bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gut bacterial metabolite Urolithin A (UA) mitigates Ca2+ entry in T cells by regulating miR-10a-5p
Authors: Zhang Shaqiu , Al-Maghout Tamer , Cao Hang , Pelzl Lisann , Salker Madhuri S , Cheng Anchun , Lang Florian , Singh Yogesh 
Published: January 2018

ABSTRACTThe gut microbiota influences several biological functions including immune response. Inflammatory bowel disease is favourably influenced by consumption of several dietary natural plant products such as pomegranate, walnuts and berries containing polyphenolic compounds such as ellagitannins and ellagic acid. The gut microbiota metabolises ellagic acid leading to formation of bioactive urolithins A, B, C and D. Urolithin A (UA) is the most active and effective gut metabolite and acts as a potent anti-inflammatory and anti-oxidant agent. However, how gut metabolite UA affects the function of immune cells remained incompletely understood. T cell proliferation is stimulated by store operated Ca2+ entry (SOCE) resulting from stimulation of Orai1 by STIM1/STIM2. We show here that treatment of murine CD4+ T cells with UA (10 µM, 3 days) significantly blunted SOCE in CD4+ T cells, an effect paralleled by significant downregulation of Orai1 and STIM1/2 transcript levels and protein abundance. UA treatment further increased miR-10a-5p abundance in CD4+ T cells in a dose dependent fashion. Overexpression of miR-10a-5p significantly decreased STIM1/2 and Orai1 mRNA and protein levels as well as SOCE in CD4+ T cells. UA further decreased CD4+ T cell proliferation. Thus, bacterial metabolite UA up-regulates miR-10a-5p thus interfering with Orai1/STIM1/STIM2 expression, store operated Ca2+ entry and proliferation of murine CD4+ T cells.
The chromatin modifiers SET-25 and SET-32 are required for initiation but not long-term maintenance of transgenerational epigenetic inheritance
Authors: Woodhouse Rachel , Buchmann Gabrielle , Hoe Matthew , Harney Dylan , Larance Mark , Boag Peter R. , Ashe Alyson 
Published: January 2018

SummarySome epigenetic modifications are inherited from one generation to the next, providing a potential mechanism for the inheritance of environmentally acquired traits. Transgenerational inheritance of RNA interference phenotypes in Caenorhabditis elegans provides an excellent model to study this phenomenon, and whilst studies have implicated both chromatin modifications and small RNA pathways in heritable silencing their relative contributions remain unclear. Here we demonstrate that the histone methyltransferases SET-25 and SET-32 are required for the establishment of a transgenerational silencing signal but not for long-term maintenance of this signal between subsequent generations, suggesting that transgenerational epigenetic inheritance is a multi-step process with distinct genetic requirements for establishment and maintenance of heritable silencing. Furthermore, small RNA sequencing reveals that the abundance of secondary siRNAs (thought to be the effector molecules of heritable silencing) does not correlate with silencing phenotypes. Together, our results suggest that the current mechanistic models of epigenetic inheritance are incomplete.
ClusterMine: a Knowledge-integrated Clustering Approach based on Expression Profiles of Gene Sets
Authors: Li Hong-Dong , Xu Yunpei , Zhu Xiaoshu , Liu Quan , Omenn Gilbert S. , Wang Jianxin 
Published: January 2018

ABSTRACTMotivationClustering analysis is essential for understanding complex biological data. In widely used methods such as hierarchical clustering (HC) and consensus clustering (CC), expression profiles of all genes are often used to assess similarity between samples for clustering. These methods output sample clusters, but are not able to provide information about which gene sets (functions) contribute most to the clustering. So interpretability of their results is limited. We hypothesized that integrating prior knowledge of annotated biological processes would not only achieve satisfying clustering performance but also, more importantly, enable potential biological interpretation of clusters.ResultsHere we report ClusterMine, a novel approach that identifies clusters by assessing functional similarity between samples through integrating known annotated gene sets,e.g.,in Gene Ontology. In addition to outputting cluster membership of each sample as conventional approaches do, it outputs gene sets that are most likely to contribute to the clustering, a feature facilitating biological interpretation. Using three cancer datasets, two single cell RNA-sequencing based cell differentiation datasets, one cell cycle dataset and two datasets of cells of different tissue origins, we found that ClusterMine achieved similar or better clustering performance and that top-scored gene sets prioritized by ClusterMine are biologically relevant.Implementation and availabilityClusterMine is implemented as an R package and is freely available at:www.genemine.org/clustermine.phpContactjxwang@csu.edu.cnSupplementary InformationSupplementary data are available at Bioinformatics online.
Sequence-dependent Three Interaction Site (TIS) Model for Single and Double-stranded DNA
Authors: Chakraborty Debayan , Hori Naoto , Thirumalai D. 
Published: January 2018

