bluuebunny/crossref_metadata_2025_split huggingface dataset:
Physician reimbursement and retention in HIV care: Racial disparities in the US South
Authors: Pan Zhongzhe , Dahman Bassam , Bono Rose S. , Sabik Lindsay M. , Belgrave Faye Z. , Nixon Daniel E. , Kimmel April D. 
Published: August 2021

AbstractFewer than 60% of Americans diagnosed with HIV are retained in care, with racial disparities. Addressing structural barriers to care may improve outcomes along the HIV care continuum, such as retention, and promote health equity. We examined the relationship between physician reimbursement and retention in HIV care, including racial differences. Data included person-level demographic information and administrative claims (Medicaid Analytic eXtract, 2008-12), state Medicaid-to-Medicare fee ratios (Urban Institute, 2008, 2012), and county characteristics for 15 Southern states plus District of Columbia. The fee ratio is a standardized measure of physician reimbursement capturing state variation in Medicaid relative to Medicare physician reimbursement, which is largely consistent across states. We used generalized estimating equations to assess the association between physician reimbursement ratio and retention in HIV care (≥2 claims for physician visits, antiretroviral prescriptions, or CD4 or HIV RNA viral load tests ≥90 days apart in a calendar-year). We also evaluated an increase in the fee ratio to parity, where Medicaid and Medicare physician reimbursement are equal. Stratified analysis assessed racial differences. The sample included 55,237 adult Medicaid enrollees living with HIV (179,002 enrollee-years). Enrollees were retained in HIV care for approximately three-quarters (76.8%) of their enrollment-years, with retention lower among non-Hispanic Black (76.2%) versus non-Hispanic White (81.3%, p<0.001) enrollees. A 10-percentage point increase in physician reimbursement was associated with a 4% increase in the odds of retention (aOR 1.04, 95% CI 1.01, 1.08). In stratified analysis, increased physician reimbursement was significantly associated with retention among non-Hispanic Black but not non-Hispanic White enrollees. At parity, predicted retention was 81.1% (80.0%, 82.1%) and 80.4% (79%, 81.7%) of enrollment-years, overall and for non-Hispanic Black enrollees, respectively. Higher physician reimbursement improves retention in HIV care, particularly among non-Hispanic Black individuals living with HIV, and could be a structural mechanism to promote racial equity in retention.
Cerebrospinal fluid concentration of complement component 4A is increased in first-episode schizophrenia
Authors: Gracias Jessica , Orhan Funda , Hörbeck Elin , Holmén-Larsson Jessica , Khanlarkani Neda , Malwade Susmita , Goparaju Sravan K. , Schwieler Lilly , Fatourus-Bergman Helena , Pelanis Aurimantas , Goold Carleton P. , Goulding Anneli , Annerbrink Kristina , Isgren Anniella , Sparding Timea , Schalling Martin , Yañez Viviana A. Carcamo , Göpfert Jens C. , Nilsson Johanna , Brinkmalm Ann , Blennow Kaj , Zetterberg Henrik , Engberg Göran , Piehl Fredrik , Sheridan Steven D. , Perlis Roy H. , Cervenka Simon , Erhardt Sophie , Landen Mikael , Sellgren Carl M. 
Published: August 2021

AbstractExcessive synapse loss is a core feature of schizophrenia and is linked to the complement component 4A gene (C4A). In two independent cohorts, we show that cerebrospinal fluid (CSF) C4A concentration is elevated in first-episode psychosis patients who develop schizophrenia and correlates with CSF measurements of synapse density. Using patient-derived cellular modeling, we find that disease-associated cytokines increase neuronal C4A expression and that IL-1β associates with C4A in patient-derived CSF.
Microfluidics-Enabled Digital Isothermal Cas13a Assay
Authors: Liu Frank X. , Cui Johnson Q. , Park Hojeong , Chan Ka Wai , Leung Tyler , Tang Ben Zhong , Yao Shuhuai 
Published: August 2021

