bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimization of subsampling, decontamination, and DNA extraction of difficult peat and silt permafrost samples
Authors: Saidi-Mehrabad Alireza , Neuberger Patrick , Cavaco Maria , Froese Duane , Lanoil Brian 
Published: January 2020

ABSTRACTThis study aims to act as a methodological guide for contamination monitoring, decontamination, and DNA extraction for peaty and silty permafrost samples with low biomass or difficult to extract DNA. We applied a biological tracer, either only in the field or both in the field and in the lab, via either spraying or painting. Spraying in the field followed by painting in the lab resulted in a uniform layer of the tracer on the core sections. A combination of bleaching, washing, and scraping resulted in complete removal of the tracer leaving sufficient material for DNA extraction, while other widely used decontamination methods did not remove all detectable tracer. In addition, of four widely used commercially available DNA extraction kits, only a modified ZymoBIOMICS™ DNA Microprep kit was able to acquire PCR amplifiable DNA. Permafrost chemical parameters, age, and soil texture did not have an effect on decontamination efficacy; however, the permafrost type did influence DNA extraction. Based on these findings, we developed recommendations for permafrost microbiologists to acquire contaminant-free DNA from permafrost with low biomass.IMPORTANCEPermafrost has the capacity to preserve microbial and non-microbial genomic material for millennia; however, major challenges are associated with permafrost samples, including decontamination of samples and acquiring pure DNA. Contamination of samples during coring and post coring handling and processing could affect downstream analyses and interpretations. Despite the use of multiple different decontamination and DNA extraction methods in studies of permafrost, the efficacy of these methods is not well known. We used a biological tracer to test the efficacy of previously published decontamination methods, as well as a bleach-based method we devised, on two chemically and structurally different permafrost core sections. Our method was the only one that removed all detectable tracer. In addition, we tested multiple DNA extraction kits and modified one that is able to acquire pure, PCR amplifiable DNA from silty, and to some extent from peaty, permafrost samples.
ERCC1-XPF Interacts with Topoisomerase IIβ to Facilitate the Repair of Activity-induced DNA Breaks
Authors: Chatzinikolaou Georgia , Stratigi Kalliopi , Agathangelou Kyriacos , Tsekrekou Maria , Goulielmaki Evi , Chatzidoukaki Ourania , Gkirtzimanaki Katerina , Aid-Pavlidis Tamara , Aivaliotis Michalis , Pavlidis Pavlos , Tsamardinos Ioannis , Topalis Pantelis , Bouwman Britta A. M. , Crosetto Nicola , Altmüller Janine , Garinis George A. 
Published: January 2020

AbstractType II DNA Topoisomerases (TOP II) generate transient double-strand DNA breaks (DSBs) to resolve topological constraints during transcription. Using genome-wide mapping of DSBs and functional genomics approaches, we show that, in the absence of exogenous genotoxic stress, transcription leads to DSB accumulation and to the recruitment of the structure-specific ERCC1-XPF endonuclease on active gene promoters. Instead, we find that the complex is released from regulatory or gene body elements in UV-irradiated cells. Abrogation of ERCC1 or re-ligation blockage of TOP II-mediated DSBs aggravates the accumulation of transcription-associated γH2Ax and 53BP1 foci, which dissolve when TOP II-mediated DNA cleavage is inhibited. Anin vivobiotinylation tagging strategy coupled to a high-throughput proteomics approach reveals that ERCC1-XPF interacts with TOP IIβ and the CTCF/cohesin complex, which co-localize with the heterodimer on DSBs. Together; our findings provide a rational explanation for the remarkable clinical heterogeneity seen in human disorders with ERCC1-XPF defects.
Using systems medicine to identify a therapeutic agent with potential for repurposing in Inflammatory Bowel Disease
Authors: Lloyd Katie , Papoutsopoulou Stamatia , Smith Emily , Stegmaier Philip , Bergey Francois , Morris Lorna , Kittner Madeleine , England Hazel , Spiller Dave , White Mike HR , Duckworth Carrie A , Campbell Barry J , Poroikov Vladimir , dos Santos Vitor AP Martins , Kel Alexander , Muller Werner , Pritchard D Mark , Probert Chris , Burkitt Michael D ,   the SysmedIBD consortium
Published: January 2020

