bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases
Authors: Staton Margaret , Cannon Ethalinda , Sanderson Lacey-Anne , Wegrzyn Jill , Anderson Tavis , Buehler Sean , Cobo-Simón Irene , Faaberg Kay , Grau Emily , Guignon Valentin , Gunoskey Jessica , Inderski Blake , Jung Sook , Lager Kelly , Main Dorrie , Poelchau Monica , Ramnath Risharde , Richter Peter , West Joe , Ficklin Stephen 
Published: June 2021

AbstractOnline, open access databases for biological knowledge serve as central repositories for research communities to store, find and analyze integrated, multi-disciplinary datasets. With increasing volumes, complexity and the need to integrate genomic, transcriptomic, metabolomic, proteomic, phenomic and environmental data, community databases face tremendous challenges in ongoing maintenance, expansion and upgrades. A common infrastructure framework using community standards shared by many databases can reduce development burden, provide interoperability, ensure use of common standards and support long-term sustainability. Tripal is a mature, open source platform built to meet this need. With ongoing improvement since its first release in 2009, Tripal provides full functionality for searching, browsing, loading and curating numerous types of data and is a primary technology powering at least 31 publicly available databases spanning plants, animals and human data, primarily storing genomics, genetics and breeding data. Tripal software development is managed by a shared, inclusive governance structure including both project management and advisory teams. Here, we report on the most important and innovative aspects of Tripal after 11 years development, including integration of diverse types of biological data, successful collaborative projects across member databases, and support for implementing FAIR principles.
wQFM: highly accurate genome-scale species tree estimation from weighted quartets
Authors: Mahbub Mahim , Wahab Zahin , Reaz Rezwana , Rahman M Saifur , Bayzid Md Shamsuzzoha 
Published: June 2021

Abstract

Motivation
Species tree estimation from genes sampled from throughout the whole genome is complicated due to the gene tree–species tree discordance. Incomplete lineage sorting (ILS) is one of the most frequent causes for this discordance, where alleles can coexist in populations for periods that may span several speciation events. Quartet-based summary methods for estimating species trees from a collection of gene trees are becoming popular due to their high accuracy and statistical guarantee under ILS. Generating quartets with appropriate weights, where weights correspond to the relative importance of quartets, and subsequently amalgamating the weighted quartets to infer a single coherent species tree can allow for a statistically consistent way of estimating species trees. However, handling weighted quartets is challenging.

Results
We propose wQFM, a highly accurate method for species tree estimation from multi-locus data, by extending the quartet FM (QFM) algorithm to a weighted setting. wQFM was assessed on a collection of simulated and real biological datasets, including the avian phylogenomic dataset, which is one of the largest phylogenomic datasets to date. We compared wQFM with wQMC, which is the best alternate method for weighted quartet amalgamation, and with ASTRAL, which is one of the most accurate and widely used coalescent-based species tree estimation methods. Our results suggest that wQFM matches or improves upon the accuracy of wQMC and ASTRAL.

Availability and implementation
Datasets studied in this article and wQFM (in open-source form) are available at https://github.com/Mahim1997/wQFM-2020.

Supplementary information
Supplementary data are available at Bioinformatics online.
HPTLC Method for the Ultrasensitive Detection of Triamterene in Plasma
Authors: Khorshed Ahmed A , Elsutohy Mohamed M , Mohamed Abobakr A , Oraby Mohamed 
Published: June 2021

