bluuebunny/crossref_metadata_2025_split huggingface dataset:
School Reopening Simulations with COVID-19 Agent-based Model for the Philippine Regions
Authors: Bongolan Vena Pearl , Francisco Nico Andrew G. , Saliba Martin Thomas D. , Celeste Jimuel 
Published: May 2022

AbstractSchools have been closed in the Philippines since March 2020 due to the COVID-19 pandemic. In 2022, the government already allowed a pilot run of limited in-person classes in low-risk areas. With such development, the present paper aims to explore the question “Is it safe to reopen schools with the current vaccination coverage?” We used an age-stratified COVID-19 agent-based model coupled with social contact probabilities to simulate school reopening and vaccination scenarios in the 17 regions of the country. Through these simulations, we found downtick points for infections and deaths—the vaccination coverage at which we do not expect increases in infections and deaths should schools reopen. We then calculated the School Reopening Viability (SRV) of the regions and visualized these scores with a stop-go map for school reopening. Simulation results suggest that all regions except Regions 7, 9, BARMM, and 13 can already reopen schools without the fear of upticks in infections nor deaths. These regions have lower vaccination coverages relative to the rest of the country, especially against the case of Luzon which has the highest vaccination coverage. We recommend that the areas of concern ramp up their vaccination efforts before reopening schools. At the same time, behavioral factors (mask-wearing, physical distancing, hand-washing) and disease resistance factors (healthy living habits) shall be enforced once schools reopen. Finally, school reopening shall be gradual to ensure the crafting of data-driven (hospital utilization, positivity rate) policies.
Modelling long-term COVID-19 hospital admission dynamics using empirical immune protection waning data
Authors: Reyné Bastien , Sofonea Mircea T. , Alizon Samuel 
Published: May 2022

AbstractImmune waning is key to the timely anticipation of COVID-19 long-term dynamics. We assess the impact of periodic vaccination campaigns using a compartmental epidemiological model with embedded multiple age structures and empiric time-dependent vaccine protection kinetics. Despite the uncertainty inherent to such scenarios, we show that vaccination campaigns decreases the yearly number of COVID-19 admissions. However, especially if restricted to individuals over 60 years old, vaccination on its own seems insufficient to prevent thousands of hospital admissions and it suffers the comparison with non-pharmaceutical interventions aimed at decreasing infection transmission. The combination of such interventions and vaccination campaigns appear to provide the greatest reduction in hospital admissions.
Quantifying the information in noisy epidemic curves
Authors: Parag Kris V , Donnelly Christl A , Zarebski Alexander E 
Published: May 2022

AbstractReliably estimating the dynamics of transmissible diseases from noisy surveillance data is an enduring problem in modern epidemiology. Key parameters, such as the instantaneous reproduction number, Rt at time t, are often inferred from incident time series, with the aim of informing policymakers on the growth rate of outbreaks or testing hypotheses about the effectiveness of public health interventions. However, the reliability of these inferences depends critically on reporting errors and latencies innate to those time series. While studies have proposed corrections for these issues, methodology for formally assessing how these sources of noise degrade Rt estimate quality is lacking. By adapting Fisher information and experimental design theory, we develop an analytical framework to quantify the uncertainty induced by under-reporting and delays in reporting infections. This yields a novel metric, defined by the geometric means of reporting and cumulative delay probabilities, for ranking surveillance data informativeness. We apply this metric to two primary data sources for inferring Rt: epidemic case and death curves. We find that the assumption of death curves as more reliable, commonly made for acute infectious diseases such as COVID-19 and influenza, is not obvious and possibly untrue in many settings. Our framework clarifies and quantifies how actionable information about pathogen transmissibility is lost due to surveillance limitations.
Evaluating specialist intensive support teams for adults with intellectual disabilities who display behaviours that challenge: The IST-ID mixed methods study
Authors: Hassiotis Angela , Kouroupa Athanasia , Hamza Leila , Marston Louise , Romeo Renee , Yaziji Nahel , Hall Ian , Langdon Peter E , Courtenay Ken , Taggart Laurence , Morant Nicola , Crossey Vicky , Lloyd-Evans Brynmor 
Published: May 2022