AbstractThe isothermal molecular diagnosis with CRISPR has attracted particular interest for the sensitive, specific detection of nucleic acids. However, most of the assays with Cas enzymes were performed in bulk assays using multistep approaches and hard to realize quantitative detection. Herein, we report Microfluidics-Enabled Digital Isothermal Cas13a Assay (MEDICA), a digital format of SHERLOCK with enhanced robustness and sensitivity. We first address the macromolecular crowding problems when combining the recombinase polymerase amplification (RPA) and Cas13a detection into a one-pot SHERLOCK assay. After the assay optimization, the enhanced one-pot SHERLOCK (E-SHERLOCK) achieves high robustness and 200-fold increased sensitivity. Leveraging droplet microfluidics, we streamline the E-SHERLOCK to eliminate undesired input targets caused by pre-amplification before partition, enabling background-free absolute quantification. From the real-time monitoring, MEDICA enables qualitative detection within 10 min and absolute quantification within 25 min. For the proof of concept, we applied MEDICA to quantify HPV 16 and 18 viral loads in 44 clinical samples, indicating perfect accordance with qPCR results. MEDICA highlights the CRISPR-based isothermal assays are promising for the next generation of point-of-care diagnostics.
Interplay of ADHD polygenic liability with birth-related, somatic and psychosocial factors in ADHD - a nationwide study
Authors: Brikell Isabell , Wimberley Theresa , Albiñana Clara , Jóhann Vilhjálmsson Bjarni , Agerbo Esben , Børglum Anders D. , Demontis Ditte , Schork Andrew J. , LaBianca Sonja , Werge Thomas , Hougaard David M. , Nordentoft Merete , Mors Ole , Mortensen Preben Bo , Petersen Liselotte Vogdrup , Dalsgaard Søren 
Published: August 2021

AbstractBackgroundADHD is multifactorial, yet the interplay ADHD polygenic risks scores (ADHD-PRS) and other ADHD associated risk-factors remains relatively unexplored. The aim of this study was to investigate associations, confounding and interactions of ADHD-PRS with birth, somatic and psychosocial risk-factors previously associated with ADHD.MethodsParticipants came from the Danish iPSYCH2012 case-cohort, including a randomly selected general population sample (N=21,578), and all ADHD cases with an ICD-10 diagnosis F90.0 (N=13,697), born in Denmark 1981-2005. We derived ADHD-PRS and identified 25 ADHD risk-factors in Danish national registers. Logistic regression was used to estimate associations of ADHD-PRS with each risk-factors in the general population. Cox models were applied in the full case-cohort to evaluate confounding of risk-factor associations by ADHD-PRS and family psychiatry history, and interactions between ADHD-PRS and each risk-factor.ResultsADHD-PRS was associated with 14 out of 25 ADHD risk-factors in the general population, e.g., maternal autoimmune disorder, mild traumatic brain injury (TBI), and most psychosocial risk-factors. In the full case-cohort, 21 risk-factors were associated with ADHD diagnosis. Adjusting for ADHD-PRS and parental psychiatric history only led to minor attenuations of these associations. Interactions were observed between ADHD-PRS and sex, maternal autoimmune disease, TBI, paternal employment and age at child-birth.ConclusionHigher ADHD-PRS is associated with exposure to certain birth and somatic ADHD risk-factors, and broadly to psychosocial adversity. Evidence of gene-environment interactions were weak and ADHD-PRS and/or family psychiatric history have limited confounding effect on ADHD risk-factor associations, suggesting that majority of the investigated risk-factors act largely independently of ADHD-PRS to increase risk of ADHD.
Telehealth in Rheumatology: The 2021 Arab League of Rheumatology Best Practice Guidelines
Authors: Ziade Nelly , Hmamouchi Ihsane , Kibbi Lina el , Daou Melissa , Abdulateef Nizar , Abutiban Fatemah , Elzorkany Bassel , Dahou-Makhloufi Chafia , Hamdi Wafa , Emadi Samar Al , Halabi Hussein , Alnaqbi Khalid A. , Abu Al Saoud Sima , Hashad Soad , Niamane Radouane , Rakawi Manal El , Kazkaz Layla , Saad Sahar , Eissa Mervat , Fraser Ilanca , Masri Basel 
Published: August 2021

