bluuebunny/crossref_metadata_2025_split huggingface dataset:
Varying crosslinking motifs drive the mesoscale mechanics of actin-microtubule composites
Authors: Ricketts Shea N. , Francis Madison L. , Farhadi Leila , Rust Michael J. , Das Moumita , Ross Jennifer L. , Robertson-Anderson Rae M. 
Published: February 2019

AbstractThe cytoskeleton dynamically tunes its mechanical properties by altering the interactions between semiflexible actin filaments, rigid microtubules, and crosslinking proteins. Here, we use optical tweezers microrheology and confocal microscopy to characterize how varying crosslinking motifs impact the microscopic and mesoscale mechanics and mobility of actin-microtubule composites. We show that, upon subtle changes in the crosslinking pattern, composites separate into two distinct classes of force response – primarily elastic versus more viscous behavior. For example, a composite in which actin and microtubules are crosslinked to each other is markedly more elastic than one in which both filaments are crosslinked but cannot link together. Notably, this distinction only emerges at mesoscopic scales in response to nonlinear forcing, whereas varying crosslinking motifs have little impact on the microscale mechanics and steady-state mobility of composites. Our unexpected scale-dependent results not only inform the physics underlying key cytoskeleton processes and structures, but, more generally, provide valuable perspective to materials engineering endeavors focused on polymer composites.
Temperature-dependent changes to host-parasite interactions alter the thermal performance of a bacterial host
Authors: Padfield Daniel , Castledine Meaghan , Buckling Angus 
Published: February 2019

AbstractThermal performance curves (TPCs) are used to predict changes in species interactions, and hence range shifts, disease dynamics and community composition, under forecasted climate change. Species interactions might in turn affect TPCs. Here, we investigate whether temperature-dependent changes in a microbial host-parasite interaction (the bacteriumPseudomonas fluorescens, and its bacteriophage, SBWФ2) changes the host TPC. The bacteriophage had a narrower infectivity range, with their critical thermal maximum ∼6°C lower than those at which the bacteria still had high growth. Consequently, in the presence of phage, the host TPC had a higher optimum temperature and a lower maximum growth rate. These changes were driven by a temperature-dependent evolution, and cost, of resistance; the largest cost of resistance occurring where bacteria grew best in the absence of phage. Our work highlights how ecological and evolutionary mechanisms can alter the effect of a parasite on host thermal performance, even over very short timescales.Data accessibility statementAll data and R code used in the analysis will be made available on GitHub and archived on Zenodo.
The inducible response of the nematodeCaenorhabditis elegansto members of its natural microbiome across development and adult life
Authors: Yang W , Petersen C , Pees B , Zimmermann J , Waschina S , Dirksen P , Rosenstiel P , Tholey A , Leippe M , Dierking K , Kaleta C , Schulenburg H 
Published: February 2019

AbstractThe biology of all organisms is influenced by the associated community of microorganisms. In spite of its importance, it is usually not well understood how exactly this microbiome affects host functions and what are the underlying molecular processes. To rectify this knowledge gap, we took advantage of the nematodeC. elegansas a tractable, experimental model system and assessed the inducible transcriptome response after colonization with members of its native microbiome. For this study, we focused on two isolates of the genusOchrobactrum. These bacteria are known to be abundant in the nematode’s microbiome and are capable of colonizing and persisting in the nematode gut, even under stressful conditions. The transcriptome response was assessed across development and three time points of adult life, using general andC. elegans-specific enrichment analyses to identify affected functions. Our assessment revealed an influence of the microbiome members on the nematode’s dietary response, development, fertility, immunity, and energy metabolism. This response is mainly regulated by a GATA transcription factor, most likely ELT-2, as indicated by the enrichment of (i) the GATA motif in the promoter regions of inducible genes and (ii) of ELT-2 targets among the differentially expressed genes. We compared our transcriptome results with a corresponding previously characterized proteome data set, highlighting a significant overlap in the differentially expressed genes and the affected functions. Our analysis further identified a core set of 86 genes that consistently responded to the microbiome members across development and adult life, including several C-type lectin-like genes and genes known to be involved in energy metabolism or fertility. We additionally assessed the consequences of induced gene expression with the help of metabolic network model analysis, using a previously established metabolic network forC. elegans. This analysis complemented the enrichment analyses by revealing an influence of theOchrobactrumisolates onC. elegansenergy metabolism and furthermore metabolism of specific amino acids, fatty acids, and also folate biosynthesis. Our findings highlight the multifaceted impact of naturally colonizing microbiome isolates onC. eleganslife history and thereby provide a framework for further analysis of microbiome-mediated host functions.
Biologically indeterminate yet ordered promiscuous gene expression in single medullary thymic epithelial cells
Authors: Dhalla F. , Baran-Gale J. , Maio S. , Chappell L. , Holländer G. , Ponting C.P. 
Published: February 2019