AbstractWe develop a robust coarse-grained model for single and double stranded DNA by representing each nucleotide by three interaction sites (TIS) located at the centers of mass of sugar, phosphate, and base. The resulting TIS model includes base-stacking, hydrogen bond, and electrostatic interactions as well as bond-stretching and bond angle potentials that account for the polymeric nature of DNA. The choices of force constants for stretching and the bending potentials were guided by a Boltzmann inversion procedure using a large representative set of DNA structures extracted from the Protein Data Bank. Some of the parameters in the stacking interactions were calculated using a learning procedure, which ensured that the experimentally measured melting temperatures of dimers are faithfully reproduced. Without any further adjustments, the calculations based on the TIS model reproduces the experimentally measured salt and sequence dependence of the size of single stranded DNA (ssDNA), as well as the persistence lengths of poly(dA) and poly(dT) chains. Interestingly, upon application of mechanical force the extension of poly(dA) exhibits a plateau, which we trace to the formation of stacked helical domains. In contrast, the force-extension curve (FEC) of poly(dT) is entropic in origin, and could be described by a standard polymer model. We also show that the persistence length of double stranded DNA, formed from two complementary ssDNAs with one hundred and thirty base pairs, is consistent with the prediction based on the worm-like chain. The persistence length, which decreases with increasing salt concentration, is in accord with the Odijk-Skolnick-Fixman theory intended for stiff polyelectrolyte chains near the rod limit. The range of applications, which did not require adjusting any parameter after the initial construction based solely on PDB structures and melting profiles of dimers, attests to the transferability and robustness of the TIS model for ssDNA and dsDNA.
Inclusive estimations of ball screw-based CNC feed drive system over positioning and pre-loading factor
Authors: Verma Kuldeep , Belokar R.M. 
Published: January 2018

Purpose
This paper aims to investigate the performance and positioning accuracy of computer numerical controlled (CNC) feed drive system using a ball screw-based pre-loading impact factor.

Design/methodology/approach
Initially, axial displacement of support bearings has been computed in relation to the different preload values. Among the computed values, a basic rule equation has been developed for the calculation of elongation in the bearings. The value of displacements computed from the developed equation has been considered as a pre-loading value, and its behavior on the feed drive system has been analyzed.

Findings
The elongation of bearings impacts the positioning accuracy and repeatability of the feed drive system and of CNC machines. Next, an analytical model for the rigorous assessment of CNC feed drive system has been designed and developed. The positioning accuracy of CNC machine in relation with different pre-loading values has been analyzed.

Practical implications
The results obtained from these investigations enhance the positioning accuracy of CNC machining centers. The optimum pre-loading value has been analyzed among the available ranges, and it has been proposed that optimal results have been achieved at 5 per cent of dynamic load rating.

Originality/value
This paper proposes improved explorations toward the performance of the CNC machines by optimizing the positioning accuracy through pre-loading. Finally, analytical estimations have been carried out to prove the validity of the proposal.
Enhancing hospital care of patients with cognitive impairment
Authors: Isaac Loretta M. , Buggy Elaine , Sharma Anita , Karberis Athena , Maddock Kim M. , Weston Kathryn M. 
Published: January 2018

Purpose
The patient-centred management of people with cognitive impairment admitted to acute health care facilities can be challenging. The TOP5 intervention utilises carers’ expert biographical and social knowledge of the patient to facilitate personalised care. The purpose of this paper is to explore whether involvement of carers in the TOP5 initiative could improve patient care and healthcare delivery.

Design/methodology/approach
A small-scale longitudinal study was undertaken in two wards of one acute teaching hospital. The wards admitted patients with cognitive impairment, aged 70 years and over, under geriatrician care. Data for patient falls, allocation of one-on-one nurses (“specials”), and length-of-stay (LOS) over 38 months, including baseline, pilot, and establishment phases, were analysed. Surveys of carers and nursing staff were undertaken.

Findings
There was a significant reduction in number of falls and number of patients allocated “specials” over the study period, but no statistically significant reduction in LOS. A downward trend in complaints related to communication issues was identified. All carers (n=43) completing the feedback survey were satisfied or very satisfied that staff supported their role as information provider. Most carers (90 per cent) felt that the initiative had a positive impact and 80 per cent felt that their loved one benefitted. Six months after implementation of the initiative, 80 per cent of nurses agreed or strongly agreed that it was now easier to relate to carers of patients with cognitive impairment. At nine-ten months, this increased to 100 per cent.