AbstractBackgroundTelehealth use is increasing and will undeniably continue to play a role beyond the COVID-19 era. Best practice guidelines (BPG) for telehealth add credibility, standardize approaches, facilitate reimbursement, and decrease liability.ObjectivesTo develop BPG for the use of Telehealth In Rheumatology in the Arab region, to identify the top barriers and facilitators of telehealth in the Arab region, and to provide rheumatologists with a practical toolkit for the implementation of telehealth.MethodsGuidelines were drafted by a core steering committee from the Arab League of Associations for Rheumatology (ArLAR) after performing a literature search. A multidisciplinary task force (TF), including 18 rheumatologists, 2 patients, and 2 regulators from 15 Arab countries, assessed the BPG using 3 rounds of anonymous online voting by modified Delphi process. The voting on barriers and facilitators was performed through one voting round. The toolkit was developed based on available literature and discussions during the Delphi rounds.ResultsFour General Principles and twelve Statements were formulated. All statements reached >80% consensus. A teleconsultation was specifically defined for the purpose of these guidelines. The concept of choice in telehealth was highlighted, emphasizing patient confidentiality, medical information security, rheumatologist’s clinical judgment, and local jurisdictional regulations. The top barrier for telehealth was the concern about the quality of care. The toolkit emphasized technical aspects of teleconsultation and proposed a triage system.ConclusionsThe ArLAR BPG provides rheumatologists with a series of strategies about the most reliable, productive, and rational approaches to apply telehealth.Article SummaryStrengths and limitations of this studyBest practice guidelines (BPG) the use of Telehealth In Rheumatology in the Arab region were developed herein under the umbrella of the Arab League of Associations for Rheumatology (ArLAR)A teleconsultation was specifically defined for the purpose of these guidelinesThe concept of choice in telehealth was highlighted, emphasizing patient confidentiality, medical information security, rheumatologist’s clinical judgment, and local jurisdictional regulationsThe top barrier for telehealth was the concern about the quality of careThe ArLAR BPG provides rheumatologists with a series of strategies about the most reliable, productive, and rational approaches to apply telehealth in the rheumatology clinic
Evolutionary dynamics of a virus in a vaccinated population
Authors: Bell Graham 
Published: August 2021

SummaryThe progress of an epidemic in a small closed community is simulated by an agent-based model which allows vaccination and variation. The attributes of the virus are governed by two genetic loci: the P-locus, which determines growth, and the M-locus, which determines immune characteristics. Mutation at either locus modifies the attributes of the virus and leads to evolution through natural selection. For both loci the crucial variable is the potential mutation supply UPot, because evolution is likely to happen when UPot> 1. Mutation at the P-locus causes a limited increase in virulence, which may be affected by vaccine design. Mutation at the M-locus may cause a qualitative shift of dynamic regime from a simple limited epidemic to a perennial endemic disease by giving rise to escape mutants which may themselves mutate. A broad vaccine that remains efficacious despite several mutations at the M-locus prevents this shift and provides protection despite the evolution of the virus. Escape variants may nevertheless arise through recombination after coinfection, and can be suppressed by timely revaccination, using the prevalent strain to design the vaccine.
COVID-19 mitigation measures in primary schools and association with infection and school staff wellbeing: an observational survey linked with routine data in Wales, UK
Authors: Marchant Emily , Griffiths Lucy , Crick Tom , Fry Richard , Hollinghurst Joe , James Michaela , Cowley Laura , Abbasizanjani Hoda , Torabi Fatemeh , Thompson Dan , Kennedy Jonathan , Akbari Ashley , Gravenor Michael , Lyons Ronan A , Brophy Sinead 
Published: August 2021

AbstractIntroductionSchool-based COVID-19 mitigation strategies have greatly impacted the primary school day (children aged 3-11) including: wearing face coverings, 2-metre distancing, no mixing of children, and no breakfast clubs or extra-curricular activities. This study examines these mitigation methods and association with COVID-19 infection, respiratory infection, and school staff wellbeing between October to December 2020 in Wales, UK.MethodsA school staff survey captured self-reported COVID-19 mitigation measures in the school, participant anxiety and depression, and open-text responses regarding experiences of teaching and implementing measures. These survey responses were linked to national-scale COVID-19 test results data to examine association of measures in the school and the likelihood of a positive (staff or pupil) COVID-19 case in the school (clustered by school, adjusted for school size and free school meals using logistic regression). Linkage was conducted through the SAIL (Secure Anonymised Information Linkage) Databank.ResultsResponses were obtained from 353 participants from 59 primary schools within 15 of 22 local authorities. Having more direct non-household contacts was associated with a higher likelihood of COVID-19 positive case in the school (1-5 contacts compared to none, OR 2.89 (1.01, 8.31)) and a trend to more self-reported cold symptoms. Staff face covering was not associated with a lower odds of school COVID-19 cases (mask vs. no covering OR 2.82 (1.11, 7.14)) and was associated with higher self-reported cold symptoms. School staff reported the impacts of wearing face coverings on teaching, including having to stand closer to pupils and raise their voices to be heard. 67.1% were not able to implement 2-metre social distancing from pupils. We did not find evidence that maintaining a 2-metre distance was associated with lower rates of COVID-19 in the school.ConclusionsImplementing, adhering to and evaluating COVID-19 mitigation guidelines is challenging in primary school settings. Our findings suggest that reducing non-household direct contacts lowers infection rates. There was no evidence that face coverings, 2-metre social distancing or stopping children mixing was associated with lower odds of COVID-19 or cold infection rates in the school. Primary school staff found teaching challenging during COVID-19 restrictions, especially for younger learners and those with additional learning needs.
Reconstructing the biogeography of a hunter-gatherer planet using machine-learning
Authors: Hamilton Marcus J. , Walker Robert S. , Buchanan Briggs , Blasi Damian E. , Bowern Claire L. 
Published: August 2021

