bluuebunny/crossref_metadata_2025_split huggingface dataset:
Numerical parameter space compression and its application to microtubule dynamic instability
Authors: Hsu Chieh-Ting (Jimmy) , Brouhard Gary J. , François Paul 
Published: November 2018

ABSTRACTPhysical models of biological systems can become difficult to interpret when they have a large number of parameters. But the models themselves actually depend on (i.e. are sensitive to) only a subset of those parameters. Rigorously identifying this subset of “stiff” parameters has been made possible by the development of parameter space compression (PSC). However, PSC has only been applied to analytically-solvable physical models. We have generalized this powerful method by developing a numerical approach to PSC that can be applied to any computational model. We validated our method against analytically-solvable models of random walk with drift and protein production and degradation. We then applied our method to an active area of biophysics research, namely to a simple computational model of microtubule dynamic instability. Such models have become increasingly complex, perhaps unnecessarily. By adding two new parameters that account for prominent structural features of microtubules, we identify one that can be “compressed away” (the “seam” in the microtubule) and another that is essential to model performance (the “tapering” of microtubule ends). Furthermore, we show that the microtubule model has an underlying, low-dimensional structure that explains the vast majority of our experimental data. We argue that numerical PSC can identify the low-dimensional structure of any computational model in biophysics. The low-dimensional structure of a model is easier to interpret and identifies the mechanisms and experiments that best characterize the system.
Mammalian SWI/SNF collaborates with a polycomb-associated protein to regulate male germ line transcription in the mouse
Authors: Menon Debashish U. , Shibata Yoichiro , Mu Weipeng , Magnuson Terry 
Published: November 2018

AbstractA deficiency in BRG1, the catalytic subunit of the SWI/SNF chromatin remodeling complex, results in a meiotic arrest during spermatogenesis. Here, we explore the causative mechanisms. BRG1 is preferentially enriched at active promoters of genes essential for spermatogonial pluripotency and meiosis. In contrast, BRG1 is also associated with the repression of somatic genes. Chromatin accessibility at these target promoters is dependent upon BRG1. These results favor a model where BRG1 coordinates spermatogenic transcription to ensure meiotic progression. In spermatocytes, BRG1 interacts with SCML2, a testes specific PRC1 factor that is associated with the repression of somatic genes. We present evidence to suggest that BRG1 and SCML2 concordantly regulate genes during meiosis. Furthermore, BRG1 is required for the proper localization of SCML2 and its associated deubiquitinase, USP7, to the sex chromosomes during pachynema. SCML2 associated, mono ubiquitination of histone H2A lysine 119 (H2AK119ub1) and acetylation of histone lysine 27 (H3K27ac) are elevated inBrg1cKOtestes. Coincidentally, the PRC1 ubiquitin ligase, RNF2 is activated while a histone H2A/H2B deubiquitinase, USP3 is repressed. Thus, BRG1 impacts the male epigenome by influencing the localization and expression of epigenetic modifiers. This mechanism highlights a novel paradigm of co-operativity between SWI/SNF and PRC1.Summary statementBRG1, a catalytic subunit of SWI/SNF chromatin remodeling complex, interacts with SCML2 (Sexcomb onmidleg-like 2), a polycomb repressive 1 (PRC1) factor, to regulate transcription during spermatogenesis. This represents a novel paradigm of SWI/SNF-PRC1 co-operation during gametogenesis.
Comprehensive analysis of miRNA and protein profiles within exosomes derived from canine lymphoid tumour cell lines
Authors: Asada Hajime , Tomiyasu Hirotaka , Uchikai Takao , Ishihara Genki , Goto-Koshino Yuko , Ohno Koichi , Tsujimoto Hajime 
Published: November 2018