Originality/value
Actively engaging carers in management of people with cognitive impairment may improve the patient, staff, and carer journeys, and may improve outcomes for patient care and service delivery.
Antecedents and consequences of nurses’ burnout
Authors: Chen Shu-Chuan , Chen Ching-Fu 
Published: January 2018

Purpose
Healthcare is recognized as a fertile field for service research, and due to the fact that nurses are stressed physically and emotionally, reducing burnout among frontline healthcare staff is an emerging and important research issue. The purpose of this paper is to explore the possible antecedents and consequences of nurses’ burnout and to examine the moderating effects of personal trait and work-environment issue.

Design/methodology/approach
Drawing on Bagozzi’s (1992) reformulation of attitude theory (appraisal→emotional response→behavior), data from a survey of 807 nurses working in a major hospital in Taiwan were analyzed using the structural equation modeling technique and hierarchical regression analysis.

Findings
The results reveal the positive causality between job stressors and nurses’ burnout, whereas supervisor support negatively relates to burnout. In addition, the full moderating effects of leadership effectiveness and partly moderating effect of emotional intelligence on the relationships among job demands, job resources, and burnout are confirmed.

Practical implications
The findings provide practical insight regarding how supervisors play an essential role in alleviating nurses’ burnout. The supportive attitude and leadership effectiveness are recommended to be effectual managerial strategies.

Originality/value
The empirical results support the job demands-resources model by applying reformulation of attitude theory. The work-environment issue surpasses the personal trait in moderating the relationships among job demands, job resources, and burnout.
Bibliometric study on relationship of agricultural credit with farmer distress
Authors: Pandey Bhavna , Bandyopadhyay Prabir , Kadam Sanjeev , Singh Manju 
Published: January 2018

PurposeThe purpose of this paper is to provide quantitative analysis of the extant literature on farmer distress resulting from agricultural credit and identify research gaps.Design/methodology/approachThe authors have used the citation analysis which is based on the citation graph. For the current study, the authors have used SCOPUS database.FindingsThe study reveals that the farmer distress is one of the social sustainability issues which have attracted major attentions from academia. Most of the studies in recent years are from South Asian perspectives and the extant literature focusing on some of the important issues like farmer challenges and pesticide poisoning. Most of the studies provide anecdotal evidences. Hence, the empirical research is scant.Originality/valueThe study is an attempt to provide an in-depth analysis, so that future research directions can be formulated.
Skills use in the workplace and its effects on wages and on job satisfaction
Authors: Mateos Romero Lucía , Salinas-Jiménez Maria del Mar 
Published: January 2018

Purpose
The purpose of this paper is to analyze the effects of labor mismatches on wages and on job satisfaction for the Spanish case, with a distinction been made between educational and skills-related measures of mismatch.

Design/methodology/approach
The focus is placed on the usage that the individuals do of their skills in the workplace and different measures of skills use are considered to check the robustness of the results.

Findings
Using data from PIAAC, the results suggest that whereas educational mismatch shows greater effects on wages, the effects of labor mismatch on job satisfaction are better explained by the relative use of individual skills in the workplace.

Research limitations/implications
Both educational and skills mismatches are relevant for understanding the economic effects of labor mismatch. Nevertheless, it should be taken into account that educational mismatch is not an accurate proxy for skills mismatch, mainly when the non-monetary effects of labor mismatch are addressed.

Practical implications
There is room to increase workers’ skills utilization in the workplace, which, in turn, would contribute to enhance individual job satisfaction and, consequently, workers productivity.

Social implications
A process of upgrading in the Spanish labor market would allow to take full advantage of recent investments in education and skills formation done in the country in the last decades.

Originality/value
This study contributes to the literature on labor mismatch by explicitly considering that educational and skills mismatch might reflect different phenomena and by analyzing the effects of both types of mismatches on different labor market outcomes.
Psychological processes linking organizational commitment and change-supportive intentions
Authors: Straatmann Tammo , Nolte Janna K. , Seggewiss Britta J. 
Published: January 2018

Purpose
With employees’ support of organizational changes being vital for today’s organizations, the purpose of this paper is to enhance the understanding of how organizational commitment is linked to change-supportive intentions. Based on the theory of planned behavior (TPB, Ajzen, 1991), mediated effects of affective organizational commitment were empirically tested to explore the underlying psychological processes.

