bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of an unannounced standardized veteran program on access to community-based services for veterans experiencing homelessness
Authors: Weiner Saul J , Schwartz Alan , Binns-Calvey Amy , Kass Benjamin , Underwood Timothy D , Kane Vincent 
Published: February 2021

Abstract

Background
The United States Department of Veterans Affairs established a program in which actors incognito portray veterans experiencing homelessness with pre-determined needs to identify barriers to access and services at community-based organizations.

Methods
From 2017 to 2019, actors who varied in gender, skin color and age portrayed one of three scripts at all VA Community-Based Resource and Referral Centers (CRRCs) serving veterans experiencing homelessness in 30 cities and completed an evaluative survey. They carried authentic VA identification and were registered in a VA patient database for each identity. CRRCs were provided with reports annually and asked to implement corrective plans. Data from the survey were analysed for change over time.

Results
Access to food, counselling, PTSD treatment, and hypertension/prediabetes care services increased significantly from 68–77% in year 2 to 83–97% in year 3 (each P &lt; 0.05 adjusted for script present). A significant disparity in access for African American actors resolved following more uniform adherence to pre-existing policies.

Conclusions
The ‘unannounced standardized veteran’ (USV) can identify previously unrecognized barriers to needed services and care. Audit and feedback programs based on direct covert observation with systematic data collection and rapid feedback may be an effective strategy for improving services to highly vulnerable populations.
TSP1 is the essential domain of SEMA5A involved in pannus formation in rheumatoid arthritis
Authors: Xiao Chipeng , Lv Chen , Sun Siyuan , Zhao Heping , Ling Hanzhi , Li Man , Qin Yang , Zhang Jinhao , Wang Jianguang , Yang Xinyu 
Published: February 2021

Abstract

Objective
In this study, we explored the effect of semaphorin5A (SEMA5A) on RA pathogenesis and its specific TSP1 domain on pannus formation.

Methods
The expression of SEMA5A was detected in the synovium, the fibroblast-like synoviocytes (FLSs) and the SF of RA patients and healthy controls (HCs) by real-time quantitative PCR (q-PCR), immunohistochemistry staining, western blot and ELISA. SEMA5A-mAb intervention was performed to appraise the severity of joints in the CIA model. Transcriptome sequencing and bioinformatics analysis in SEMA5A-transfected FLSs from HCs were performed to screen differentially expressed genes after SEMA5A overexpression. An MTT assay in RA-FLSs, a chicken embryo allantoic membrane experiment and a tube formation experiment were used to clarify the influence of SEMA5A on cell proliferation and angiogenesis. Furthermore, a rescue experiment verified the function of the TSP1 domain of SEMA5A in the progress of RA with Sema5a−/− CIA mice.

Results
The expression of SEMA5A increased in RA compared with that in HCs. Simultaneously, SEMA5A-mAbs significantly attenuated joint injury and the inflammatory response in CIA models. In addition, transcriptome sequencing and angiogenesis-related experiments verified the ability of SEMA5A to promote FLS proliferation and angiogenesis. Moreover, TSP1 was proved to be an essential domain in SEMA5A-induced angiogenesis in vitro. Additionally, rescue of TSP1-deleted SEMA5A failed to reduce the severity of arthritis in a CIA model constructed with Sema5a −/− mice.

Conclusion
In summary, upregulation of SEMA5A was first confirmed in pathological lesions of RA patients. Furthermore, treatment with SEMA5A-mAbs attenuated the progress of RA in the CIA model. Moreover, TSP1 was indicated as the key domain of SEMA5A in the promotion of pannus formation in RA.
Should we use glucocorticoids in early rheumatoid arthritis? Results at 5 years from the early RA UCLouvain Brussels cohort
Authors: Sapart Emilie , Sokolova Tatiana , de Montjoye Stéphanie , Dierckx Stéphanie , Nzeusseu Adrien , Avramovska Aleksandra , Durez Patrick 
Published: February 2021

Abstract

Objectives
To evaluate the proportion of patients with early RA (ERA) who had or had not initiated glucocorticoids, to analyse the baseline characteristics, and to assess the clinical benefit and side effects of glucocorticoids during 5 years of follow-up.

Methods
We included patients with ERA from the UCLouvain Brussels cohort who met the ACR/EULAR 2010 classification criteria and were naïve to conventional DMARDs (cDMARDs). We retrospectively collected patient characteristics prior to the introduction of cDMARDs with or without glucocorticoids. Efficiency and serious adverse events were analysed at 6, 12, 36 and 60 months.