Estimating the total human population size (i.e., abundance) of the preagricultural planet is important for setting the baseline expectations for human-environment interactions if all energy and material requirements to support growth, maintenance, and well-being were foraged from local environments. However, demographic parameters and biogeographic distributions do not preserve directly in the archaeological record. Rather than attempting to estimate human abundance at some specific time in the past, a principled approach to making inferences at this scale is to ask what the human demography and biogeography of a hypothetical planet Earth would look like if populated by ethnographic hunter-gatherer societies. Given ethnographic hunter-gatherer societies likely include the largest, densest, and most complex foraging societies to have existed, we suggest population inferences drawn from this sample provide an upper bound to demographic estimates in prehistory. Our goal in this paper is to produce principled estimates of hunter-gatherer abundance, diversity, and biogeography. To do this we trained an extreme gradient boosting algorithm (XGBoost) to learn ethnographic hunter-gatherer population densities from a large matrix of climatic, environmental, and geographic data. We used the predictions generated by this model to reconstruct the hunter-gatherer biogeography of the rest of the planet. We find the human abundance of this world to be 6.1±2 million with an ethnolinguistic diversity of 8,330±2,770 populations, most of whom would have lived near coasts and in the tropics.Significance StatementUnderstanding the abundance of humans on planet Earth prior to the development of agriculture and the industrialized world is essential to understanding human population growth. However, the problem is that these features of human populations in the past are unknown and so must be estimated from data. We developed a machine learning approach that uses ethnographic and environmental data to reconstruct the demography and biogeography of planet Earth if populated by hunter-gatherers. Such a world would house about 6 million people divided into about 8,330 populations with a particular concentration in the tropics and along coasts.
Getting the gist faster: Blurry images enhance the early temporal similarity between neural signals and convolutional neural networks
Authors: Tovar David A. , Grootswagers Tijl , Jun James , Cha Oakyoon , Blake Randolph , Wallace Mark T. 
Published: August 2021

AbstractHumans are able to recognize objects under a variety of noisy conditions, so models of the human visual system must account for how this feat is accomplished. In this study, we investigated how image perturbations, specifically reducing images to their low spatial frequency (LSF) components, affected correspondence between convolutional neural networks (CNNs) and brain signals recorded using magnetoencephalography (MEG). Using the high temporal resolution of MEG, we found that CNN-Brain correspondence for deeper and more complex layers across CNN architectures emerged earlier for LSF images than for their unfiltered broadband counterparts. The early emergence of LSF components is consistent with the coarse-to-fine theoretical framework for visual image processing, but surprisingly shows that LSF signals from images are more prominent when high spatial frequencies are removed. In addition, we decomposed MEG signals into oscillatory components and found correspondence varied based on frequency bands, painting a full picture of how CNN-Brain correspondence varies with time, frequency, and MEG sensor locations. Finally, we varied image properties of CNN training sets, and found marked changes in CNN processing dynamics and correspondence to brain activity. In sum, we show that image perturbations affect CNN-Brain correspondence in unexpected ways, as well as provide a rich methodological framework for assessing CNN-Brain correspondence across space, time, and frequency.
Deciphering the major metabolic pathways associated with aluminum tolerance in popcorn roots using label-free quantitative proteomics
Authors: Pinto Vitor Batista , Almeida Vinícius Costa , Lima Ítalo Antunes Pereira , de Moura Vale Ellen , Araújo Wagner Luiz , Silveira Vanildo , Viana José Marcelo Soriano 
Published: August 2021