AbstractExosomes are small extracellular vesicles released from almost all cell types, which play roles in cell-cell communication. Recent studies have suggested that microenvironmental crosstalk mediated by exosomes is an important factor in the escape of tumour cells from the anti-tumour immune system in human haematopoietic malignancies. Here, we conducted comprehensive analysis of the miRNA and protein profiles within the exosomes released from four canine lymphoid tumour cell lines as a model of human lymphoid tumours. The results showed that the miRNAs and proteins abundantly contained in exosomes were similar among the four cell lines. However, the profiles of miRNA within exosomes differed among the cell lines and reflected the expression pattern of miRNAs of the parent cells. In the comparison of the amounts of miRNAs and proteins among the cell lines, those of three miRNAs (miR-151, miR-8908a-3p, and miR-486) and CD82 protein differed between exosomes derived from vincristine-sensitive and resistant cell lines. Further investigations are needed to elucidate the biological functions of the exosomal contents in the microenvironmental crosstalk of lymphoid tumours.
Long read-based de novo assembly of low complex metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system
Authors: Somerville Vincent , Lutz Stefanie , Schmid Michael , Frei Daniel , Moser Aline , Irmler Stefan , Frey Jürg E. , Ahrens Christian H. 
Published: November 2018

AbstractBackgroundComplete and contiguous genome assemblies greatly improve the quality of subsequent systems-wide functional profiling studies and the ability to gain novel biological insights. While a de novo genome assembly of an isolated bacterial strain is in most cases straightforward, more informative data about co-existing bacteria as well as synergistic and antagonistic effects can be obtained from a direct analysis of microbial communities. However, the complexity of metagenomic samples represents a major challenge. While third generation sequencing technologies have been suggested to enable finished metagenome-assembled-genomes, to our knowledge, the complete genome assembly of all dominant strains in a microbiome sample has not been shown so far. Natural whey starter cultures (NWCs) are used in the production of cheese and represent low complex microbiomes. Previous studies of Swiss Gruyère and selected Italian hard cheeses, mostly based on amplicon-based metagenomics, concurred that three species generally pre-dominate: Streptococcus thermophilus, Lactobacillus helveticus and Lactobacillus delbrueckii.ResultsTwo NWCs from Swiss Gruyère producers were subjected to whole metagenome shotgun sequencing using Pacific Biosciences Sequel, Oxford Nanopore Technologies MinION and Illumina MiSeq platforms. We achieved the complete assembly of all dominant bacterial genomes from these low complex NWCs, which was corroborated by a 16S rRNA based amplicon survey. Moreover, two distinct L. helveticus strains were successfully co-assembled from the same sample. Besides bacterial genomes, we could also assemble several bacterial plasmids as well as phages and a corresponding prophage. Biologically relevant insights could be uncovered by linking the plasmids and phages to their respective host genomes using DNA methylation motifs on the plasmids and by matching prokaryotic CRISPR spacers with the corresponding protospacers on the phages. These results could only be achieved by employing third generation, long-read sequencing data able to span intragenomic as well as intergenomic repeats.ConclusionsHere, we demonstrate the feasibility of complete de novo genome assembly of all dominant strains from low complex NWC’s based on whole metagenomics shotgun sequencing data. This allowed to gain novel biological insights and is a fundamental basis for subsequent systems-wide omic analyses, functional profiling and phenotype to genotype analysis of specific microbial communities.
Ca2+-activated K+channels reduce network excitability, improving adaptability and energetics for transmitting and perceiving sensory information
Authors: Li Xiaofeng , Tayoun Ahmad Abou , Song Zhuoyi , Dau An , Rien Diana , Jaciuch David , Dongre Sidhartha , Blanchard Florence , Nikolaev Anton , Zheng Lei , Bollepalli Murali K. , Chu Brian , Hardie Roger C. , Dolph Patrick J. , Juusola Mikko 
Published: November 2018