AbstractDuring thymic negative selection, medullary thymic epithelial cells (mTEC) collectively express most protein coding genes, a process termed promiscuous gene expression (PGE). Although PGE is crucial for inducing central T-cell tolerance, this process has not been established definitively as being either stochastic or coordinated. To resolve this question, we sequenced the transcriptomes of 6,894 single mTEC, including 1,795 rare cells expressing either of two tissue-restricted antigens, TSPAN8 or GP2. Transcriptional heterogeneity allowed partitioning of mTEC into 15 robustly-defined subpopulations representing distinct maturational stages and subtypes. Although 50 gene co-expression groups were robustly identified, few could be explained by chromosomal location, biological pathway, or tissue specificity. Further, GP2+ mTEC were randomly dispersed spatially within medullary islands. Thus although PGE exhibits ordered co-expression, biologically it is indeterminate. This likely enhances the presentation of diverse antigens to passing thymocytes during their medullary residency, while simultaneously maintaining mTEC identity throughout PGE.
The oncoprotein DEK affects the outcome of PARP1/2 inhibition during replication stress
Authors: Ganz Magdalena , Vogel Christopher , Czada Christina , Jörke Vera , Kleiner Rebecca , Pierzynska-Mach Agnieszka , Zanacchi Francesca Cella , Diaspro Alberto , Kappes Ferdinand , Bürkle Alexander , Ferrando-May Elisa 
Published: February 2019

ABSTRACTDNA replication stress is a major source of genomic instability and is closely linked to tumor formation and progression. Poly(ADP-ribose)polymerases1/2 (PARP1/2) enzymes are activated in response to replication stress resulting in poly(ADP-ribose) (PAR) synthesis. PARylation plays an important role in the remodelling and repair of impaired replication forks, providing a rationale for targeting highly replicative cancer cells with PARP1/2 inhibitors. The human oncoprotein DEK is a unique, non-histone chromatin architectural protein whose deregulated expression is associated with the development of a wide variety of human cancers. Recently, we showed that DEK is a high-affinity target of PARylation and that it promotes the progression of impaired replication forks. Here, we investigated a potential functional link between PAR and DEK in the context of replication stress. Under conditions of mild replication stress induced either by topoisomerase1 inhibition with camptothecin or nucleotide depletion by hydroxyurea, we found that the effect of acute PARP1/2 inhibition on replication fork progression is dependent on DEK expression. Reducing DEK protein levels also overcomes the restart impairment of stalled forks provoked by blocking PARylation. Non-covalent DEK-PAR interaction via the central PAR-binding domain of DEK is crucial for counteracting PARP1/2 inhibition as shown for the formation of RPA positive foci in hydroxyurea treated cells. Finally, we show by iPOND and super resolved microscopy that DEK is not directly associated with the replisome since it binds to DNA at the stage of chromatin formation. Our report sheds new light on the still enigmatic molecular functions of DEK and suggests that DEK expression levels may influence the sensitivity of cancer cells to PARP1/2 inhibitors.
Prey abundance drives habitat occupancy by jaguars in Amazonian floodplain river islands
Authors: Rabelo Rafael M. , Aragón Susan , Bicca-Marques Júlio César 
Published: February 2019

AbstractThe jaguar (Panthera onca) is widely distributed across a broad range of habitat types, where its feeding habits and habitat use patterns vary significantly. The jaguar and its main arboreal prey – the brown-throated sloth (Bradypus variegatus) and the red howler monkey (Alouatta juara) – are widespread in the Amazonian floodplain forests of the Mamirauá Reserve. These forest-dwelling species are the most common mammal species both in the continuous forest and the forest patches surrounded by a river matrix – the fluvial islands – of the Solimões and Japurá rivers. We used sign surveys along line-transects to assess the pattern of habitat occupancy by jaguars in Amazonian floodplain forests. Specifically, we (i) tested whether habitat occupancy by jaguars differs between river islands and continuous forest; and (ii) evaluated whether and how the local abundance of sloths and howler monkeys influence the probability of site occupancy by jaguars. We built an occupancy model and used Bayesian inference to reach these goals. The proportion of sites estimated to be used by jaguars wasψ= 0.75 (HPD95: 0.36–1.00), and it did not differ between islands and continuous forest. The abundance of both prey species had a direct influence on jaguar’s habitat use, whereas the aquatic matrix seems to have a negligible effect on the use of islands by jaguars. We conclude that the isolation of the river islands within the aquatic matrix does not hamper jaguars to use them. We also conclude that prey search modulates jaguars’ habitat occupancy patterns with both prey species having a similar effect. This finding is compatible with the previously reported importance of sloths to the diet of jaguars in the study region despite its lower abundance than howlers. Finally, we suggest that sign surveys are an alternative method to assess the pattern of jaguar habitat occupancy in floodplain forests.
Immunohistochemical and ultrastructural analysis of the maturing larval zebrafish enteric nervous system reveals the formation of a neuropil pattern
Authors: Baker Phillip A. , Meyer Matthew D. , Tsang Ashley , Uribe Rosa A. 
Published: February 2019