AbstractObjectiveInflammatory bowel diseases cause significant morbidity and mortality. Aberrant NF-κB signalling is strongly associated with these conditions, and several established drugs influence the NF-κB signalling network to exert their effect. This study aimed to identify drugs which alter NF-κB signalling and may be repositioned for use in inflammatory bowel disease.DesignThe SysmedIBD consortium established a novel drug-repurposing pipeline based on a combination of in-silico drug discovery and biological assays targeted at demonstrating an impact on NF-kappaB signalling, and a murine model of IBD.ResultsThe drug discovery algorithm identified several drugs already established in IBD, including corticosteroids. The highest-ranked drug was the macrolide antibiotic Clarithromycin, which has previously been reported to have anti-inflammatory effects in aseptic conditions.Clarithromycin’s effects were validated in several experiments: it influenced NF-κB mediated transcription in murine peritoneal macrophages and intestinal enteroids; it suppressed NF-κB protein shuttling in murine reporter enteroids; it suppressed NF-κB (p65) DNA binding in the small intestine of mice exposed to LPS, and it reduced the severity of dextran sulphate sodium-induced colitis in C57BL/6 mice. Clarithromycin also suppressed NF-κB (p65) nuclear translocation in human intestinal enteroids.ConclusionsThese findings demonstrate that in-silico drug repositioning algorithms can viably be allied to laboratory validation assays in the context of inflammatory bowel disease; and that further clinical assessment of clarithromycin in the management of inflammatory bowel disease is required.
Benchmarking logistics facilities: a rating model to assess building quality and functionality
Authors: Baglio Martina , Perotti Sara , Dallari Fabrizio , Garagiola Elisabetta Rachele 
Published: January 2020

PurposeLogistics real estate has been experiencing a recent rebirth led by the growth of retailing and e-commerce. Although these sectors are looking for facilities matching their logistics needs, the identification of the most suitable building becomes a challenging task. To date, from both the practitioner’s and academic perspectives there is a lack of models for assessing the quality of logistics facilities together with functionality (i.e. whether a warehouse is suitable for hosting a given logistics activity). The purpose of this paper is to fill this gap by developing a rating model for assessing the quality and functionality of logistics facilities.Design/methodology/approachA three-pronged methodology was adopted. First, a Systematic Literature Network Analysis (SLNA) was carried out to identify the relevant features that must be taken into consideration when assessing logistics real estate. Second, a Delphi method involving experts in the field was used to fine-tune the list of features that emerged from the SLNA process and to evaluate the importance of each feature from a company perspective. The rating model was developed and validated through pilot tests on 27 logistics facilities.FindingsThe rating model is divided into four sections: location, technical specifications, external spaces and internal areas. As an output, the model determines the building quality and main functionality, together with a gap analysis to detect the weakest emerging elements.Originality/valueThis research fills an identified research gap in the logistics real estate literature. Specifically, it offers a quantitative and shared evaluation method, which can be used to estimate building quality and functionality, thus extending the scope of the previous assessment methods available.
How host-country nationals manage the demands of hosting expatriates
Authors: Fee Anthony 
Published: January 2020

Purpose
Using job demands-resources (JD-R) theory as a conceptual apparatus, the purpose of this paper is to report an empirical exploration of the experiences of host-country national (HCN) employees when their organization hosts an expatriate assignment.

Design/methodology/approach
Semi-structured interviews were conducted with 23 Vietnamese HCNs who had vast experience hosting multiple self-initiated expatriates with organizational development objectives.

Findings
The study reveals previously hidden costs associated with locals’ support for expatriates, including a range of extra-role demands and more complex and stressful interpersonal interactions. These demands exceeded the current intercultural capabilities of many respondents, and while offset to some extent by their positive pre-arrival attitudes and culture-specific knowledge, led to sometimes counterproductive coping responses such as withdrawal behaviors.