AbstractCa2+-activated K+channels (BK and SK) are ubiquitous in synaptic circuits, but their role in network adaptation and sensory perception remains largely unknown. Using electrophysiological and behavioral assays and biophysical modelling, we discover how visual information transfer in mutants lacking the BK channel (dSlo−), SK channel (dSK−) or both (dSK−;;dSlo−) is shaped in the female fruit fly (Drosophila melanogaster) R1-R6 photoreceptor-LMC circuits (R-LMC-R system) through synaptic feedforward-feedback interactions and reduced R1-R6ShakerandShabK+conductances. This homeostatic compensation is specific for each mutant, leading to distinctive adaptive dynamics. We show how these dynamics inescapably increase the energy cost of information and promote the mutants’ distorted motion perception, determining the true price and limits of chronic homeostatic compensation in anin vivogenetic animal model. These results reveal why Ca2+-activated K+channels reduce network excitability (energetics), improving neural adaptability for transmitting and perceiving sensory information.Significance statementIn this study, we directly linkin vivoandex vivoexperiments with detailed stochastically operating biophysical models to extract new mechanistic knowledge of howDrosophilaphotoreceptor-interneuron-photoreceptor (R-LMC-R) circuitry homeostatically retains its information sampling and transmission capacity against chronic perturbations in its ion-channel composition, and what is the cost of this compensation and its impact on optomotor behavior. We anticipate that this novel approach will provide a useful template to other model organisms and computational neuroscience, in general, in dissecting fundamental mechanisms of homeostatic compensation and deepening our understanding of how biological neural networks work.
Fungal symbionts produce prostaglandin E2to promote their intestinal colonization
Authors: Tan Tze Guan , Lim Ying Shiang , Tan Alrina , Leong Royston , Pavelka Norman 
Published: November 2018

AbstractCandida albicansis a ubiquitous fungal symbiont that resides on diverse human barrier surfaces. Both mammalian and fungal cells can convert arachidonic acid into the lipid mediator, prostaglandin E2 (PGE2), but the physiological significance of fungal-derived PGE2remains elusive. Here we report that aC. albicansmutant deficient in PGE2production suffered a loss of competitive fitness in the murine gastrointestinal (GI) tract and that PGE2supplementation mitigated this fitness defect. Impaired fungal PGE2production affected neither thein vitrofitness ofC. albicansnor hyphal morphogenesis and virulence in either systemic or mucosal infection models. Fungus-derived PGE2improved intra-GI fitness ofC. albicansby diminishing the killing ofC. albicansby phagocytes. Consequently, ablation of colonic phagocytes abrogated the fitness boost conferred by fungal PGE2. These observations suggest thatC. albicanshas evolved the capacity to produce PGE2from arachidonic acid, a host-derived precursor, to promote its own colonization of the host gut. Analogous mechanisms might undergird host-microbe interactions of other symbiont fungi.Author SummaryCandida albicansis a symbiont fungus that resides in the gut of a majority of people without provoking disease. However, residentC. albicanscan bloom and turn pathogenic in a subset of individuals who are immunocompromised due to infections or chemotherapy or who suffer a disruption of their intestinal microbial community due to antibiotic use. However, the fungal and host factors that regulate the fitness ofC. albicansas a symbiont or an invasive pathogen remain poorly understood. Here we focused on the physiological role of fungus-derived prostaglandin E2 (PGE2) in the fitness ofC. albicansusing a PGE2-deficientC. albicansstrain and mouse models of infections and intestinal symbiosis. We found that fungal PGE2, contrary to previously described functions of promoting virulence, played no role in fungal pathogenicityin vivo. Instead, fungal PGE2specifically augmented the ability ofC. albicansto colonize the gut, in part by reducing fungal killing by intestinal phagocytes. Our results suggest that fungal PGE2synthetic pathways may be prophylactically targeted in individuals susceptible to invasive infections.
Power distance in India
Authors: Mathew Sagi , Taylor Greig 
Published: November 2018