AbstractBackgroundIntensive Support Teams (ISTs) are recommended for individuals with intellectual disabilities who display behaviours that challenge. However, there is currently little evidence about the clinical and cost effectiveness of IST models operating in England.AimsTo investigate the clinical and cost effectiveness of IST models.MethodsWe carried out a cohort study to evaluate the clinical and cost-effectiveness of two previously identified IST models (independent and enhanced) in England. Adult participants (n=226) from 21 ISTs (10 independent and 11 enhanced) were enrolled. The primary outcome was change in challenging behaviour between baseline and 9 months measured by the Aberrant Behaviour Checklist-Community 2.ResultsWe found no statistically significant differences between models for the primary outcome (adjusted β: 4.27; 95% CI: -6.34 to 14.87; p=0.430) or any secondary outcomes. Quality Adjusted Life Years (0.0158; 95% CI: -0.0088 to 0.0508) and costs (£3409.95; 95% CI: -£9957.92 to £4039.89) of the two models were comparable.ConclusionsThe study provides evidence that both models were associated with clinical improvement for similar costs at follow-up. We recommend that the choice of service model should rest with local services. Further research should investigate the critical components of IST care to inform the development of fidelity criteria, and policy makers should consider whether roll out of such teams should be mandated.Study registration numberClinicalTrials.govNCT03586375; IRAS 239820; National Institute for Health Research (NIHR) Central Portfolio Management System (CPMS) 38554.
Deep learning for subtypes identification of pure seminoma of the testis
Authors: Medvedev Kirill E. , Acosta Paul H. , Jia Liwei , Grishin Nick V. 
Published: May 2022

AbstractThe most critical step in the clinical diagnosis workflow is the pathological evaluation of each tumor sample. Deep learning is a powerful approach that is widely used to enhance diagnostic accuracy and streamline the diagnosis process. In our previous study using omics data, we identified two distinct subtypes of pure seminoma. Seminoma is the most common histological type of testicular germ cell tumors (TGCTs). Here we developed a deep learning decision making tool for the identification of seminoma subtypes using histopathological slides. We used all available slides for pure seminoma samples from The Cancer Genome Atlas (TCGA). The developed model showed an area under the ROC curve of 0.896. Our model not only confirms the presence of two distinct subtypes within pure seminoma but also unveils the presence of morphological differences between them that are imperceptible to the human eye.
United States’ political climates and the spread of SARS-2-COVID-19 during 2020
Authors: Pratto Felicia , Cortopassi Andrew , Marrouch Natasza 
Published: May 2022

AbstractWe tested whether the political climate in each U.S. state and Washington, DC determined the nature of the spread of COVID-19 cases and deaths in those polities during 2020. Political climate for each polity was indexed as a weighted average of the proportion of Republicans in legislatures in 2018 and the degree of public trust in both the White House and President Trump to handle COVID-19 in April, 2020. We found that polities higher on the political climate index had faster increases in per capita COVID-19 cases and deaths. Such Republican-trusting polities also had lower access to health care and less public engagement in prevention behavior, both of which mediated the influence of political climate on COVID- 19 cases and deaths. Further, the relationship between incidence of COVID-19 cases and deaths was weaker in more Republican-trusting polities. Political climate can be seen as contributing to more cases and deaths due to lower access to health care and to lower public adherence to public health guidelines in polities led by Republicans and which trusted the Trump White House to handle the pandemic.
Evaluation of a disease-specific mHealth-based exercise self-tracking measure
Authors: Ensari Ipek , Horan Emma , Elhadad Noémie , Bakken Suzanne R. 
Published: May 2022