Research limitations/implications
The study extends the JD-R framework by explicating which demands and resources are pertinent to HCNs, and how these activate particular coping strategies. The cultural context of Vietnam, as both a setting for the workplace interactions and imbued in the values and assumptions of respondents, limits the study’s transferability.

Practical implications
The findings provide guideposts for organizations in ways to offset HCNs’ hindrance demands (e.g. matching demands to current capabilities) and to encourage the use of productive coping strategies via, for instance, anticipating and mitigating potential challenges.

Originality/value
The study’s insights go some way toward articulating more fully the richness and complexity of HCNs’ experiences, and a more rounded perspective of the costs and benefits inherent in international work assignments.
Clinicians’ perceptions of telephone-delivered mental health services
Authors: Mercado Micaela , Little Virna 
Published: January 2020

Purpose
The adoption of telephone-delivered mental health services (TDMHS) for scaling collaborative care or addressing access to mental health services in routine primary care practice is gradual despite the needs of the population. Although there are multi-level factors associated with efficient implementation of collaborative care, there is limited understanding of clinicians’ perceptions, experiences and acceptability providing mental health treatment exclusively over the telephone. The purpose of this paper is to explore behavioral health clinicians’ delivery of mental health services over the telephone within primary care settings.

Design/methodology/approach
This qualitative study explored behavioral health professionals’ perceptions and experiences providing remote, TDMHS. Convenience sampling was used to recruit 11 clinicians in New York, California and Arizona who provided collaborative care services to patients exclusively over the telephone. Semi-structured interviews were conducted, and analyzed using qualitative content analysis methods.

Findings
Three main themes and associated subthemes emerged from the analyses. The first theme was participants’ perceptions of TDMHS prior to implementation relating to patient characteristics, patient engagement and comparison to in-person therapy. The second main theme identified was participants’ experiences implementing TDMHS with subthemes relating to benefits, quality of care, gaps in care and concerns implementing TDMHS. The final theme that emerged from the analysis was participants’ perceived acceptability of TDMHS by patients.

Research limitations/implications
The small sample size limits the generalizability of these findings.

Practical implications
Mental health services delivered over the telephone are perceived as feasible and acceptable by behavioral health clinicians.

Originality/value
This study contributes to gaps in research about behavioral health clinicians’ beliefs, uptake and acceptability toward mental health services delivered exclusively over the telephone.
Analysis of the original influencing factors and secondary influencing factors of academic papers
Authors: Zhao Rongying , Bo Yu 
Published: January 2020

Purpose
The influencing factors of academic papers have always been the focus of attention in the field of Scientometrics. Exploring the influencing factors of altmetrics indicators and traditional literature indicators on academic papers is beneficial to better explore the potential significance and value of academic papers in the evaluation of scientific research. The paper aims to discuss these issues.

Design/methodology/approach
Based on the latest JCR citation report, this paper selects 22 academic journals in the JIF Quartile Q1 journal of Information Science and Library Science, and then obtains the evaluation data of these journal papers from WOS database and Altmetric.com. This paper uses literature measurement, correlation analysis and regression analysis to explore the influencing factors of the paper.

Findings
The results show that the original influencing factors of academic papers have a significant impact on secondary influencing factors. What is more obvious is that the number of references (nr) presents a significant positive correlation with the total number of times (Z9), the number of uses (U1) and (U2).

Originality/value
This paper combines traditional literature indicators with Altmetrics indicators to study the influencing factors through primary influencing factors and secondary influencing factors. Through research, it denies the phenomenon that academic circles have published academic papers in the world in recent years to overemphasize certain factors to improve the influence of the paper.
Assessment of proteolysis in ultra‐high temperature milk using attenuated total reflectance–Fourier transform infrared spectroscopy
Authors: Ranvir Suvartan , Sharma Rajan , Gandhi Kamal , Upadhyay Neelam , Mann Bimlesh 
Published: January 2020

