bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel Cluster AZArthrobacterphages Powerpuff, Lego, and YesChef exhibit close functional relationships withMicrobacteriumphages
Authors: Kapinos Andrew , Aghamalian Pauline , Capehart Erika , Alag Anya , Angel Heather , Briseno Eddie , Farag Emily , Foster Hilory , Hakim Abbas , Hernandez-Casas Daisy , Huang Calvin , Lam Derek , Mendez Maya , Min Ashley , Nguyen Nikki , Ortiz Emily , Saldivar Lizbeth Shelly , Shannon Jack Arthur , Smith Rachel , Sridhar Mihika V. , Ta An , Theophilus Malavika C. , Ngo Ryan , Torres Canela , Reddi Krisanavane , Freise Amanda C. , Parker Jordan Moberg 
Published: November 2020

AbstractBacteriophages exhibit a vast spectrum of relatedness and there is increasing evidence of close genomic relationships independent of host genus. The variability in phage similarity at the nucleotide, amino acid, and gene content levels confounds attempts at quantifying phage relatedness, especially as more novel phages are isolated. This study describes three highly similar novelArthrobacter globiformisphages–Powerpuff, Lego, and YesChef–which were assigned to Cluster AZ using a nucleotide-based clustering parameter. Phages in Cluster AZ andMicrobacteriumCluster EH, as well as the formerMicrobacteriumsingleton Zeta1847, exhibited low nucleotide similarity but gene content similarity in excess of the recently adoptedMicrobacteriumclustering parameter, which resulted in the reassignment of Zeta1847 to Cluster EH. Additionally, Clusters AZ and EH phages encode a shared integrase indicative of a lysogenic life cycle; in the first experimental verification of a Cluster AZ phage’s life cycle, we show that phage Powerpuff is a true temperate phage and forms stable lysogens that exhibit immunity to superinfection by related phages, despite lacking identifiable repressors typically required for lysogenic maintenance and superinfection immunity. The ability of phage Powerpuff to undergo and maintain lysogeny suggests that other closely related phages encoding an integrase but lacking an identified repressor may be temperate as well. Our findings further highlight the importance of using multiple metrics to capture phage relatedness, provide additional evidence of significant shared phage genomic content spanning multiple actinobacterial host genera, and demonstrate the continued need for verification and characterization of life cycles in newly isolated phages.
THE VARIATION OF GENOME SITES ASSOCIATED WITH SEVERE COVID-19 ACROSS POPULATIONS: THE WORLDWIDE AND NATIONAL PATTERNS
Authors: Balanovsky Oleg , Petrushenko Valerie , Mirzaev Karin , Abdullaev Sherzod , Gorin Igor , Chernevskiy Denis , Agdzhoyan Anastasiya , Balanovska Elena , Alexander Kryukov , Sychev Dmitriy 
Published: November 2020