AbstractThe gastrointestinal tract is constructed with an intrinsic series of interconnected ganglia that span its entire length, called the enteric nervous system (ENS). The ENS exerts critical local reflex control over many essential gut functions; including peristalsis, water balance, hormone secretions and intestinal barrier homeostasis. ENS ganglia exist as a collection of neurons and glia that are arranged in a series of plexuses throughout the gut: the myenteric plexus and submucosal plexus. While it is known that enteric ganglia are derived from a stem cell population called the neural crest, mechanisms that dictate final neuropil plexus organization remain obscure. Recently, the vertebrate animal, zebrafish, has emerged as a useful model to understand ENS development, however knowledge of its developing myenteric plexus architecture was unknown. Here, we examine myenteric plexus of the maturing zebrafish larval fish histologically over time and find that it consists of a series of tight axon layers and long glial cell processes that wrap the circumference of the gut tube to completely encapsulate it, along all levels of the gut. By late larval stages, complexity of the myenteric plexus increases such that a layer of axons is juxtaposed to concentric layers of glial cells. Ultrastructurally, glial cells contain glial filaments and make intimate contacts with one another in long, thread-like projections. Conserved indicators of vesicular axon profiles are readily abundant throughout the larval plexus neuropil. Together, these data extend our understanding of myenteric plexus architecture in maturing zebrafish, thereby enabling functional studies of its formation in the future.
Biological Process Activity Transformation of Single Cell Gene Expression for Cross-Species Alignment
Authors: Ding Hongxu , Blair Andrew , Yang Ying , Stuart Joshua M. 
Published: February 2019

ABSTRACTThe maintenance and transition of cellular states are controlled by biological processes. Here we present a gene set-based transformation of single cell RNA-Seq data into biological process activities that provides a robust description of cellular states. Moreover, as these activities represent species-independent descriptors, they facilitate the alignment of single cell states across different organisms.
Dyadic alignment in capital goods companies
Authors: Moori Roberto Giro , Nafal Kalid A. , Kimura Herbert , Sobreiro Vinicius Amorim 
Published: February 2019

PurposeThe purpose of this paper is to identify the main factors of the dyadic alignment in the supply chain of capital goods companies.Design/methodology/approachA survey was conducted among 159 respondents (53 supplier companies, 53 manufacturers and 53 clients).FindingsUsing structural equation modelling, no evidence of alignment between suppliers and manufacturers was identified. However, for the manufacturers, there is a partial mediation effect of the operational capabilities in the relationship between supply chain management and business performance.Originality/valueThis research investigates whether there is a dyadic alignment among supplier–manufacturer, manufacturer–customer and supplier–customer from the capital goods manufacturers’ perspective.
Impacts of Lean Six Sigma on improving a higher education system: a case study
Authors: Haerizadeh Milad , Sunder M. Vijaya 
Published: February 2019

Purpose
The purpose of this paper is to demonstrate the applicability and impact of Lean Six Sigma (LSS), a contemporary quality excellence methodology, for improving education system in a reputed University in Iran.

Design/methodology/approach
The paper follows a case study approach illustrating how theory has been put into practice, explaining how to implement the LSS define-measure-analyze-improve-control framework in a field-setting in a higher education institution (HEI), and to highlight the subsequent challenges occurred and lessons learned during the implementation.

Findings
The key finding from the study is the confirmation of LSS applicability in education systems. The goals of the LSS team were to baseline student satisfaction levels and improve the overall rating by 10 percent; to decrease student advising wait times by 15 percent; and increase enrollment by 5 percent. The application of the LSS methodology has delivered promising results to improve the education system of the University by achieving the set goals. Further, the implementation of LSS has demonstrated student-facing benefits of improved quality on the education system.

Research limitations/implications
LSS implementation in HEIs is relatively a new topic for research. Hence, this case study adds to the body of knowledge with directions to progress future research in this area.

Practical implications
The outputs of the case study have provided greater stimulus within the facilities for wider full-blown deployment of LSS as a strategic resource for problem solving. Additionally, this case study sets the foundation for many other future projects, and to trigger interest among the HEIs in their journeys for quality excellence.

Social implications
Higher education sector being a socially responsible field of service, LSS offers continuous improvement benefits, highlighted as part of this paper.