This study investigated the suitability of attenuated total reflectance–Fourier transform infrared spectroscopy (ATR‐FTIR) as an alternative technique to assess proteolysis in ultra‐high temperature (UHT) milk. Commercial UHT milk samples were stored (5 and 30 °C) and analysed for four months. Milk samples were treated with acetic acid and trichloroacetic acid to obtain milk extracts containing peptides. The concentrated extracts were subjected to ATR‐FTIR, and the spectrum was obtained. Results were compared with techniques like high‐performance liquid chromatography, fluorescamine and 2,4,6‐trinitrobenzenesulphonic acid. The present study indicated that ATR‐FTIR‐based method can be used as an alternative method for assessing proteolysis in UHT milk.
Quantifying the spatial distribution and trends of supplementary feeding sites in South Africa and their potential contribution to vulture energetic requirements
Authors: Brink C. W. , Santangeli A. , Amar A. , Wolter K. , Tate G. , Krüger S. , Tucker A. S. , Thomson R. L. 
Published: January 2020

AbstractOld world vultures are the most threatened group of raptors globally. Supplementary feeding sites (SFS) are a popular conservation tool, widely used to assist vulture populations. Despite their popularity, the impact of SFS on vultures remains largely unstudied. A lack of knowledge on the number, distribution and management of SFS is a key factor hindering such research. In this study, we compile records of SFS in South Africa and conduct questionnaires with SFS managers to characterize SFS. We identify 143 currently active SFS. Our data suggest that SFS numbers have been stable over the last decade. The average provisioning rate for all SFS was 64.6 kg day−1. Overall SFS provide an estimated 3301 tonnes of food to scavengers each year, the equivalent of 83% of the energetic needs of all vultures in the region. This contribution was highly skewed, however, with just 17% of active SFS sites providing 69% of all food. Furthermore, these resources were not equally distributed, with SFS in Limpopo, North West and Kwazulu‐Natal provinces providing 83% of the total meat provisioned. The three most common meat types provided at SFS were beef (39%), pork (33%) and game (19%). Worryingly, we found that 68% and 28% of SFS managers were unaware of the potential harmful effects of lead and veterinary drugs, respectively, which highlights potential poisoning risks associated with SFS. Examining exposure to SFS by different vulture species, we found that whilst SFS are accessible across the distribution range of vultures with large home ranges (e.g. African white‐backed and Cape vultures), those species with smaller home ranges have relatively poor accessibility. With this study, we demonstrate the potential importance, but also associated risks, of SFS to vultures in South Africa, and provide the information base to assess the impacts of this popular but as yet largely unassessed conservation tool.
Long‐term safety and efficacy of psoas bladder hitch in infants aged <12 months with unilateral obstructive megaureter
Authors: Nakamura Shigeru , Hyuga Taiju , Tanabe Kazuya , Inoguchi Satoru , Kawai Shina , Nakai Hideo 
Published: January 2020

ObjectiveTo determine the long‐term safety and efficacy of ureteric reimplantation with psoas bladder hitch (PBH) in patients aged <12 months with unilateral obstructive megaureter (OM).Patients and MethodsWe retrospectively compared a group of patients aged <12 months (study group) with an group of patients aged ≥12 months (comparison group), who underwent PBH for OM between September 2007 and April 2017, in terms of preoperative patient characteristics, intra‐ and peri‐operative results, and postoperative results.ResultsThe study group comprised seven infants, five boys and two girls. The median (range) age at the time of PBH was 3 (2–8) months; OM was detected by ultrasonography during the fetal period. The left side was affected in four infants and the right side in three. Four infants had primary OM (POM). In all three infants who had ectopic OM in the complete double renal pelvis and ureter, the OM involved the ureter from the upper half of the kidney. The median (range) follow‐up period after PBH was 45 (33–129) months. Comparison of the two groups showed no significant difference in terms of surgical time (P = 0.948) and length of hospital stay (P = 0.125). In both groups, hydroureteronephrosis improved postoperatively in all patients. There was no significant difference between the two groups in terms of postoperative complications, such as vesico‐ureteric reflux, febrile urinary tract infection and deterioration of ipsilateral renal function. Notably, no patient underwent reoperation in either group.ConclusionPsoas bladder hitch for unilateral OM including POM appears to be safe and effective in the long term for patients aged <12 months and for those aged ≥12 months. Although not routinely recommended, PBH appears to be a viable option for selected infants with POM.
Quality of life in adolescents with epilepsy, cerebral palsy, and population norms
Authors: Boldyreva Uliana , Streiner David L , Rosenbaum Peter L , Ronen Gabriel M 
Published: January 2020