Design/methodology/approach
The study was conducted in the context of a complex change process at a production facility of a large international manufacturing company (n=667). Data from the change survey were analyzed employing Hayes’ (2012) PROCESS macro.

Findings
The results showed that organizational commitment relates to change-supportive intentions directly and, as suggested by the TPB, its effects are mediated via change-related attitudes, subjective norms, and perceived behavioral control. Furthermore, results suggest additional effects of change recipients’ age and occupational status.

Practical implications
Employing the TPB offers specific insights for tailored interventions to create conditions facilitating organizational changes. The results indicate that commitment lays the ground for employees’ change reactions. Moreover, the psychological processes suggested by the TPB serve as additional levers for explaining change-supportive intentions.

Originality/value
The study provides valuable information on the relationship between commitment and change-supportive intentions. Specifically, affective organizational commitment is shown to be an important resource in times of change, as it relates to more positive psychological reactions to change.
Hunger mediates apex predator's risk avoidance response in wildland–urban interface
Authors: Blecha Kevin A. , Boone Randall B. , Alldredge Mathew W. 
Published: January 2018

Abstract

Conflicts between large mammalian predators and humans present a challenge to conservation efforts, as these events drive human attitudes and policies concerning predator species. Unfortunately, generalities portrayed in many empirical carnivore landscape selection studies do not provide an explanation for a predator's occasional use of residential development preceding a carnivore–human conflict event. In some cases, predators may perceive residential development as a risk–reward trade‐off.

We examine whether state‐dependent mortality risk‐sensitive foraging can explain an apex carnivore's (Puma concolor) occasional utilization of residential areas. We assess whether puma balance the risk and rewards in a system characterized by a gradient of housing densities ranging from wildland to suburban. Puma GPS location data, characterized as hunting and feeding locations, were used to assess landscape variables governing hunting success and hunting site selection. Hunting site selection behaviour was then analysed conditional on indicators of hunger state.

Residential development provided a high energetic reward to puma based on increases in prey availability and hunting success rates associated with increased housing density. Despite a higher energetic reward, hunting site selection analysis indicated that pumas generally avoided residential development, a landscape type attributed with higher puma mortality risk. However, when a puma experienced periods of extended hunger, risk avoidance behaviour towards housing waned.

This study demonstrates that an apex carnivore faces a trade‐off between acquiring energetic rewards and avoiding risks associated with human housing. Periods of hunger can help explain an apex predator's occasional use of developed landscapes and thus the rare conflicts in the wildland–urban interface. Apex carnivore movement behaviours in relation to human conflicts are best understood as a three‐player community‐level interaction incorporating wild prey distribution.
Pulsed flows, tributary inputs and food‐web structure in a highly regulated river
Authors: Sabo John L. , Caron Melanie , Doucett Rick , Dibble Kimberly L. , Ruhi Albert , Marks Jane C. , Hungate Bruce A. , Kennedy Ted A. 
Published: January 2018

Abstract

Dams disrupt the river continuum, altering hydrology, biodiversity and energy flow. Although research indicates that tributary inputs have the potential to dilute these effects, knowledge at the food‐web level is still scarce.

Here, we examined the riverine food‐web structure of the Colorado River below Glen Canyon Dam, focusing on organic matter sources, trophic diversity and food chain length. We asked how these components respond to pulsed flows from tributaries following monsoon thunderstorms that seasonally increase streamflow in the American Southwest.

Tributaries increased the relative importance of terrestrial organic matter, particularly during the wet season below junctures of key tributaries. This contrasted with the algal‐based food‐web present immediately below Glen Canyon Dam.

Tributary inputs during the monsoon also increased trophic diversity and food chain length: food chain length peaked below the confluence with the largest tributary (by discharge) in Grand Canyon, increasing by >1 trophic level over a 4–5 km reach possibly due to aquatic prey being flushed into the mainstem during heavy rain events.

Our results illustrate that large tributaries can create seasonal discontinuities, influencing riverine food‐web structure in terms of allochthony, food‐web diversity and food chain length.

Synthesis and applications. Pulsed flows from unregulated tributaries following seasonal monsoon rains increase the importance of terrestrially derived organic matter in large, regulated river food webs, increasing food chain length and trophic diversity downstream of tributary inputs. Protecting unregulated tributaries within hydropower cascades may be important if we are to mitigate food‐web structure alteration due to flow regulation by large dams. This is critical in the light of global hydropower development, especially in megadiverse, developing countries where dam placement (including completed and planned structures) is in tributaries.