AbstractObjectivesThis study investigates the concurrent and construct validity of a brief, customizable exercise self-tracking item from a research mHealth App (“Phendo”) for use as a measure of day-level and habitual exercise behavior in endometriosis.Study SampleStudy 1 included 52 participants who were recruited online and provided data for up to 14 days. Study 2 included 359 Phendo users who had retrospectively-collected data on the study measures.MethodsIn Study 1, we evaluated the responses on the self-tracking exercise item as estimates of day-level moderate-to-vigorous intensity exercise (MVE) and total step counts. Comparison measures included recall-based MVE minutes and accelerometry-based step counts, which were self-reported through daily surveys. In Study 2, we derived a measure of habitual exercise using each individual’s longitudinal self-tracked responses. We assessed its concurrent validity using the Nurses’ Health Study II Physical Activity Scale (NHS-II) as the comparison measure. We assessed its discriminant validity through known-group differences analysis where the sample was dichotomized based on Health Survey Short Form-36 (SF-36) and body mass index (BMI).Data AnalysisWe assessed bivariate associations between the scores on the self-tracking and comparison measures using Kendall’s rank correlations. We estimated daily MVE and step counts (Study 1), and weekly exercise (Study 2) from the self-tracking item scores through adjusted linear and polynomial regression models. We used t-tests and linear regression to conduct known-group differences analyses.ResultsIn Study 1, self-tracked exercise responses were moderately correlated with survey based MVE and step counts. Regression analyses indicated that overall exercise responses were associated with ∼17 minutes of MVE for the average participant (B=16.09, t=3.11, p=0.045). Self-tracked aerobic-type exercise was a stronger predictor of MVE minutes and step counts (B=27.561, t=5.561, p<0.0001). In Study 2, each self-tracked exercise instance corresponded to ∼19 minutes of exercise per week on the NHS-II Scale (B=19.80, t=2.1, p=0.028). Finally, there were statistically significant differences between the groups dichotomized based on SF-36 subscale scores and BMI.ConclusionThis study presents preliminary evidence on the concurrent and discriminant validity of a brief mHealth App measure for exercise self-tracking among individuals with endometriosis. These findings have implications in the context of large-scale studies that involve monitoring a diverse group of participants over long durations of time, as well as engaging and retaining research participants.
Allergen recognition by specific effector Th2 cells enables IL-2-dependent activation of regulatory T cell responses in humans
Authors: Lozano-Ojalvo Daniel , Tyler Scott R. , Aranda Carlos J. , Wang Julie , Sicherer Scott , Sampson Hugh A. , Wood Robert A. , Burks A. Wesley , Jones Stacie M. , Leung Donald Y. M. , Curotto de Lafaille Maria , Berin M. Cecilia 
Published: May 2022

AbstractType 2 allergen-specific T cells are essential for the induction and maintenance of allergies to foods, and Tregs specific for these allergens are assumed to be involved in their resolution. However, it has not been convincingly demonstrated whether allergen-specific Treg responses are responsible for the generation of oral tolerance in humans. We observed that sustained food allergen exposure in the form of oral immunotherapy resulted in increased frequency of Tregs only in individuals with lasting clinical tolerance. We sought to identify regulatory components of the CD4+ T cell response to food allergens by studying their functional activation over time in vitro and in vivo. Two subsets of Tregs expressing CD137 or CD25/OX40 were identified with a delayed kinetics of activation compared to clonally enriched pathogenic effector Th2 cells. Treg activation was dependent on IL-2 derived from effector T cells. In vivo exposure to peanut in the form of an oral food challenge of allergic subjects induced a delayed and persistent activation of Tregs after initiation of the allergen-specific Th2 response. Our results reveal a dependency of Tregs on effector Th2 cells for their activation and highlight the important role of IL-2 in the generation of a regulatory response to food allergens.One Sentence SummaryInitiation of allergen-specific Th2 cell responses induces an IL-2-mediated activation of Tregs with suppressive properties.
Mitochondrial DNA heteroplasmy distinguishes disease manifestation in PINK1- and PRKN-linked Parkinson’s disease
Authors: Trinh Joanne , Hicks Andrew A. , König Inke R. , Delcambre Sylvie , Lüth Theresa , Schaake Susen , Wasner Kobi , Ghelfi Jenny , Borsche Max , Vilariño-Güell Carles , Hentati Faycel , Germer Elisabeth L. , Bauer Peter , Takanashi Masashi , Kostić Vladimir , Lang Anthony E. , Brüggemann Norbert , Pramstaller Peter P. , Pichler Irene , Rajput Alex , Hattori Nobutaka , Farrer Matthew J. , Lohmann Katja , Weissensteiner Hansi , May Patrick , Klein Christine , Grünewald Anne 
Published: May 2022

