies of each chromosome and are therefore more difficult to be haplotyped compared to diploids. We develop a novel method, PopPoly, to estimate polyploid haplotypes in an F1-population from short sequence data by considering the transmission of the haplotypes from the parents to the offspring. In addition, PopPoly employs this information to improve genotype dosage estimation and to call missing genotypes in the population. Through realistic simulations, we compare PopPoly to other haplotyping methods and show its better performance in terms of phasing accuracy and the accuracy of phased genotypes. We apply PopPoly to estimate the parental and offspring haplotypes for a tetraploid potato cross with 10 offspring, using Illumina HiSeq sequence data of 9 genomic regions involved in plant maturity and tuberisation.
A guide to using a multiple-matrix animal model to disentangle genetic and nongenetic causes of phenotypic variance
Authors: Thomson Caroline E. , Winney Isabel S. , Salles Oceane C. , Pujol Benoit 
Published: May 2018

AbstractNon-genetic influences on phenotypic traits can affect our interpretation of genetic variance and the evolutionary potential of populations to respond to selection, with consequences for our ability to predict the outcomes of selection. Long-term population surveys and experiments have shown that quantitative genetic estimates are influenced by nongenetic effects, including shared environmental effects, epigenetic effects, and social interactions. Recent developments to the “animal model” of quantitative genetics can now allow us to calculate precise individual-based measures of non-genetic phenotypic variance. These models can be applied to a much broader range of contexts and data types than used previously, with the potential to greatly expand our understanding of nongenetic effects on evolutionary potential. Here, we provide the first practical guide for researchers interested in distinguishing between genetic and nongenetic causes of phenotypic variation in the animal model. The methods use matrices describing individual similarity in nongenetic effects, analogous to the additive genetic relatedness matrix. In a simulation of various phenotypic traits, accounting for environmental, epigenetic, or cultural resemblance between individuals reduced estimates of additive genetic variance, changing the interpretation of evolutionary potential. These variances were estimable for both direct and parental nongenetic variances. Our tutorial outlines an easy way to account for these effects in both wild and experimental populations. These models have the potential to add to our understanding of the effects of genetic and nongenetic effects on evolutionary potential. This should be of interest both to those studying heritability, and those who wish to understand nongenetic variance.
Cargo Transport Shapes the Spatial Organization of a Microbial Community
Authors: Shrivastava Abhishek , Patel Visha K. , Tang Yisha , Yost Susan Connolly , Dewhirst Floyd E. , Berg Howard C. 
Published: May 2018

AbstractThe human microbiome is an assemblage of diverse bacteria that interact with one another to form communities. Bacteria in a given community are arranged in a three-dimensional matrix with many degrees of freedom. Snapshots of the community display well-defined structures, but the steps required for their assembly are not understood. Here, we show that this construction is carried out with the help of gliding bacteria. Gliding is defined as the motion of cells over a solid or semi-solid surface without the necessity of growth or the aid of pili or flagella. Genomic analysis suggests that gliding bacteria are present in human microbial communities. We focus on Capnocytophaga gingivalis which is present in abundance in the human oral microbiome. Tracking of fluorescently-labeled single cells and of gas bubbles carried by fluid flow shows that swarms of C. gingivalis are layered, with cells in the upper layers moving more rapidly than those in the lower layers. Thus, cells also glide on top of one another. Cells of non-motile bacterial species attach to the surface of C. gingivalis and are propelled as cargo. The cargo cell moves along the length of a C. gingivalis cell, looping from one pole to the other. Multi-color fluorescent spectral imaging of cells of different live but non-motile bacterial species reveals their long-range transport in a polymicrobial community. A swarm of C. gingivalis transports some non-motile bacterial species more efficiently than others and helps shape the spatial organization of a polymicrobial community.SignificanceWe describe a situation in which bacteria typical of the human oral microbiome are organized spatially by gliding cells, species of Capnocytophaga, that move backwards and forwards over the substratum. The mobile adhesins that pull the cells over the substratum also attach to cells of non-motile bacterial species, which are carried up and down the motile cells as cargo. The synchronized transport of non-motile cargo bacteria helps shape a polymicrobial community.
Soft drinks and monogenetic diabetes: a study on the Wolfram syndrome 1 (Wfs1) deficient mouse model
Authors: Porosk Rando , Pintšuk Julia , Punapart Marite , Soomets Ursel , Terasmaa Anton , Kilk Kalle 
Published: May 2018