Results
Data from 474 eligible ERA patients were collected; 180 patients initiated glucocorticoids compared with 294 who did not. At baseline, the increased CRP was the main factor that favoured the initiation of glucocorticoids followed by smoking, absence of ACPA, prescription of MTX as a monotherapy and age. Five years’ follow-up of DAS28-CRP, HAQ or visual analog score (VAS) pain values did not differ between the two groups. We also analysed a subgroup of 139 patients who received &gt;1 g of prednisolone during the 5-year period. We confirmed the same baseline differences and observed in addition more men and higher DAS-28CRP values. During the 5 years’ follow-up, DAS-28CRP, VAS pain and HAQ remained significantly higher in this subgroup. More severe infections were also reported.

Conclusion
In our ERA cohort, the initiation of glucocorticoid treatment did not bring additional benefit for the short- and long-term control of the disease. Glucocorticoid was more prescribed in seronegative RA patients with a higher level of inflammation.
Field-Relevant New Sources of Resistance to Anthracnose Caused by Colletotrichum truncatum in a Mungbean Mini-Core Collection
Authors: Pandey Abhay K. , Basandrai Ashwani K. , Basandrai Daisy , Boddepalli Venkata Naresh , Rathore Abhishek , Adapala Gopikrishna , Nair Ramakrishnan M. 
Published: February 2021

Anthracnose is a prevalent disease of mungbean in Asian countries and Sub-Saharan Africa. It is caused by multiple Colletotrichum species. The high levels of anthracnose resistance in mungbean have not been studied in depth in India, but genetic resistance is desired. In this study, we identified the causal agent of mungbean anthracnose in two regions of India as Colletotrichum truncatum through morphological and molecular methods. A set of 296 mungbean mini-core accessions developed by WorldVeg was screened under a natural disease pressure from July to September (kharif season) in 2016, 2017, and 2018 in Hyderabad (a hot spot for anthracnose) to identify anthracnose resistance. Based on disease severity scores, 22 accessions were consistently anthracnose resistant under the categories of immune, highly resistant, and resistant with scores ranging from ≥1.0 to ≤3.0 during the period of study. Furthermore, based on the agronomic performance, anthracnose resistance in Hyderabad, and other desirable traits, a subset of 74 mungbean accessions was selected from 296 mini-core accessions. These accessions were evaluated under natural disease pressure from July to September in 2018 and 2019 in Palampur (another hot spot for anthracnose) to determine the variation in anthracnose resistance. Out of the 74 accessions, two accessions were resistant in 2018; in 2019, one was immune, nine were highly resistant, and 15 were resistant. Combined analysis of variance of 65 accessions common in Hyderabad and Palampur revealed highly significant effects of environment, genotype (accessions), and genotype × environment interaction on the disease severity. The combined GGE biplot analysis of data across years and locations confirmed that the seven accessions MC-24, MC-51, MC-75, MC-127, MC-207, MC-208, and MC-292 were resistant during 2016 to 2018 in Hyderabad, and only in 2019 in Palampur, and the same accessions were moderately resistant in 2018 in Palampur. The seven resistant accessions identified from both test locations could be used as potential donors in the anthracnose resistance breeding program. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Seroprevalence of anti-SARS-CoV-2 IgG antibodies among truck drivers and assistants in Kenya
Authors: Kagucia E Wangeci , Gitonga John N , Kalu Catherine , Ochomo Eric , Ochieng Benard , Kuya Nickline , Karani Angela , Nyagwange James , Karia Boniface , Mugo Daisy , Karanja Henry K , Tuju James , Mutiso Agnes , Maroko Hosea , Okubi Lucy , Maitha Eric , Ajuck Hossan , Bogita Mary , Mudindi Richmond , Mukabi David , Moracha Wycliffe , Bulimu David , Andanje Nelson , Shiraku Evans , Okuku Rosemary , Ogutu Monicah , Aman Rashid , Mwangangi Mercy , Amoth Patrick , Kasera Kadondi , Ng’ang’a Wangari , Mariga Rodgers , Munabi Tobias , Ramadhan Susan M , Mwikali Janet , Nasike Rose , Andera Cornelius , Nechesa Roselyne , Kiplagat Benson K , Omengo Julius , Oteba Simon , Mwangi Arthur , Mkanyi Dorcas , Karisa George , Migosi Judith K , Msili Patrick , Mwambire Samson , Boniface Anthony M , Nyaguara Amek , Voller Shirine , Otiende Mark , Bottomley Christian , Agoti Charles N , Ochola-Oyier Lynette I , Adetifa Ifedayo M O , Etyang Anthony O , Gallagher Katherine E , Uyoga Sophie , Barasa Edwine , Bejon Philip , Tsofa Benjamin , Agweyu Ambrose , Warimwe George M , Scott J Anthony G 
Published: February 2021