PurposeThe purpose of this paper is to explore how cultural differentiation can affect the successful transplantation of lean management and production techniques from the parent country to subsidiary countries in the developing world. In particular, the focus will be on car manufacture in India and the role of hierarchy in Indian society, with reflection on how this seeps into workplace and power relations.Design/methodology/approachLean production techniques have been hailed as revolutionising modern manufacturing, particularly in the automotive sector. In developed world countries, car manufacturers have made significant gains in efficiency and productivity as a result of their implementation. However, as many of these multinational companies (MNCs) have expanded production into rapidly-developing nations to take advantage of both their market and low-labour costs, the introduction of lean production practices have met some resistance. This is because certain underpinning concepts and values of the lean system, such as team work, delegation of authority and upward communication can be considered incompatible with aspects of local culture and employees’ attitude towards work and their superiors. The analysis presented is based on a series of semi-structured interviews with managers and workers from an India-based subsidiary of a MNC car manufacturer and engagement with the existing literature.FindingsIt concludes that paternal relationships, religious values and group orientation in Indian society have a significant impact on the dynamics of the workplace and result in a brand of power distance that is specific to this national context, raising questions about the suitability of universal implementation of lean production practices.Originality/value“Power distance” has become a catch-all term for cultures with an orientation towards hierarchy and status in society. However, this categorisation masks some of the factors belying the phenomenon and intricacies relating to how it plays out in the workplace. It is simplistic to postulate that high power distance cultures might be incompatible with management approaches that decentralise authority and increase worker participation. Rather than rely on overgeneralisations, the analysis provided has attempted to deconstruct the composition of power distance in the Indian context and document systematically how features of Indian culture conflict with the principles of lean production techniques, using a case study from an Indian subsidiary of a MNC. In particular, the study finds that religion, caste and paternalism create an India-specific power distance that manifests itself in worker behaviour and workplace relationships.
Customers satisfaction by fuzzy synthetic evaluation and genetic algorithm (case study)
Authors: Nayebpour Hamid , Bokaei Mohsen Nazem 
Published: November 2018

Purpose
The purpose of this paper is to present a new technique for the determination of effective criteria weight on satisfaction using genetic algorithm and fuzzy synthetic evaluation.

Design/methodology/approach
The weight values express the relative importance of criteria. In most of research works, weight values depend heavily on expert knowledge, and customer’s perspective have not been considered. The proposed approach determines the criteria weight on satisfaction using genetic algorithm and fuzzy synthetic evaluation considering Euclidean distance between the computed overall satisfaction evaluation and the surveyed overall satisfaction evaluation.

Findings
The research findings show that different segments of customer have various needs and explain causes of various needs in customers using genetic algorithm and fuzzy synthetic evaluation.

Originality/value
The value of the paper is in it using a new approach in order to determine the weight of criteria. The main advantage of proposed approach is that it will help managers and researchers to determine the weight of criteria on satisfaction, and this process will no longer just rely on expert knowledge.
New Education beyond the school: Rosemarie Benjamin’s Theatre for Children, 1937-1957
Authors: McIntyre John Alexander 
Published: November 2018

Purpose
The purpose of this paper is to examine the work of Rosemary Benjamin’s Theatre for Children in Sydney as a compelling narrative of the New Education in Australia in the late 1930s, an historical moment when theatre for children emerged as a cultural experiment rich in educational ideas.

Design/methodology/approach
Contemporary sources and archival records are explored through several interpretive frames to develop a historical account of Benjamin’s Theatre for Children from 1937 to 1957.

Findings
Benjamin’s concept of children’s theatre was shaped by English progressive education as much as the Soviet model she extolled. She pursued her project in Sydney from 1937 because she found there a convivial European emigré community who encouraged her enterprise. They understood her Freudian ideas, which commended the use of the symbolic resources of myth and fairy tales to help children deal with difficult unconscious material. Benjamin also analysed audience reactions applying child study principles, evidence of the influence of Susan Isaacs and the New Education Fellowship. More successful as a Publicist than a Producer, Benjamin was able to mobilise support for her educational cause among performers, parents, cultural figures and educational authorities. Her contribution was to pave the way for those who would succeed with different models of theatre for children.

Originality/value
This is the first study to employ archival sources to document the history of the Theatre for Children, Sydney and address its neglect as a theatre project combining educational and theatrical values.
The Pransky interview: Dr Aaron Edsinger, CEO and cofounder at Hello Robot Inc
Authors: Pransky Joanne 
Published: November 2018

Purpose
The purpose of this paper is to present a “Q&A interview” conducted by Joanne Pransky of Industrial Robot Journal as a method to impart the combined technological, business and personal experience of a prominent, robotic industry PhD-turned entrepreneur regarding the evolution, commercialization and challenges of bringing a technological invention to market.