AbstractIn a modern society, the risk of developing type II diabetes and obesity may be linked to the increased consumption of carbohydrate-rich drinks. Several genes, including Wolfram Syndrome 1 (WFS1), have been reported to increase susceptibility for developing type II diabetes. In this study we aimed to investigate the effect of chronic consumption of carbohydrate-rich drinks on weight gain, overall consumption of liquids, glucose tolerance and liver metabolism in Wfs1-deficient mice. Wfs1-deficient and wild-type mice were divided into three groups that consumed regular Coca-Cola, 20% sucrose solution or water ad libitum as the only source of liquid. During the experiment, daily liquid consumption was determined. After 30 days, total weight gain of mice was calculated and glucose tolerance test was performed. The liver tissue was analysed by means of untargeted and targeted metabolomics using liquid chromatography-mass spectrometry. Weight gain was strongly affected by mouse genotype (p<0.001), their drink (p<0.001) and the interaction of both genotype and drink (p<0.001). Coca-Cola significantly increased liquid consumption in knock-out mice. There was an effect of the drink (p<0.001) and the interaction between the genotype and treatment (p=0.02) on blood glucose level while Coca-Cola and 20% sucrose solution exacerbated glucose intolerance in the knock-out mice. In untargeted metabolic profiling, the water consuming wild-type and heterozygous mice were found to be the most distinctive from the mice with all other genotype and drink combinations. Targeted analysis revealed interactions between the genotype and drink regarding to glycolysis and lipogenesis. In the wild-type animals, carbohydrate overload was alleviated by converting glucose to lipids. However, the same mechanism is not implemented in knock-out animals, as lipolysis and gluconeogenesis are upregulated by Wfs1 deficiency. In conclusion, our study demonstrates a significant interaction between the genotype and the drink when comparing wild-type and Wfs1 knock-out mice consuming soft drinks.
Testing soil nematode extraction efficiency using different variations of the Baermann funnel method
Authors: Schulz Annika Eva , Eisenhauer Nico , Cesarz Simone 
Published: May 2018

AbstractNematodes are increasingly used as powerful bioindicators of soil food web composition and functioning in ecological studies. Todays’ ecological research aims to investigate not only local relationships but global patterns, which requires consistent methodology across locales. Thus, a common and easy extraction protocol of soil nematodes is needed. In this study, we present a detailed protocol of the Baermann funnel method and highlight how different soil pre-treatments and equipment (soil type, amount of soil, sieving, filter type) can affect extraction efficiency and community composition by using natural nematode communities. We found that highest nematode extraction efficiency was achieved using lowest soil weight (25 g instead of 50 g or 100 g) in combination with soil sieving, and by using milk filters (instead of paper towels). PCA at the family level revealed that different pre-treatments significantly affected nematode community composition. Increasing the amount of soil increased the proportion of larger-sized nematodes being able to overcome long distances. Sieving is suggested to break up soil aggregates and, therefore, facilitate moving in general. Interestingly, sieving did not negatively affect larger nematodes that are supposed to have a higher probability of getting bruised during sieving. The present study shows that variations in the extraction protocol can alter the total density and community composition of extracted nematodes and provides recommendations for an efficient and standardized approach in future studies. Having a simple, cheap, and standardized extraction protocol can facilitate the assessment of soil biodiversity in global contexts.
Development of a conceptual framework on real options theory for strategic human resource management
Authors: Bhattacharyya Som Sekhar 
Published: May 2018