AbstractIn October 2020, anti-SARS-CoV-2 IgG seroprevalence among truck drivers and their assistants (TDA) in Kenya was 42.3%, higher than among other key populations. TDA transport essential supplies during the COVID-19 pandemic, placing them at increased risk of being infected and of transmitting SARS-CoV-2 infection over a wide geographical area.
Evaluation of a fully automated high-throughput SARS-CoV-2 multiplex qPCR assay with build-in screening functionality for DelHV69/70- and N501Y variants such as B.1.1.7
Authors: Nörz Dominik , Grunwald Moritz , Olearo Flaminia , Fischer Nicole , Aepfelbacher Martin , Pfefferle Susanne , Lütgehetmann Marc 
Published: February 2021

1AbstractBackgroundNew SARS-CoV-2 variants with increased transmissibility, like B.1.1.7 from England or B1.351 from South Africa, have caused considerable concern worldwide. In order to contain the spread of these lineages, it is of utmost importance to have rapid, sensitive and high-throughput detection methods at hand.MethodsAnalytical sensitivity was assessed for both wild-type SARS-CoV-2 and B.1.1.7 lineage by serial dilution. A total of 141 clinical samples were subjected to the test and results compared to a commercial manual typing-PCR assay and NGS.ResultsThe multiplex assay is highly sensitive for detection of SARS-CoV-2 RNA in clinical samples, with an LoD of 25.82 cp/ml (CI: 11.61 – 57.48). LoDs are slightly higher for the HV68/70 deletion (111.36 cp/ml; CI: 78.16 – 158.67) and the N501Y SNP (2548.04 cp/ml, CI: 1592.58 – 4076.73). A total of 141 clinical samples were tested with the assay, including 16 samples containing SARS-CoV-2 of the B.1.1.7 lineage. Three non-B.1.1.7 samples contained a HV69/70 deletion. All were correctly identified by the multiplex assay.ConclusionWe describe here a highly sensitive, fully automated multiplex PCR assay for the simultaneous detection of del-HV69/70 and N501Y that can distinguish between lineages B.1.1.7 and B1.351. The assay allows for high-throughput screening for relevant variants in clinical samples prior to sequencing.
ClinGen Variant Curation Interface: A Variant Classification Platform for the Application of Evidence Criteria from ACMG/AMP Guidelines
Authors: Preston Christine G. , Wright Matt W. , Madhavrao Rao , Harrison Steven M. , Goldstein Jennifer L. , Luo Xi , Wand Hannah , Wulf Bryan , Cheung Gloria , Mandell Mark E. , Tong Howard , Cheng Shaung , Iacocca Michael A. , Pineda Arturo Lopez , Popejoy Alice B. , Dalton Karen , Zhen Jimmy , Dwight Selina S. , Babb Lawrence , DiStefano Marina , O’Daniel Julianne M. , Lee Kristy , Riggs Erin R. , Zastrow Diane B. , Mester Jessica L. , Ritter Deborah I. , Patel Ronak Y. , Subramanian Sai Lakshmi , Milosavljevic Aleks , Berg Jonathan S. , Rehm Heidi L. , Plon Sharon E. , Cherry J. Michael , Bustamante Carlos D. , Costa Helio A. 
Published: February 2021

AbstractBackgroundIdentification of clinically significant genetic alterations involved in human disease has been dramatically accelerated by developments in next-generation sequencing technologies. However, the infrastructure and accessible comprehensive curation tools necessary for analyzing an individual patient genome and interpreting genetic variants to inform healthcare management have been lacking.ResultsHere we present the ClinGen Variant Curation Interface (VCI), a global open-source variant classification platform for supporting the application of evidence criteria and classification of variants based on the ACMG/AMP variant classification guidelines. The VCI is among a suite of tools developed by the NIH-funded Clinical Genome Resource (ClinGen) Consortium, and supports an FDA-recognized human variant curation process. Essential to this is the ability to enable collaboration and peer review across ClinGen Expert Panels supporting users in comprehensively identifying, annotating, and sharing relevant evidence while making variant pathogenicity assertions. To facilitate evidence-based improvements in human variant classification, the VCI is publicly available to the genomics community and is available athttps://curation.clinicalgenome.org. Navigation workflows support users providing guidance to comprehensively apply the ACMG/AMP evidence criteria and document provenance for asserting variant classifications.ConclusionThe VCI offers a central platform for clinical variant classification that fills a gap in the learning healthcare system, and facilitates widespread adoption of standards for clinical curation.
Excess Mortality in Suicide caused by COVID-19 in Japan
Authors: Kurita Junko , Sugawara Tamie , Ohkusa Yasushi 
Published: February 2021