SUMMARYBackgroundThe knowledge of clinically relevant markers distribution might become a useful tool in COVID-19 therapy using personalized approach in the lack of unified recommendations for COVID-19 patients management during pandemic. We aimed to identify the frequencies and distribution patterns of rs11385942 and rs657152 polymorphic markers, associated with severe COVID-19, among populations of the world, as well at the national level within Russia. The study was also dedicated to reveal whether population frequencies of both polymorphic markers are associated with COVID-19 cases, recovery and death rates.MethodsWe genotyped 1883 samples from 91 ethnic populations from Russia and neighboring countries by rs11385942 and rs657152 markers. Local populations which were geographically close and genetically similar were pooled into 28 larger groups. In the similar way we compiled a dataset on the other regions of the globe using genotypes extracted or imputed from the available datasets (32 populations worldwide). The differences in alleles frequencies between groups were estimated and the frequency distribution geographic maps have been constructed. We run the correlation analysis of both markers frequencies in various populations with the COVID-19 epidemiological data on the same populations.FindingsThe cartographic analysis revealed that distribution of rs11385942 follows the West Eurasian pattern: it is frequent in Europeans, West Asians, and particularly in South Asians but rare or absent in all other parts of the globe. Notably, there is no abrupt changes in frequency across Eurasia but the clinal variation instead. The distribution of rs657152 is more homogeneous. Higher population frequencies of both risk alleles correlated positively with the death rate. For the rs11385942 we can state the tendency only (r=0,13, p=0.65), while for rs657152 the correlation was significantly high (r=0,59, p=0,02). These reasonable correlations were obtained on the Russian dataset, but not on the world dataset.InterpretationUsing epidemiological statistics on Russia and neighboring countries we revealed the evident correlation of the risk alleles frequencies with the death rate from COVID-19. The lack of such correlations at the world level should be attributed to the differences in the ways epidemiological data have been counted in different countries. So that, we believe that genetic differences between populations make small but real contribution into the heterogeneity of the pandemic worldwide. New studies on the correlations between COVID-19 recovery/mortality rates and population’s gene pool are urgently needed.
Integrative Brain Transcriptome Analysis Links Complement Component 4 andHSPA2to theAPOEε2 Protective Effect in Alzheimer Disease
Authors: Panitch Rebecca , Hu Junming , Chung Jaeyoon , Zhu Congcong , Meng Gaoyuan , Xia Weiming , Bennett David A. , Lunetta Kathryn L. , Ikezu Tsuneya , Au Rhoda , Stein Thor D. , Farrer Lindsay A. , Jun Gyungah R. 
Published: November 2020

AbstractMechanisms underlying the protective effect of apolipoprotein E (APOE) ε2 against Alzheimer’s disease (AD) are not well understood. We analyzed gene expression data derived from autopsied brains donated by 982 individuals including 135APOEε 2/ε 3 carriers. Complement pathway genesC4AandC4Bwere among the most significantly differentially expressed genes between ε 2/ε 3 AD cases and controls. We also identified anAPOEε2/ε3 AD-specific co-expression network enriched for astrocytes, oligodendrocytes and oligodendrocyte progenitor cells containing the genesC4A, C4B, andHSPA2. These genes were significantly associated with the ratio of phosphorylated tau at position 231 to total Tau but not with amyloid-β 42 level, suggesting thisAPOEε 2 related co-expression network may primarily be involved with tau pathology.HSPA2expression was oligodendrocyte specific and significantly associated with C4B protein. Our findings provide the first evidence of a crucial role of the complement pathway in the protective effect ofAPOEε2 for AD.
SalivaSTAT: Direct-PCR and pooling of saliva samples collected in healthcare and community setting for SARS-CoV-2 mass surveillance
Authors: Sahajpal Nikhil S , Mondal Ashis K , Ananth Sudha , Njau Allan , Ahluwali Pankaj , Newnam Gary , Lozoya-Colinas Adriana , Hud Nicholas V. , Kota Vamsi , Ross Ted M , Reid Michelle D. , Fulzele Sadanand , Chaubey Alka , Hegde Madhuri , Rojiani Amyn M , Kolhe Ravindra 
Published: November 2020