PurposeThe purpose of this paper is to propose a conceptual real options theory framework for the firms to use options to mitigate both investment risks and retention of the trained human resources.Design/methodology/approachThis conceptual paper is built with logical argumentation.FindingsThe growth of IT firms has created a demand for quality IT industry employees in substantive quantity in India. IT firms provide training and development (T&D) inputs for developing better skills of employees for better employee and superior firm performance. T&D input requires firm investment. It also creates enhanced market demand for the trained employee. High growth area like IT firms not only competes for market but also for employees. A trained employee might leave the firm that provided the training to join a rival firm which offers relatively better salary, a catch -22 situation. This paper develops a real options-based framework for strategic human resource management (HRM).Research limitations/implicationsThis work integrates the theory of real options and strategic HRM.Originality/valueThis conceptual work is one of the first attempts to use real options theory on strategic HRM.
Housing demand in Indian metros: a hedonic approach
Authors: Roy Debarpita 
Published: May 2018

Purpose
This paper aims to understand housing demand of urban Indian households in terms of housing and household-level characteristics. Because a house is a bundle of certain characteristics which vary across houses, each characteristic has an implicit price. Finding this implicit price for certain important characteristics is the first objective of this study. The second objective of the paper is to compute the income elasticity and price elasticity of housing demand for these cities.

Design/methodology/approach
To achieve comparable estimates, household-level data from India’s National Sample Survey Organisation housing surveys for the years 2002 and 2008-2009 have been used. A hedonic price function is estimated using ordinary least squares (OLS) and Box-Cox functional forms to estimate the implicit prices of housing characteristics. This exercise is attempted for owned and rented houses separately. Demand function required for computing the elasticities, uses the hedonic price index derived from the implicit prices and household characteristics.

Findings
The study finds housing demand to be income elastic and price inelastic for the six cities across both the time periods.

Originality/value
Firstly, this study includes housing characteristics such as individual access to drinking water, modern sanitation facility, separate kitchen, condition of the structure, existence of a road with street light and whether the house is in a slum or non-slum area in the hedonic price function. These variables were not used in any of the earlier studies pertaining to India. Secondly, it uses the Box-Cox non-linear form to derive the hedonic price function, a specification not used earlier. Thirdly, this is the first study analysing housing demand across the six largest Indian cities.
Leveraging supply chain collaboration in pursuing radical innovation
Authors: Yunus Erlinda N. 
Published: May 2018

PurposeThe purpose of this study is to examine the relationship between supply chain collaboration and innovation. It particularly investigates the effect of collaboration on radical innovation and highlights the positive impact of innovation, both radical and incremental, on business performance.Design/methodology/approachA survey of 230 Indonesian firms was conducted and the instrument was tested for reliability and validity to warrant its psychometric properties. The data were analyzed using structural equation modeling.FindingsThis study reveals that collaboration with suppliers brings radical innovation, while collaboration with customers brings incremental innovation. Contrary to this study’s conjecture, albeit interesting, collaboration with customers negatively affects radical innovation. Both radical and incremental innovations further exert a positive influence over firm performance.Research limitations/implicationsThis study focuses on the relationships between supply chain collaboration, innovation and firm performance. The results enhance our understanding of types of innovation that are promoted by each dimension of collaboration. Further studies could extend the research by using a more elaborate measure of innovation or perform a longitudinal examination.Practical implicationsManagers are encouraged to pursue innovation as it improves firm performance. They could exploit their current partnership with customers to generate incremental innovation or leverage their supplier network to develop radical innovation.Originality/valueStudies that specifically investigate the impact of firms’ collaboration with their supply chain partners on radical innovation are quite scarce. This empirical study is among the very few to fill this void by providing an integrative assessment of customer, supplier and internal collaborations and their impact on both radical and incremental innovation.
Africa-China investment and growth link
Authors: Koomson-Abekah Isaac , Nwaba Eugene Chinweokwu 
Published: May 2018