AbstractA high-performance thin-layer chromatographic (HPTLC) method has developed for the selective detection of a diuretic drug, triamterene (TRIAM), in pure form, tablets and human plasma. The method was based on chromatographic separation of TRIAM using HPTLC plates, precoated with silica gel, and a mobile phase consisted of ethyl acetate: dimethylformamide: ammonia (7.0: 2.7: 0.3, by volume). The native fluorescence signal of TRIAM was detected at 440 nm and used to quantify TRIAM using the proposed method, improving the method sensitivity to ~250-folds in comparison to that reported in previous HPTLC studies. The developed method enabled the detection of TRIAM in pure drug and biological samples (human plasma) within linear concentrations ranged from 0.8 to 60 ng/band or 1.0 to 60 ng/band for pure drug and plasma samples, respectively. Furthermore, the method was validated according to the official guidelines to permit its applicability in quality control and clinical laboratories.
Antibodies to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in All of Us Research Program Participants, 2 January to 18 March 2020
Authors: Althoff Keri N , Schlueter David J , Anton-Culver Hoda , Cherry James , Denny Joshua C , Thomsen Isaac , Karlson Elizabeth W , Havers Fiona P , Cicek Mine S , Thibodeau Stephen N , Pinto Ligia A , Lowy Douglas , Malin Bradley A , Ohno-Machado Lucila , Williams Carolyn , Goldstein David , Kouame Aymone , Ramirez Andrea , Roman Adrienne , Sharpless Norman E , Gebo Kelly A , Schully Sheri D 
Published: June 2021

Abstract

Background
With limited severe acute respiratory syndrome coronavirus (SARS-CoV-2) testing capacity in the United States at the start of the epidemic (January–March 2020), testing was focused on symptomatic patients with a travel history throughout February, obscuring the picture of SARS-CoV-2 seeding and community transmission. We sought to identify individuals with SARS-CoV-2 antibodies in the early weeks of the US epidemic.

Methods
All of Us study participants in all 50 US states provided blood specimens during study visits from 2 January to 18 March 2020. Participants were considered seropositive if they tested positive for SARS-CoV-2 immunoglobulin G (IgG) antibodies with the Abbott Architect SARS-CoV-2 IgG enzyme-linked immunosorbent assay (ELISA) and the EUROIMMUN SARS-CoV-2 ELISA in a sequential testing algorithm. The sensitivity and specificity of these ELISAs and the net sensitivity and specificity of the sequential testing algorithm were estimated, along with 95% confidence intervals (CIs).

Results
The estimated sensitivities of the Abbott and EUROIMMUN assays were 100% (107 of 107 [95% CI: 96.6%–100%]) and 90.7% (97 of 107 [83.5%–95.4%]), respectively, and the estimated specificities were 99.5% (995 of 1000 [98.8%–99.8%]) and 99.7% (997 of 1000 [99.1%–99.9%]), respectively. The net sensitivity and specificity of our sequential testing algorithm were 90.7% (97 of 107 [95% CI: 83.5%–95.4%]) and 100.0% (1000 of 1000 [99.6%–100%]), respectively. Of the 24 079 study participants with blood specimens from 2 January to 18 March 2020, 9 were seropositive, 7 before the first confirmed case in the states of Illinois, Massachusetts, Wisconsin, Pennsylvania, and Mississippi.

Conclusions
Our findings identified SARS-CoV-2 infections weeks before the first recognized cases in 5 US states.
Design-based research approach for teacher learning: a case study from Singapore
Authors: Lim Fei Victor , Nguyen Thi Thu Ha 
Published: June 2021

Abstract
In this article, we describe how a design-based research approach brought about teacher learning in terms of both confidence and competence to design and enact a multiliteracies lesson package. This study is situated within the efforts to grow a community of practice comprising teacher champions across schools as they work closely with researchers. Based on a single case study of a teacher, the article discusses her discernible trajectory of growth as evident from her reflections collected after each of the lesson co-design sessions, the lesson plans that she designed, and her actual classroom practices. The findings from the study suggest that the design-based research approach, given its features, can be productive in bringing about a deeper and more reflective teacher learning and as a platform to strengthen the nexus between research and practice.
Management of acute coronary syndromes in older adults
Authors: Morici Nuccia , De Servi Stefano , De Luca Leonardo , Crimi Gabriele , Montalto Claudio , De Rosa Roberta , De Luca Giuseppe , Rubboli Andrea , Valgimigli Marco , Savonitto Stefano 
Published: June 2021