ABSTRACTAluminum toxicity is one of the most important abiotic stresses that affect crop production worldwide. The soluble form (Al3+) inhibits root growth by altering water and nutrients uptake, which also reduces plant growth and development. Under a long term Al3+ exposure, plants can activate several tolerance mechanisms, and to date, there are no reports of large-scale proteomic data of maize in response to this ion. To investigate the post-transcriptional regulation in response to Al toxicity, we performed a label-free quantitative proteomics for comparative analysis of two Al-contrasting popcorn inbred lines and an Al-tolerant commercial hybrid during 72 h under Al-stress. A total of 489 differentially accumulated proteins (DAPs) were identified in the Al-sensitive inbred line, 491 in the Al-tolerant inbred line, and 277 in the commercial hybrid. Among them, 120 DAPs were co-expressed in both Al tolerant genotypes. Bioinformatics analysis indicated that starch and sucrose metabolism, glycolysis/gluconeogenesis, and carbohydrate metabolism were significant biochemical processes regulated in response to Al toxicity. The up accumulation of sucrose synthase and the increase of sucrose content and starch degradation suggest that these components may enhance popcorn tolerance to Al stress. The up-accumulation of citrate synthase suggests a key role of this enzyme in the detoxification process in the Al-tolerant inbred line. The integration of transcriptomic and proteomic data indicated that the Al tolerance response presents a complex regulatory network into the transcription and translation dynamics of popcorn roots development.
The loss of enzymatic activity of the PHARC associated lipase ABHD12 results in increased phagocytosis that causes neuroinflammation
Authors: Singh Shubham , Kamat Siddhesh S. 
Published: August 2021

ABSTRACTPhagocytosis is an important evolutionary conserved process, essential for clearing pathogens and cellular debris in higher organisms, including humans. This well-orchestrated innate immunological response is intricately regulated by numerous cellular factors, important amongst which, are the immunomodulatory lysophosphatidylserines (lyso-PSs) and the pro-apoptotic oxidized phosphatidylserines (PSs) signaling lipids. Interestingly, in mammals, both these signaling lipids are physiologically regulated by the lipase ABHD12, mutations of which, cause the human neurological disorder PHARC. Despite the biomedical significance of this lipase, detailed mechanistic studies and the specific contribution of ABHD12 to innate processes like phagocytosis remain poorly understood. Here, by immunohistochemical and immunofluorescence approaches, using the murine model of PHARC, we show, that upon an inflammatory stimulus, activated microglial cells in the cerebellum of mice deficient in ABHD12 have an amoeboid morphology, increased soma size, and display heightened phagocytosis activity. We also report that upon an inflammatory stimulus, cerebellar levels of ABHD12 increase to possibly metabolize the heightened oxidized PS levels, temper phagocytosis and in turn control neuroinflammation during oxidative stress. Next, to complement these findings, using biochemical approaches in cultured microglial cells, we show that the pharmacological inhibition and/or genetic deletion of ABHD12 results in increased phagocytic uptake in a fluorescent bead uptake assay. Together, our studies provide compelling evidence that ABHD12 plays an important role in regulating phagocytosis in cerebellar microglial cells, and provides a possible explanation, as to why human PHARC subjects display neuroinflammation and atrophy in the cerebellum.
Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions
Authors: Carrascoza Francisco , Antczak Maciej , Miao Zhichao , Westhof Eric , Szachniuk Marta 
Published: August 2021

AbstractIn silico prediction is a well-established approach to derive a general shape of an RNA molecule based on its sequence or secondary structure. This paper reports an analysis of the stereochemical quality of the RNA three-dimensional models predicted using dedicated computer programs. The stereochemistry of 1,052 RNA 3D structures, including 1,030 models predicted by fully automated and human-guided approaches within 22 RNA-Puzzles challenges and reference structures, is analysed. The evaluation is based on standards of RNA stereochemistry that the Protein Data Bank requires from deposited experimental structures. Deviations from standard bond lengths and angles, planarity or chirality are quantified. A reduction in the number of such deviations should help in the improvement of RNA 3D structure modelling approaches.