PurposeThis paper aims to investigate China–Africa Investment link, using over two decades of FDI’s data. During the specified periods, African economic growth path has been predominantly upward trending, despite multiple external threats. This impressive growth was partly because of the growth of FDI stock across the region. This study explores the various sources of FDI to Africa, mainly China’s FDI’s and how they influence African macroeconomic indicators, i.e. unemployment, export and import activities.Design/methodology/approachPesaran autoregressive distributive lag (ARDL) is used as a framework to test the short-run and long-run relationship of indicators. Granger causality test checked the causality between growth and macroeconomic indicators.FindingsThe link between China’s FDI and African economic growth reported a negative/declining effect in both short and long run. In the long run, the effect of world FDI on growth was significant but not the in the short run. However, US FDI to Africa, China Export and Import from Africa reported an insignificant effect on growth. There was no evidence of Okun’s law, as a decrease in Africa unemployment does not increase growth. Overall, China’s FDI’s inflows to Africa are allocated to capital-intensive activities which has less labor employability. The Granger causality test reported a uni-directional link between growth and all series, except for human capital which experienced no link at all in all directions. Despite the issue of socio-infrastructure militating against growth in the region, African economy is likely to perform better, if more FDI’s are channeled into labor-intensive activities, because it has a reductive effect on unemployment.Research limitations/implicationsThe research considered point annual FDI data but not accumulated stock and is a macro-based study, i.e. regional economy.Practical implicationsThis paper bridged the literature gap in African investment performance by providing an empirical justification in understanding the inflow of FDI, especially China. This is a useful guard in policy design and implementations in the attraction of the right type of investment, so as to reduce unemployment and promote growth.Originality/valueThe authors confirm that this study has not been published elsewhere and is not under consideration in whole or in part by another journal.
Community participation in the management of palm leaf manuscripts as Lanna cultural material in Thailand
Authors: Jarusawat Piyapat , Cox Andrew , Bates Jo 
Published: May 2018

Purpose
The cultural heritage of the Lanna region of upper Northern Thailand is unique. One of its distinctive features is palm leaf manuscripts (PLMs), which are viewed simultaneously as examples of sacred writing and religious symbols, means of transferring cultural knowledge, artefacts of beauty and fragile historical documents. Local people still care about these objects, and speak the language but knowledge of the script is limited. The purpose of this paper is to explore the views of community members and experts about the value and management of PLMs as the basis for developing a model of community-based collection management.

Design/methodology/approach
Because the purpose was to explore differing perceptions and beliefs around PLMs the study adopted an interpretivist worldview. Data were collected through interviews with local people with an interest in PLMs and experts who advised on organising them. In addition, observation and a photo inventory method was used to collect data. Data were analysed thematically.

Findings
The results showed that while both groups saw the value of the knowledge PLMs contained, the community placed particular importance on the earning of “merit” through activities related to them as Buddhist objects. Experts gave particular emphasis to the knowledge of herbal medicine contained in the PLMs. The community valued indigenous storage and preservation practices. Experts were particularly pre-occupied with the intellectual property issue around medical knowledge and convenient storage and digitisation.

Research limitations/implications
Existing theory around libraries, archives and museums suggest some starting points for how community participation might be managed, but the unique circumstances of Lanna PLMs calls for a distinctive approach.

Practical implications
The paper identifies a pathway suitable to the Lanna context that can build on current local practices, to enhance community participation in the management of PLMs, including a consideration of the role of information professionals.

Originality/value
This paper is one of the first to extend thinking about participatory practices in the library, archive and museum literature to the context of Thailand and specifically to the case of PLMs, in the Lanna region. Rigorous data analysis of a substantial body of evidence has enhanced the understanding of the different types of value placed on PLMs. It identifies an important but not unbridgeable tension between how local people and experts view PLMs. It builds on previous library, archive and museum theory to propose a realistic model of how communities and experts (including librarians) can work together to protect the rich cultural resource represented by PLMs.