AbstractOlder patients are underrepresented in prospective studies and randomized clinical trials of acute coronary syndromes (ACS). Over the last decade, a few specific trials have been conducted in this population, allowing more evidence-based management. Older adults are a heterogeneous, complex, and high-risk group whose management requires a multidimensional clinical approach beyond coronary anatomic variables. This review focuses on available data informing evidence-based interventional and pharmacological approaches for older adults with ACS, including guideline-directed management. Overall, an invasive approach appears to demonstrate a better benefit–risk ratio compared to a conservative one across the ACS spectrum, even considering patients’ clinical complexity and multiple comorbidities. Conversely, more powerful strategies of antithrombotic therapy for secondary prevention have been associated with increased bleeding events and no benefit in terms of mortality reduction. An interdisciplinary evaluation with geriatric assessment should always be considered to achieve a holistic approach and optimize any treatment on the basis of the underlying biological vulnerability.
Can mental health competence reduce the higher risk of smoking initiation among teenagers with parents who smoke?
Authors: Pearce Anna , Rougeaux Emeline , Deighton Jessica , Viner Russell M , Law Catherine , Hope Steven 
Published: June 2021

Abstract

Background
Parental smoking strongly influences adolescent smoking, yet few studies have examined factors that may protect against this. We investigated whether skills-based components of positive mental health (‘mental health competence’, MHC) modified the association between parental and teenager smoking, in the UK-representative Millennium Cohort Study (approximately 18 000 children, born 2000–02; analytic sample: n = 10 133).

Methods
Cohort members (CMs) reported at 14 years (y) whether they had ever smoked cigarettes. A dichotomized variable indicated whether one/both parents smoked when CMs were 11 y. A four-class latent MHC measure captured learning skills and prosocial behaviours at 11 y: High, High–Moderate, Moderate, Low. We examined effect measure modification (on the additive scale) by comparing risk differences (RDs) for CM smoking according to parental smoking, within each MHC class. We then estimated RDs for CM smoking according to combinations of parental smoking and MHC. Analyses accounted for confounding, sample design, attrition and item missingness.

Results
CMs were more likely to smoke cigarettes if their parent(s) smoked (27%) than CMs with no parent(s) who smoked (11%; RD: 16%). When stratified by MHC, RDs were stronger for low MHC (21%; 95% CI 11–31%) than other MHC classes (ranging: 7–11%). Compared to CMs with high MHC and non-smoker parents, those with low MHC and parent(s) who smoked had an RD of 28% (95% CI 20–36%). This was greater than the sum of RDs for those with low MHC and non-smoker parent(s) [7% (2–14%)] plus those with high MHC and whose parent(s) smoked [11% (7–15%)]. There was limited effect measure modification by moderate or High–Moderate MHC.

Conclusion
Improving MHC to moderate levels may help reduce intergenerational transference of smoking.
Social distancing measures: barriers to their implementation and how they can be overcome – a systematic review
Authors: Sadjadi Mahan , Mörschel Katharina S , Petticrew Mark 
Published: June 2021

Abstract

Background
Despite their central role in the global response to the COVID-19 pandemic and previous infectious disease outbreaks, factors influencing the acceptability and implementation of social distancing measures are poorly understood. This systematic review aims to identify such factors drawing on qualitative literature.

Methods
A systematic search was carried out in eleven databases. Papers were included in the review if they reported on qualitative studies of factors influencing the implementation of social distancing measures in potentially epidemic infectious diseases. An adapted meta-ethnographical approach was used for synthesis. Review findings were assessed for strength and reliability using GRADE-CERQual.

Results
Twenty-nine papers were included from the systematic search that yielded 5620 results, and supplementary methods. The review identifies two broad categories of barriers to social distancing measures: individual- or community-level psychosocial phenomena, and shortcomings in governmental action or communication. Based on this, 25 themes are identified that can be addressed to improve the implementation of social distancing.