AbstractBiallelic mutations in PINK1 and PRKN cause recessively inherited Parkinson’s disease (PD). Though some studies suggest that PINK1/PRKN monoallelic mutations may not contribute to risk, deep phenotyping assessment showed that PINK1 or PRKN monoallelic pathogenic variants were at a significantly higher rate in PD compared to controls. Given the established role of PINK1 and Parkin in regulating mitochondrial dynamics, we explored mitochondrial DNA (mtDNA) integrity and inflammation as potential disease modifiers in carriers of mutations in these genes. MtDNA integrity, global gene expression and serum cytokine levels were investigated in a large collection of biallelic (n=84) and monoallelic (n=170) carriers of PINK1/PRKN mutations, iPD patients (n=67) and controls (n=90). Affected and unaffected PINK1/PRKN monoallelic mutation carriers can be distinguished by heteroplasmic mtDNA variant load (AUC=0.83, CI:0.74-0.93). Biallelic PINK1/PRKN mutation carriers harbor more heteroplasmic mtDNA variants in blood (p=0.0006, Z=3.63) compared to monoallelic mutation carriers. This enrichment was confirmed in iPSC-derived and postmortem midbrain neurons from biallelic PRKN-PD patients. Lastly, the heteroplasmic mtDNA variant load was found to correlate with IL6 levels in PINK1/PRKN mutation carriers (r=0.57, p=0.0074). PINK1/PRKN mutations predispose individuals to mtDNA variant accumulation in a dose- and disease-dependent manner. MtDNA variant load over time is a potential marker of disease manifestation in PINK1/PRKN mutation carriers.
HUMAN PAPILLOMAVIRUS SEROTYPES IN ABNORMAL CERVICAL SMEARS IN CALABAR CROSS RIVER STATE A CROSS SECTIONAL STUDY
Authors: Orji Ocheze Chinwendu , Eyong Edu Michael , Nnoli Martins Anadozo , Ugbem Theophilus Ipeh , Samaila Modupeola , Rotimi Solomon Oladapo , Ekanem Ima-obong Asuquo 
Published: May 2022

ABSTRACTBackgroundHuman Papillomavirus (HPV) is sexually transmitted and constitutes the major cause of cancer of the cervix and could be detected using cervical smear screening test.Aim and objectiveTo determine the frequency of high risk HPV serotypes (16,18,33,45)in abnormal cervical smears in women aged 18-65 years in Calabar, Cross River State using cytological method over a period of one year from 1stMarch, 2017 to 28thFebruary, 2018 in Cross River State, Nigeria.Materials and methodThe study was a cross sectional study carried out in University of Calabar Teaching Hospital, Calabar on women aged 18-65 years who met the study inclusion criteria and were consecutively selected for conventional cervical screening test from the three provinces of Efik, Efut and Qua provinces. Females who were positive for squamous intraepithelial lesion after screening results were subjected to Human papillomavirus deoxyribonucleic acid (HPV DNA) testing.Results304 women aged 18-65 years were recruited into the study. Of these only 30 had intraepithelial lesions. Low grade squamous lntraepithelial lesions (LSIL) predominated with 63.3%(19) as compared with High grade squamous lntraepithelial lesion of 36.6%(11). HPV DNA was observed in all the abnormal cytology subjected to HPV DNA test. The prevalence rate of high risk HPV in this study was 9.9 %. The commonest serotypes found among study participants were HPV 16,33,and 45 with prevalence of 4.7%, 100% and 61.9% respectively.Among participants infected with HPV 33 and HPV 45, 13(61.9%) and 8(38.1%) had low grade squamous Intraepithelial lesion respectively while 8(38.1%) and 5(23.8%) had high grade squamous Intraepithelial lesion respectivelyIn this study,66.67%(14) out of 21 participants had HPV DNA co – infection.ConclusionThe prevalent HPV serotypes were 16,33 and 45 from this study with serotypes 33 being the commonest. Advocacy for HPV vaccine for reproductive age females should be encouraged and this should be included with established cervical cancer screening programs in government hospitals.
Antibody response to SARS-CoV2 among COVID-19 confirmed cases, and correlates with neutralizing assay in a subgroup of patients in Delhi National Capital Region, India
Authors: Misra Puneet , Kant Shashi , Guleria Randeep , Rai Sanjay , Jaiswal Abhishek , Mandal Suprakash , Medigeshi Guruprasad R , Ahmad Mohammad , Rahman Anisur , Sangral Meenu , Yadav Kapil , Bairwa Mohan , Haldar Partha , Kumar Parveen 
Published: May 2022