BackgroundThe limitations of widespread current COVID-19 diagnostic testing lie at both pre-analytical and analytical stages. Collection of nasopharyngeal swabs is invasive and is associated with exposure risk, high cost, and supply-chain constraints. Additionally, the RNA extraction in the analytical stage is the most significant rate-limiting step in the entire testing process. To alleviate these limitations, we developed a universal saliva processing protocol (SalivaSTAT) that would enable an extraction free RT-PCR test using any of the commercially available RT-PCR kits.MethodsWe optimized saliva collection devices, heat-shock treatment and homogenization. The effect of homogenization on saliva samples for extraction-free RT-PCR assay was determined by evaluating samples with and without homogenization and preforming viscosity measurements. Saliva samples (872) previously tested using the FDA-EUA method were reevaluated with the optimized SalivaSTAT protocol using two widely available commercial RT-PCR kits. Further, a five-sample pooling strategy was evaluated as per FDA guidelines using the SalivaSTAT protocol.ResultsThe saliva collection (done without any media) performed comparable to the FDA-EUA method. The SalivaSTAT protocol was optimized by incubating saliva samples at 95°C for 30-minutes and homogenization, followed by RT-PCR assay. The clinical sample evaluation of 630 saliva samples using the SalivaSTAT protocol with PerkinElmer (600-samples) and CDC (30-samples) RT-PCR assay achieved positive (PPA) and negative percent agreement (NPA) of 95.8% and 100%, respectively. The LoD was established as ∼20-60 copies/ml by absolute quantification. Further, a five-sample pooling evaluation using 250 saliva samples achieved a PPA and NPA of 92% and 100%, respectively.ConclusionWe have optimized an extraction-free direct RT-PCR assay for saliva samples that demonstrated comparable performance to FDA-EUA assay (Extraction and RT-PCR). The SalivaSTAT protocol is a rapid, sensitive, and cost-effective method that can be adopted globally, and has the potential to meet testing needs and may play a significant role in management of the current pandemic.
Grant Review Feedback: Appropriateness and Usefulness
Authors: Gallo Stephen , Schmaling Karen , Thompson Lisa , Glisson Scott 
Published: November 2020

AbstractThe primary goal of the peer review of research grant proposals is to evaluate their quality for the funding agency. An important secondary goal is to provide constructive feedback to applicants for their resubmissions. However, little is known about whether review feedback achieves this goal. In this paper, we present a mixed methods analysis of responses from grant applicants regarding their perceptions of the effectiveness and appropriateness of peer review feedback they received from grant submissions. Overall, 56%-60% of applicants determined the feedback to be appropriate (fair, well-written, and well-informed), although their judgments were more favorable if their recent application was funded. Importantly, independent of funding success, women found the feedback better written than men, and more white applicants found the feedback to be fair than non-white applicants. Also, perceptions of a variety of biases were specifically reported in respondents’ feedback. Less than 40% of applicants found the feedback to be very useful in informing their research and improving grantsmanship and future submissions. Further, negative perceptions of the appropriateness of review feedback were positively correlated with more negative perceptions of feedback usefulness. Importantly, respondents suggested that highly competitive funding pay-lines and poor inter-panel reliability limited the usefulness of review feedback. Overall, these results suggest that more effort is needed to ensure that appropriate and useful feedback is provided to all applicants, bolstering the equity of the review process and likely improving the quality of resubmitted proposals.
Diversity as job quality: toward the inclusion of trade unions in public procurement of social services
Authors: Benjamin Orly 
Published: November 2020

PurposeWhen union representatives are included in government procurement procedures for contracting-out of social welfare services, organizational diversity is enhanced if the job quality parameter, as reflected in the contract, is improved. Asking how unions are treated in government procurement procedures, this paper discusses an approach to diversity management based on the inclusion of unions.Design/methodology/approachAs part of a broader research project, interviews were conducted with six budget administrators and 16 occupational standards administrators employed by the Israeli ministries of Welfare, Education and Health; and with eight trade union activists. Grounded theory was applied for data analysis, revealing meanings of “trade unions” and “job quality.”FindingsBudgeting administrators manifested diversity resistance by means of only partially supporting trade union demands to enhance job quality. Their power position enabled them to prioritize the profit imperative of service providers; the diverse labor force operating the contracted-out service were consequently denied the ostensible benefits of workplace diversity.Practical implicationsUnionization, and trade union participation in social welfare procurement processes, is a potentially effective path to improving job quality and enhancing workplace diversity. However, more must be done to develop the institutional-level processes that will ensure that this potential is utilized to the full.Social implicationsIncluding trade unions in social welfare procurement processes is a potentially effective path to improving job quality and enhancing workplace diversity. However, specific actions are required to develop the willingness of budgeting administrators to recognize the association between union participation, job quality and the acknowledged benefit of promoting organizational diversity.Originality/valueAn institutional work perspective was used to detail how budgeting administrators involved in public procurement processes resisted diversity by undermining trade union action for job quality. By identifying three social processes deployed to side-track trade union campaigns for improved job quality, this research shows how the power struggle between budgeting administrators and union representatives ultimately undermines workplace diversity.
An emergency response system created to combat injuries during physical education training in a university using deep learning
Authors: Leilei Wang , Rajendiran Sowmipriya , Gayathri K. 
Published: November 2020