Conclusion
Among other findings, the review identifies the need for good communication as well as the need for authorities to provide comprehensive support as two key opportunities to increase acceptability and adherence. Further important enablers of adherence are adequate preparedness and appropriate legislation, the presence of community involvement, solidarity within communities and trust in governments and authorities.
OCT1 – a yeast mitochondrial thiolase involved in the 3-oxoadipate pathway
Authors: Vrzoňová Romana , Tóth Renáta , Siváková Barbara , Moťovská Anna , Gaplovská-Kyselá Katarína , Baráth Peter , Tomáška Ľubomír , Gácser Attila , Gabaldón Toni , Nosek Jozef , Neboháčová Martina 
Published: June 2021

ABSTRACT
The 3-oxoacyl-CoA thiolases catalyze the last step of the fatty acid β-oxidation pathway. In yeasts and plants, this pathway takes place exclusively in peroxisomes, whereas in animals it occurs in both peroxisomes and mitochondria. In contrast to baker's yeast Saccharomyces cerevisiae, yeast species from the Debaryomycetaceae family also encode a thiolase with predicted mitochondrial localization. These yeasts are able to utilize a range of hydroxyaromatic compounds via the 3-oxoadipate pathway the last step of which is catalyzed by 3-oxoadipyl-CoA thiolase and presumably occurs in mitochondria. In this work, we studied Oct1p, an ortholog of this enzyme from Candida parapsilosis. We found that the cells grown on a 3-oxoadipate pathway substrate exhibit increased levels of the OCT1 mRNA. Deletion of both OCT1 alleles impairs the growth of C. parapsilosis cells on 3-oxoadipate pathway substrates and this defect can be rescued by expression of the OCT1 gene from a plasmid vector. Subcellular localization experiments and LC-MS/MS analysis of enriched organellar fraction-proteins confirmed the presence of Oct1p in mitochondria. Phylogenetic profiling of Oct1p revealed an intricate evolutionary pattern indicating multiple horizontal gene transfers among different fungal groups.
Migration and Economic Coercion
Authors: Connell Brendan J , Moya Samantha L , Shin Adrian J 
Published: June 2021

Abstract
Sender costs of economic sanctions exacerbate the enforcement problem associated with multilateral coercive measures. When third-country sanctioners share strategic interests with the target state, they have commercial and diplomatic incentives to defect from multilateral sanctions arrangements. In addition to these well-documented sender costs, this article argues that migration pressure from the target state has become an important consideration for potential sanctioners. Economic sanctions often increase the economic distress on the target country, which in turn causes more people to migrate to countries where their co-ethnics reside. Countries hosting a large number of nationals from the target country face a disproportionately high level of migration pressure when sanctions increase emigration from the target country. Therefore, policymakers of these countries oppose economic sanctions on the target country as an attempt to preempt further migration. Analyzing the sanctions bills in the European Parliament from 2011 to 2015, we find empirical support for our prediction.
Dose–Response Relationships Between Polypharmacy and All-Cause and Cause-Specific Mortality Among Older People
Authors: Huang Yun-Ting , Steptoe Andrew , Wei Li , Zaninotto Paola 
Published: June 2021

Abstract

Background
Although medicines are prescribed based on clinical guidelines and expected to benefit patients, both positive and negative health outcomes have been reported associated with polypharmacy. Mortality is the main outcome, and information on cause-specific mortality is scarce. Hence, we investigated the association between different levels of polypharmacy and all-cause and cause-specific mortality among older adults.

Method
The English Longitudinal Study of Ageing is a nationally representative study of people aged 50+. From 2012/2013, 6 295 individuals were followed up to April 2018 for all-cause and cause-specific mortality. Polypharmacy was defined as taking 5–9 long-term medications daily and heightened polypharmacy as 10+ medications. Cox proportional hazards regression and competing-risks regression were used to examine associations between polypharmacy and all-cause and cause-specific mortality, respectively.

Results
Over a 6-year follow-up period, both polypharmacy (19.3%) and heightened polypharmacy (2.4%) were related to all-cause mortality, with hazard ratios of 1.51 (95% CI: 1.05–2.16) and 2.29 (95% CI: 1.40–3.75) respectively, compared with no medications, independently of demographic factors, serious illnesses and long-term conditions, cognitive function, and depression. Polypharmacy and heightened polypharmacy also showed 2.45 (95% CI: 1.13–5.29) and 3.67 (95% CI: 1.43–9.46) times higher risk of cardiovascular disease deaths, respectively. Cancer mortality was only related to heightened polypharmacy.