AbstractBackgroundPlaque reduction neutralization test (PRNT) is the gold standard to detect neutralizing capacity of the serum antibodies. Neutralizing antibody confers protection against further infection. The present study was done with the objective to measure the antibody level against SARS-CoV2 among laboratory confirmed COVID-19 cases and to evaluate whether the presence of anti-SARS-CoV2 antibodies indicate virus neutralizing capacity.MethodsOne hundred COVID-19 confirmed cases were recruited. Sociodemographic details and history of COVID-19 vaccination, contact with positive COVID-19 cases, and symptoms were ascertained using a self-developed semi-structured interview schedule. Serum samples of the participants were collected within three months from date of the positive report of COVID-19. The presence of anti-SARS-CoV-2 antibodies (IgA, IgG and IgM antibodies), receptor binding domain antibodies (anti-RBD), and neutralizing antibodies were measured.FindingsAlmost all participants had Anti-SARS-CoV2 antibodies (IgA, IgG and IgM) (99%) and Anti-RBD IgG antibodies (97%). However, only 69% had neutralizing antibodies against SARS-CoV2. Anti-RBD antibody levels were significantly higher among participants having neutralizing antibodies compared to those who didn’t.InterpretationThe present study highlights that presence of antibodies against SARS-CoV2, or presence of anti-RBD antibody doesn’t necessarily imply presence of neutralizing antibodies.FundingWorld Health Organisation
How might postprandial ‘extras’ fatten? Simulation of a gastric mixing hypothesis
Authors: Booth David A. 
Published: May 2022

ABSTRACTIt was suggested that the ingestion of extra calories towards the end of or shortly after a meal might be especially fattening. That hypothesis was based on the intuition that mixing of the sugared drink and accompaniments while the stomach was emptying rapidly would delay the release of hunger less than the same intake in the hour before the next meal. This paper presents an examination of that mechanism by calculating the time course of gastric emptying with extra intake at different times after the meal. The output from these simulations confirmed that early further energy would delay the end of emptying less than later. However, within the parameters tested, the effect is not large. Fattening effects of calories after meals could arise by a variety of mechanisms that remain to be tested without disrupting daily life.“Highlights”Extra intake may be more fattening shortly after meals than later.That proposal was supported by theoretical calculations of gastric emptying.Hence the timing of energy intake well before a meal seems critical to its effect on weight.The eater’s own concepts of meal, snacks and drinks are key to research on weight control.
‘Self-Management Intervention through Lifestyle Education for Kidney health’ (the SMILE-K study): protocol for a single-blind longitudinal randomised control trial with nested pilot study
Authors: Lightfoot Courtney J. , Wilkinson Thomas J. , Yates Thomas , Davies Melanie J , Smith Alice C. 
Published: May 2022

ABSTRACTIntroductionMany people living with chronic kidney disease (CKD) are expected to self-manage their condition. Patient activation is the term given to describe the knowledge, skills, and confidence a person has in managing their own health and is closely related to the engagement in preventive health behaviors. Self-management interventions have the potential to improve remote disease management and health outcomes. We are testing an evidence- and theory-based digital self-management structured 10-week programme developed for CKD patients called ‘My Kidneys & Me’. The primary aim of the study (SMILE-K) is to assess the effect on patient activation levels.Methods and analysisA single-blind randomised control trial (RCT) with a nested pilot study will assess the feasibility of the intervention and study design before continuation to a full RCT. Individuals aged 18 years or older, with established CKD stage 3-4 (eGFR of 15-59 ml/min/1.73m2) will be recruited through both primary and secondary care pathways. Participants will be randomised into two groups: intervention group and control group. The primary outcome is the Patient Activation Measure (PAM-13). The full RCT will assess the effect of the programme on online self-reported outcomes which will be assessed at baseline, after 10-weeks, and then after 20-weeks in both groups. A total sample size of n=432 participants are required based on a 2:1 randomisation. A sub-study will measure physiological changes (e.g., muscle mass, physical function) and patient experience (qualitative semi-structured interviews).Ethics and disseminationThis study was fully approved by the Research Ethics Committee-Leicester South on the 19/11/2020 (reference: 17/EM/0357). All participants are required to provide informed consent obtained online. The results are expected to be published in scientific journals and presented at clinical research conferences. This is protocol version 1.0 dated 27/01/2021.Trial registration numberThe study was prospectively registered as ISRCTN18314195 in December 2020.