AbstractBackgroundCountermeasures against COVID-19 outbreak such as lockdown and voluntary restrictions against going out adversely affect human stress and economic activity. Particularly, this stress might lead to suicide.ObjectWe examined excess mortality attributable to suicide caused by COVID-19. Method: We applied the NIID model to suicide deaths from October 2009 through September, 2021 for the whole of Japan by gender. Effects of the great earthquake that struck in eastern Japan on March 11, 2011 were incorporated into the estimation model. Results: Significant excess mortality in suicide was found between July, 2020 and July, 2021 for both genders. However, in August and September, 2021, excess mortality in suicide was detected only in female. It was greater among females than among males. In total, 2950 excess cases of mortality were identified.Discussion and ConclusionExcess mortality during the four months was more than two times greater than the number of COVID-19 deaths confirmed by PCR testing. Countermeasures against COVID-19 should be chosen carefully in light of suicide effects.
Genome-wide association studies of 27 accelerometry-derived physical activity measurements identified novel loci and genetic mechanisms
Authors: Qi Guanghao , Dutta Diptavo , Leroux Andrew , Ray Debashree , Muschelli John , Crainiceanu Ciprian , Chatterjee Nilanjan 
Published: February 2021

AbstractPhysical inactivity (PA) is an important risk factor for a wide range of diseases. Previous genome-wide association studies (GWAS), based on self-reported data or a small number of phenotypes derived from accelerometry, have identified a limited number of genetic loci associated with habitual PA and provided evidence for involvement of central nervous system in mediating genetic effects. In this study, we derived 27 PA phenotypes from wrist accelerometry data obtained from 88,411 UK Biobank study participants. Single-variant association analysis based on mixed-effects models and transcriptome-wide association studies (TWAS) together identified 5 novel loci that were not detected by previous studies of PA, sleep duration and self-reported chronotype. For both novel and previously known loci, we discovered associations with novel phenotypes including active-to-sedentary transition probability, light-intensity PA, activity during different times of the day and proxy phenotypes to sleep and circadian patterns. Follow-up studies including TWAS, colocalization, tissue-specific heritability enrichment, gene-set enrichment and genetic correlation analyses indicated the role of the blood and immune system in modulating the genetic effects and a secondary role of the digestive and endocrine systems. Our findings provided important insights into the genetic architecture of PA and its underlying mechanisms.
Systematic Review and Scientific Rating of Commercial Apps Available in India for Diabetes Prevention
Authors: Ranjani H , Nitika S , Hariharan R , Charumeena H , Oliver N , Pradeepa R , Chambers J C , Unnikrishnan R , Mohan V , Avari P , Anjana RM 
Published: February 2021

ABSTRACTBACKGROUNDScientific evidence for digital health applications (apps) which claim to help in the prevention and management of Type 2 diabetes (T2D) is limited.OBJECTIVESWe aimed to evaluate the quality of currently available health apps for prevention of T2D amongst Asian Indians.METHODSUsing the keywords, ‘diabetes prevention’, ‘healthy lifestyle’ and ‘fitness’, a total of 1486 apps available in India via Google Play were assessed for eligibility by two independent reviewers. After initial screening using specific inclusion and exclusion criteria, 50 apps underwent a pre-specified rating based on user reviews, number of downloads and app size. Sixteen apps that scored ≥ 9 were shortlisted for further review using the Mobile App Rating Scale (MARS). MARS contains 2 main categories: Category I (Application Quality) and Category II (Application Subjective Quality). The mean MARS scores were used to identify the top ranked apps.RESULTSThe mean score for Category I of MARS rating was highest for ‘Google Fit: Health and Activity Tracking’ (4.55/5). This was followed by ‘Healthifyme - Diet Plan, Health and Weight Loss’ (4.45/5). For Category II of MARS, ‘Diabetes M’, ‘Google Fit: Health and Activity Tracking’ and Calorie Counter- My fitness pal’, ‘Healthifyme - Diet plan, Health and Weight Loss’ all scored equally well. On comparing the advantages and disadvantages of each of these applications, ‘Google Fit: Health and Activity Tracking’ and ‘Healthifyme - Diet plan, Health and Weight Loss’ again ranked the best.CONCLUSIONSOur review identifies two commercially available apps ‘Google Fit: Health and Activity Tracking’ and ‘Healthifyme - Diet plan, Health and Weight Loss’ as being user friendly and good quality. Although encouraging, further research is needed to evaluate the efficacy of these apps for prevention of diabetes.
Artificial Intelligence Applications for COVID-19 in Intensive Care and Emergency Settings: A Systematic Review
Authors: Chee Marcel Lucas , Ong Marcus Eng Hock , Siddiqui Fahad Javaid , Zhang Zhongheng , Lim Shir Lynn , Ho Andrew Fu Wah , Liu Nan 
Published: February 2021