Conclusion
Structured medication reviews are currently advised for heightened polypharmacy, but our results suggest that greater attention to polypharmacy in general for older people may reduce adverse effects and improve older adults’ health.
BIM-based analysis of energy efficiency design of building thermal system and HVAC system based on GB50189-2015 in China
Authors: Zhao Tianyi , Qu Ziyi , Liu Chao , Li Kuishan 
Published: June 2021

Abstract
Recently, the application of building information modeling (BIM) in building energy efficiency design programs has been emphasized in research. In China, faced with requirements in building energy efficiency design standards and specifications, researchers have been using BIM as a platform for breaking up bottlenecks in energy simulation and design software, and BIM is considered the key to improve the efficiency of building energy efficiency design. Firstly, based on the trade-off energy consumption judgment method proposed in the ‘Public Building Energy Efficiency Design Standard (GB50189-2015)’, this study combines the BIM platform with an orthogonal simulation design adopting an experimental building construction project in a cold region of China, to thereby study the influences of different envelope structural parameters on cooling and heating loads. Then, this study analyzes the continuity and consistency of data exchange between different BIM-related software, through the modeling software Revit and the sustainable analysis software Ecotect. Finally, through the experiment, the critical factors of the optimized design of the building envelope are investigated and applied for the optimized design of the building thermal system. In addition, this study uses BIM to complete an energy efficiency design for a laboratory heating, ventilation and air conditioning (HVAC) system. According to the experimental results, the following conclusions can be drawn: this study proposes a BIM-based optimized design method of building thermal system, which complies with various Chinese building energy efficiency standards and polices and can be used as a reference for Chinese designers. Also, the issues and challenges in building consumption simulation based on BIM technology and the application of BIM technology in the design of building thermal HVAC systems are discussed, and the development trends of BIM technology in China are analyzed. Building thermal system and HVAC system design are the key points of building efficiency design. The optimized design method proposed in this paper is of great significance to this system design. The optimized design method can improve the design efficiency of designers while complying with China’s standards and policies. Therefore, it can save costs, improve the economic benefits of the projects and, at the same time, obtain an ideal building efficiency design.
Telling the story of complex change: an Impact Framework for the real world
Authors: Willett Jo , Barclay Michelle , Mukoro Felix , Sweeney Grace 
Published: June 2021

AbstractBackgroundIn the National Health Service (NHS) in England, traditional approaches to evidencing impact and value have an important role to play but are unlikely to demonstrate the full value of national quality improvement programmes and large-scale change initiatives in health and care. This type of work almost always takes place in complex and complicated settings, in that it involves multiple players, numerous interventions and a host of other confounding factors. Improvement work is usually emergent, with cause and effect only understood in hindsight; challenges around contribution and attribution can lead the key players to question how they can be certain that the described or observed changes are due to their intervention and would not have happened without them. In this complex environment, there is a risk of oversimplifying the observed impact and focusing instead on those things that are easier to measure, missing that which is important but more difficult to evidence.MethodsBetween 2016 and 2019, an action-orientated approach, drawing on realist and development evaluation approaches, was taken to designing and testing the Impact Framework. First, we undertook a pragmatic review of tools and approaches used by others to capture and demonstrate their impact both within and outside the health and care environment. Following the identification and review of these tools and approaches, and in consultation with national improvement teams in England about their evaluation challenges and aspirations, we developed a set of underpinning principles to inform the design and build of the framework. The principles were informed and finessed following conversations with improvement teams and programme leads in NHS England with respect to the challenges that they were facing and their aspirations in terms of demonstrating their impact and learning as they worked.ResultsThe ‘Impact Framework’ described in this article offers a practical approach to capturing the impact of improvement work at any scale, taking account of unintended outcomes, considering attribution and contribution, and using a narrative approach to uncover the difference made by improvement initiatives in rich detail. In this article, we describe how the Impact Framework has been used with one of NHS England’s national programmes, Time for Care, which was delivered between 2016 and 2020.ConclusionsThe Impact Framework continues to be used, developed and further tested by national improvement programmes being delivered by NHS England and NHS Improvement and is updated regularly. The framework has been developed to be accessible to frontline teams and is supported by a set of resources to help improvement teams and individuals to use by themselves (https://www.england.nhs.uk/sustainableimprovement/impact-framework/).