AimTo compare: (1) self‐ and proxy‐reported quality of life (QoL) in adolescents with epilepsy, cerebral palsy (CP), both epilepsy and CP, and a representative general population sample; and (2) parental stress between parents of adolescents with epilepsy, CP, or both epilepsy and CP.MethodThis was a cross‐sectional observational study with 362 adolescents with epilepsy, 468 with CP, 192 with both CP and epilepsy, and 15 396 from the general population, assessed with the KIDSCREEN‐52 and Parenting Stress Index (PSI).ResultsAll KIDSCREEN‐52 domains showed statistically significant differences across groups. The epilepsy population showed clinically better scores for ‘school environment’ than the general population (Cohen’s d=0.62). Parents scored adolescents with CP lower than adolescents with epilepsy or general populations on ‘physical health’ (d=0.57, d=0.55) and ‘social‐support and peers’ (d=0.82, d=0.91). Parents of adolescents with CP scored them lower than parents of the epilepsy group on ‘autonomy’ (d=0.62). Parents of adolescents with epilepsy scored them lower on ‘mood and emotions’ (d=0.52) and ‘social acceptance’ (d=0.66) than the general population. PSI scores were better for parents of adolescents with epilepsy than for parents of adolescents with CP (d=0.587) and with both CP and epilepsy (d=1.03,
d=0.613, d=0.528).InterpretationAdolescents with epilepsy or CP self‐report equal or better QoL than the general adolescent population, which should comfort families and allow clinicians to address parental concerns.What this paper adds

Adolescents with epilepsy, with or without cerebral palsy (CP), self‐reported better school environment than adolescents in the general population.

Proxy quality of life (QoL) results showed clinically important differences across groups in 6 out of 10 domains of the KIDSCREEN‐52.

Proxy‐reported results showed poorer QoL scores for adolescents with epilepsy or CP than the general population.

Parental stress level was higher in parents of children with CP or both CP and epilepsy, than in those with only epilepsy.
Parent recommendations to support physical activity for families with young children: Results of interviews in deprived and affluent communities in South Wales (United Kingdom)
Authors: Khanom Ashrafunnesa , Evans Bridie Angela , Lynch Rebecca , Marchant Emily , Hill Rebecca A. , Morgan Kelly , Rapport Frances , Lyons Ronan A. , Brophy Sinead 
Published: January 2020

AbstractBackgroundPhysical inactivity is the fourth leading cause of mortality worldwide. Early childhood is a critical period when healthy behaviours can be instilled for a future active lifestyle. We explored community, societal and environmental factors affecting child and family physical activity and sought parent recommendations to support physical activity in families with young children.MethodsWe interviewed 61 parents expecting a child or with a baby ≤12 months (35 mother and father paired interviews and 26 interviews with mothers only). We purposively sampled families for neighbourhood deprivation status (Townsend Index; 26 affluent; 35 deprived). We conducted thematic analysis of interview transcripts using Bronfenbrenner's socio‐ecological framework to guide interpretation.ResultsWe identified four themes: work family‐life balance; spaces for activity; beliefs and attitudes; and physical activity facilitators. We found that parents from deprived neighbourhoods were more likely to be underactive because of a complex web of community, social and personal factors which reduced motivation and hindered opportunity for physical activity. To increase knowledge and opportunity, respondents suggested ‘help not tell’ messages covering ‘why’, ‘how’ and ‘where’ information about physical activity, and using physical activity to support community engagement and social interaction.ConclusionsRecommendations from parents highlight effective communication about the importance of early child and family physical activity and improved community access to safe facilities and opportunities. Both parents need to be engaged in designing interventions to support greater physical activity and healthy behaviours which are relevant and achievable in individuals’ lives.