AbstractBackgroundLittle is known about the role of artificial intelligence (AI) as a decisive technology in the clinical management of COVID-19 patients. We aimed to systematically review and critically appraise the current evidence on AI applications for COVID-19 in intensive care and emergency settings, focusing on methods, reporting standards, and clinical utility.MethodsWe systematically searched PubMed, Embase, Scopus, CINAHL, IEEE Xplore, and ACM Digital Library databases from inception to 1 October 2020, without language restrictions. We included peer-reviewed original studies that applied AI for COVID-19 patients, healthcare workers, or health systems in intensive care, emergency or prehospital settings. We assessed predictive modelling studies using PROBAST (prediction model risk of bias assessment tool) and a modified TRIPOD (transparent reporting of a multivariable prediction model for individual prognosis or diagnosis) statement for AI. We critically appraised the methodology and key findings of all other studies.ResultsOf fourteen eligible studies, eleven developed prognostic or diagnostic AI predictive models, all of which were assessed to be at high risk of bias. Common pitfalls included inadequate sample sizes, poor handling of missing data, failure to account for censored participants, and weak validation of models. Studies had low adherence to reporting guidelines, with particularly poor reporting on model calibration and blinding of outcome and predictor assessment. Of the remaining three studies, two evaluated the prognostic utility of deep learning-based lung segmentation software and one studied an AI-based system for resource optimisation in the ICU. These studies had similar issues in methodology, validation, and reporting.ConclusionsCurrent AI applications for COVID-19 are not ready for deployment in acute care settings, given their limited scope and poor quality. Our findings underscore the need for improvements to facilitate safe and effective clinical adoption of AI applications, for and beyond the COVID-19 pandemic.
Phase-based cortical synchrony is affected by prematurity
Authors: Yrjölä Pauliina , Stjerna Susanna , Palva J. Matias , Vanhatalo Sampsa , Tokariev Anton 
Published: February 2021

AbstractInter-areal synchronization by phase-phase correlations (PPC) of cortical oscillations mediates many higher neurocognitive functions, which are often affected by prematurity, a globally prominent neurodevelopmental risk factor. Here, we used electroencephalography (EEG) to examine brain-wide cortical PPC networks at term-equivalent age, comparing human infants after early prematurity to a cohort of healthy controls. We found that prematurity affected these networks in a sleep state-specific manner, and the differences between groups were also frequency-selective, involving brain-wide connections. The strength of synchronization in these networks was predictive of clinical outcomes in the preterm infants. These findings show that prematurity affects PPC networks in a clinically significant manner suggesting early functional biomarkers of later neurodevelopmental compromise to be used in clinical and translational studies after early neonatal adversity.
Structural basis for the Pr-Pfr long-range signaling mechanism of a full-length bacterial phytochrome at the atomic level
Authors: Otero Lisandro H. , Foscaldi Sabrina , Antelo Giuliano T. , Sirigu Serena , Klinke Sebastián , Defelipe Lucas A. , Sánchez-Lamas Maximiliano , Battocchio Giovanni , Chavas Leonard M. G. , Goldbaum Fernando A. , Mroginski Maria-Andrea , Rinaldi Jimena , Bonomi Hernán R. 
Published: February 2021

ABSTRACTLight sensing allows organisms to adapt to constantly changing environmental factors. Phytochromes constitute a widespread biological photoreceptor family that typically interconvert between two photostates called Pr (red light-absorbing) and Pfr (far-red light-absorbing). Despite the vast structural information reported on phytochromes, the lack of full-length structures at the (near-)atomic level in both pure Pr and Pfr states leaves gaps in the structural mechanisms involved in the signal transmission pathways during the photoconversion. Here we present three crystallographic structures from the plant pathogenXanthomonas campestrisvirulence regulator bacteriophytochrome, including two full-length proteins, in the Pr and Pfr states. The structural findings, combined with mutational, biochemical and computational studies, allow us to describe the signaling mechanism of a full-length bacterial phytochrome at the atomic level, from the isomerization of the chromophore and the β-sheet/α-helix tongue transition to the remodeling of the quaternary assembly of the protein.TEASERCrystal structures of the full-length bacteriophytochromeXccBphP in both Pr and Pfr states unveil photoswitching mechanism