Originality/value
The applicability of LSS in HEIs is relatively an upcoming research area with immense potential and value. This paper would serve as a valuable means for both researchers and practitioners working in HEIs, in terms of understanding the systematic application of the LSS methodology, and implications in a real-world situation.
Viewpoint: CPS guidance on prosecuting rape and sexual assault cases
Authors: Foley Marian , Cummins Ian 
Published: February 2019

PurposeThe purpose of this paper is to highlight concerns about recent CPS guidance on the prosecution of rape and sexual assault cases.Design/methodology/approachThe paper places the CPS guidance in the wider policy context of concerns about sexual violence on mental health wards.FindingsThe paper concludes that the reported CPS guidance appears to run counter to other policy directives particularly the recent report from the CQC.Originality/valueThe paper is a first response to these issues.
Antecedents of supplier selection decisions in the public sector in Nigeria
Authors: Essien Eyo , Lodorfos George , Kostopoulos Ioannis 
Published: February 2019

PurposeThis paper aims to develop and test a conceptual model of supplier selection decisions in the public sector. The study seeks to determine the relative importance of a broad range of non-economic variables in explaining supplier selection decisions during strategic organizational purchases.Design/methodology/approachData were collected from a national sample of 341 senior staff and top management team (TMT) members in 40 public sector organizations in Nigeria by using structured questionnaires.FindingsResults of structural equation modeling (SEM) analysis shows that government policy requirements, social ties of organizational actors, party politics, decision-makers’ experience and the perception of instrumental ethical work climates are the most important determinants of strategic supplier selection decisions, followed in a descending order of importance by the perception of rules ethical work climates, self-enhancement personal values, CEOs’ structural position, self-transcendent personal values and the perception of time pressure. Findings also indicate that the choice of a supplier per se is not an important determinant of organizational performance.Originality/valueNo prior study has brought together, in a single model, the broad range of variables employed in this study with a view to exploring their relative importance in explaining public sector supplier selection decisions in a non-western country context. The findings of this study have implications for Marketing Managers looking to do business with public sector firms in emerging markets.
An empirical framework for soft CSFs of TQM in Chinese manufacturing companies
Authors: Yan Jianwen , Zhang Kexin , Zhu Weiwei , Fan Yu 
Published: February 2019

Purpose
The purpose of this paper is to frame an empirical model with the priority of implementing soft critical successful factors (CSFs) of total quality management (TQM) in Chinese manufacturing companies.

Design/methodology/approach
In total, 23 hypotheses regarding the relationships among TQM factors and business results have been developed through literature review and are tested using the structural equation modelling (SEM). The data used in this study are collected from 228 manufacturing companies in the central area of China.

Findings
Of the 23 hypotheses, 11 were statistically significant, and according to the empirical results a conceptual framework complying to Chinese condition is constructed and discussed in the finding parts to group soft CSFs of TQM into different levels of importance.

Research limitations/implications
Researchers can use the framework to further study soft CSFs of TQM in detail, and extend it to explore their impact mechanism for a clearer and deeper understanding of the TQM.

Practical implications
The empirical framework for soft CSFs of TQM provides a new perspective for managers to implement the soft CSFs and optimise the quality management system of their manufacturing companies.

Originality/value
This research uses multiple, distinct indicators for each soft factor to test an elaborate SEM model of the relationships among them, according to the empirical results constructs a holistic framework classifying the importance level of soft CSFs of TQM, which is novel and subjected with Chinese condition and manufacturing characteristics.
Issues and challenges in implementing the Skill India movement
Authors: De Debpriya 
Published: February 2019

Purpose
The purpose of this paper is to discuss the issues and challenges that become a hurdle towards implementation of the “Skill India Movement” at the ground level. It is critical to identify the challenges that are faced or experienced by training partners with the National Skill Development Corporation (NSDC), skills councils and other bodies if an effort to resolve the same is to be made.

Design/methodology/approach
A round-table discussion was organised to seek feedback from all the stakeholders who are directly or indirectly involved in strategising, decision-making and implementing the government’s skills initiative. The primary data were collected through discussions and questionnaires, and the official sites of NSDC and Pradhan Mantri Kaushal Vikas Yojna, along with ministry reports, were referred to as well.

Findings
The research is likely to identify gaps in administration of the initiative at various levels and will hopefully provide guidance on removing bottlenecks to achieve effective implementation. It is imperative that the challenges be understood and solutions found, with focus on a long-term sustainable approach, rather than short-term gains for political propaganda purposes alone.

Practical implications
This paper will try to bring value to the stakeholders by exploring the various measures that can be taken to take this mission in a more meaningful direction and work towards giving more employability to the youth and supporting the respective industry segments with much needed trained manpower.

Originality/value
This study discusses the issues and challenges that are impeding effective implementation of the Skill India initiative at the local level and identifies the gaps in administration. Also, it outlines how bottlenecks could be addressed to ensure that the mission is back on track and that the employability of youth is enhanced.