Purpose
The main goal of the physical education (PE) environment is that each individual trained should achieve self-fulfillment with the large group of students involved with their own efforts. Deep learning is applying transferrable knowledge in new situations to help the students master in tough circumstances. In PE training, injuries occur when working together as a team. Safety measures are taken immediately as an emergency response to reduce the potential risk in students by providing first aid. To provide safety measures for the injured student immediately, the environment is monitored in real-time using a GPS.

Design/methodology/approach
Theory of Humanities Education (ToHE) infers that it has less collection of theories and a wide range of applications than the state-of-the-art systems. ToHE allows students to think creatively and play a vital role in one’s health which is a critical aspect in PE. The ToHE theory focuses on two main concepts, i.e. by using a methodological approach to analyse and deep learning to solve the problem. PE motivates college students to follow a healthy and active lifestyle.

Findings
The proposed system is deployed in real time for monitoring the student’s performance and provides an emergency response with an accuracy rate of 90%.

Originality/value
The deep learning offers solutions to the injuries by using the deep convolutional neural network to provide interpretability of the consequence by training it with various injuries that occur in the playground and inappropriate use of sports equipment. A case study provided in this paper outlines an emergency response scenario to an injured student in sports training.
Supply chain finance is not for everyone
Authors: Elliot Viktor Hugo , De Goeij Christiaan , Gelsomino Luca Mattia , Woxenius Johan 
Published: November 2020

PurposeLogistics service providers (LSPs) have unique resources and capabilities that position them to deliver supply chain finance (SCF) solutions. The study aims to discuss and illustrate the necessary resources and process of value creation and capture of LSPs, potentially offering SCF solutions.Design/methodology/approachRelying on a theoretical framework, combining a resource-based view (RBV) with the literature on SCF, the authors apply an abductive case study methodology, including 11 interviews with representatives from four LSPs.FindingsThe main findings are as follow: (1) although an LSP has sufficient resources for value-added SCF solutions, it may not capture enough value to motivate realising them; (2) an LSP considering offering SCF should account for the interaction between its resources and cargo transit times, risk and regulatory restrictions and (3) future studies should distinguish between financing the logistics services and the moved products.Research limitations/implicationsThe authors contribute to the growing field of SCF research by analysing motives and barriers for LSPs to offer SCF service to their customers. Because none of our case companies decided to move beyond experimentation further research is needed on the resources and capabilities needed for LSPs to successfully venture into SCF.Practical implicationsThe study provides LSPs with clear indications of the difficulties involved when contemplating a move into SCF solutions and discusses the potential value of offering such services.Originality/valueDespite evidence of LSPs engaging in SCF in various industries, academic contributions do not go beyond operational conditions or quantification of benefits. The authors add evidence on how LSPs are currently evaluating the prominence of adding SCF to their value offerings, including a new perspective on resources, value generation and capture mechanisms.
The Power of Playgroups: Key components of supported and therapeutic playgroups from the perspective of parents
Authors: Armstrong Jodie , Elliott Catherine , Davidson Emma , Mizen Joanne , Wray John , Girdler Sonya 
Published: November 2020