Design/methodology/approach
The interviewee is Dr Aaron Edsinger, a proven entrepreneur and inventor in the field of human-collaborative robotics. Dr Edsinger shares his journey that led him from developing humanoids at Rodney Brooks’ Computer Science and Artificial Intelligence Laboratory at MIT, to cofounding four companies, two of which got purchased by Google.

Findings
Dr Edsinger received a BS degree in Computer Systems Engineering from Stanford, an MS in Computer Science from the Massachusetts Institute of Technology (MIT) and a PhD in Computer Science from MIT and did post-doctorate research in the Humanoid Robotics Group at the MIT Computer Science and Artificial Intelligence Lab. He co-founded his first company Meka Robotics in 2007 and that same year, he started his second company, HStar Technologies. In 2011, he cofounded Redwood Robotics, and in 2013, he sold Meka and Redwood to Google. From 2013 to 2017, he was a Robotics Director at Google. In August of 2017, he cofounded Hello Robot Inc.

Originality/value
Dr Edsinger’s work in robotics grew out of the San Francisco robotic art scene in the 1990s. Since then, he has collaborated and built over a dozen research and artistic robot platforms and has been granted 28 patents. His world-class robotic systems encompass Dr Edsinger’s innovative research in dexterous manipulation in unstructured environments, force controlled compliant actuation, human safe robotics, integrated mechatronic engineering and the design of humanoid robots. Domo, the humanoid robot he built, was named one of Time magazine’s Best Inventions of the Year for 2007. Out of the eight robot companies Google purchased in 2013, two were cofounded by Dr Edsinger. In 2017, Dr Edsinger left Google to cofound his new company, Hello Robot Inc, a stealth mode consumer robot company.
Interactive effect of consumer affinity and consumer ethnocentrism on product trust and willingness-to-buy: a moderated-mediation model
Authors: Guo Gongxing , Tu Hongwei , Cheng Bao 
Published: November 2018

Purpose
This study aims to clarify the relationship between two plausible conflicting attitudes in cross-cultural context-consumer affinity and consumer ethnocentrism (CET) and to explore their interactive effect on product trust and willingness-to-buy.

Design/methodology/approach
A total of 392 usable responses were obtained. Previously validated scales of consumer affinity, CET, product trust and willingness-to-buy were used and showed good reliability. Hierarchical multiple regression and the bootstrapping method were conducted to test the hypotheses.

Findings
This study revealed that consumer affinity is positively associated with product trust, which in turn promotes consumers’ intention to buy products from the affinity country; CET moderates the relationship between consumer affinity and product trust; and CET also moderates the mediating effect of product trust on the relationship between consumer affinity and willingness-to-buy.

Research limitations/implications
First, this study helps to explain how consumer affinity boosts willingness-to-buy, and it reveals the type of consumers whose product trust is most notably influenced by their level of ethnocentrism. Second, this study examines the moderating effects of CET on the relationship between consumer affinity and product trust, which can help to identify the situations in which consumer affinity influences product trust most strongly. Third, this study examined the interactive effect of consumer affinity and CET on product trust and its subsequent effect on willingness-to-buy. The findings help to explain the CET’s critical role in the effect of consumer affinity by relating it to the literature of product trust and willingness-to-buy.

Practical implications
Given the crucial role that consumer affinity plays in improving consumers’ trust in and buying intention for a country’s products, governments, multinational enterprises and international marketers should strategically construct, maintain and magnify a positive national image to the world. This study’s results also clarify that consumer affinity does not conflict with CET; not only can they coexist but also they are positively related. The crucial implication is that CET is not always a barrier to purchasing foreign products.

Originality/value
Although research interest in consumer attitudinal conflict issues is increasing, the real relationship and interactive effects of plausible conflicting attitudes between consumer affinity and CET remain to be understood. This study bridges a gap between CET and willingness-to-buy by considering the boundary conditions of consumer attitudes toward a specific country (inherent in consumer affinity). Furthermore, this study is, to the best of the author’s knowledge, the first to link consumer affinity with willingness-to-buy through the mediating effect of product trust. These findings are helpful for understanding how consumer affinity positively effects willingness-to-buy.