AbstractIntroductionPlaygroups are community‐based programs for children and families aiming to improve child outcomes, enhance family and community networks and increase parenting capacity. Despite the prevalence of playgroups in Australian communities there is a lack of research clearly articulating the key components of playgroups, specifically from the perspective of parents attending these groups. This study aimed to identify the key components of supported and therapeutic playgroups impacting on perceived effectiveness from the perspective of parents with a child with a developmental delay and/or disability.MethodsThis study explored the experiences of 23 parents attending supported or therapeutic playgroups using a qualitative interpretive phenomenological approach. Data were collected through three focus groups and seven individual interviews and analysed using Colaizzi's (1978) qualitative method of data analysis.ResultsFindings indicated playgroup components that most strongly impacted on perceived effectiveness were feeling accepted; providing opportunities for child development, socialisation and enjoyment; and enhancing parental knowledge and skills. Findings reinforced the importance of family centred practice and facilitating peer support for families of children with developmental delay and/or disability.ConclusionSupported and therapeutic playgroups emerged as a valuable model for parents of children with developmental delays and/or disabilities but require an interplay of specific facilitator, parent and child characteristics to be effective. This study contributes to the understanding of key components of successful supported and therapeutic playgroup models, highlighting the importance of engaging consumers in developing evidence‐based meaningful interventions for children with developmental delay and/or disabilities and their families.
Play profiles of children with HIV/Aids: A comparative study
Authors: Munambah Nyaradzai , Cordier Reinie , Chiwaridzo Matthew , Ramugondo Elelwani L. 
Published: November 2020

AbstractIntroductionDespite play being widely used in occupational therapy practice as a means and ends in intervention, no research has explored how the play of children with HIV/AIDS is affected. Therefore, the specific processes through which play can be used in therapy with children with HIV/AIDS remains underexplored, especially in low resourced settings. This study aims to compare the level of playfulness of children with HIV/AIDS to that of age and gender matched typically developing children living in the same low resourced community.MethodsThe Test of Playfulness (ToP) was used to examine the differences and similarities of play between children aged 4–7 years who are typically developing children (n = 52) and children with HIV/AIDS who receive antiretroviral treatment (n = 44). Each child was video recorded playing with a familiar playmate both indoors and outdoors. The videos were scored by two independent raters who were blinded to all aspects of the study. Scores were subjected to Rasch analysis to calculate interval level measure scores. Independent t‐tests were used to compare differences between the means of the groups.ResultsTypically developing children scored significantly higher when playing outdoors, as compared to children with HIV [t (94) = 3.57, p = .001]. There was no significant difference between mean measure scores for indoor play when comparing typically developing children and children with HIV. Children who are HIV positive scored significantly lower than typically developing children on items related to the ability to suspend reality and framing in both indoor and outdoor environments.ConclusionsChildren with HIV/AIDS exhibited lower levels of playfulness when compared to typically developing children. This study provides insight on the play profiles of children with HIV/AIDS, highlighting play deficits and differences between indoor and outdoor play. Occupational therapy can play a significant role in promoting playfulness in children with HIV/AIDS.
Doing justice to your child: a Dutch pilot intervention for parents in high‐conflict divorces
Authors: Geurts Teun , Gutterswijk Raymond V. 
Published: November 2020

This study examines the feasibility of a Dutch intervention for parents in high‐conflict divorces. The intervention consisted of a high‐intensity programme in which parents undergo a series of therapeutic interventions on five consecutive days. Data were collected from up to ten parents at three moments in time (prior to, immediately after, and about one year after the intervention). We showed that the intervention yielded high expectations with participating parents immediately after the intervention. One year after the intervention, however, these high expectations had not been consolidated into a perceived reduction of conflict. A comparison of pre‐ and post‐intervention conflict levels, on the other hand, suggested a decrease in conflict as well as improvement in relationship quality, although these improvements were not as high as parents had anticipated directly after the intervention. Parents might be unaware of their progress due to unmet expectations.Practitioner points

This study offers evidence of promise for Doing Justice to Your Child, an intensive, mixed‐intervention treatment programme for parents in high‐conflict divorces

Lawyers were also involved in the programme

Parents in high‐conflict divorces may be unable to see positive progress from this intervention themselves