bluuebunny/crossref_metadata_2025_split huggingface dataset:
School-level intra-cluster correlation coefficients and autocorrelations for children’s accelerometer-measured physical activity in England by age and gender
Authors: Salway Ruth , Jago Russell , de Vocht Frank , House Danielle , Porter Alice , Walker Robert , Kipping Ruth , Owen Christopher G. , Hudda Mohammed T. , Northstone Kate , van Sluijs Esther ,   International Children’s Accelerometry Database (ICAD) Collaborators, Atkin Andrew , Ekelund Ulf , Esliger Dale , Hansen Bjorge H. , Sherar Lauren , van Sluijs Esther 
Published: August 2024

Abstract
Background
Randomised, cluster-based study designs in schools are commonly used to evaluate children’s physical activity interventions. Sample size estimation relies on accurate estimation of the intra-cluster correlation coefficient (ICC), but published estimates, especially using accelerometry-measured physical activity, are few and vary depending on physical activity outcome and participant age. Less commonly-used cluster-based designs, such as stepped wedge designs, also need to account for correlations over time, e.g. cluster autocorrelation (CAC) and individual autocorrelation (IAC), but no estimates are currently available. This paper estimates the school-level ICC, CAC and IAC for England children’s accelerometer-measured physical activity outcomes by age group and gender, to inform the design of future school-based cluster trials.

Methods
Data were pooled from seven large English datasets of accelerometer-measured physical activity data between 2002–18 (> 13,500 pupils, 540 primary and secondary schools). Linear mixed effect models estimated ICCs for weekday and whole week for minutes spent in moderate-to-vigorous physical activity (MVPA) and being sedentary for different age groups, stratified by gender. The CAC (1,252 schools) and IAC (34,923 pupils) were estimated by length of follow-up from pooled longitudinal data.

Results
School-level ICCs for weekday MVPA were higher in primary schools (from 0.07 (95% CI: 0.05, 0.10) to 0.08 (95% CI: 0.06, 0.11)) compared to secondary (from 0.04 (95% CI: 0.03, 0.07) to (95% CI: 0.04, 0.10)). Girls’ ICCs were similar for primary and secondary schools, but boys’ were lower in secondary. For all ages, combined the CAC was 0.60 (95% CI: 0.44–0.72), and the IAC was 0.46 (95% CI: 0.42–0.49), irrespective of follow-up time. Estimates were higher for MVPA vs sedentary time, and for weekdays vs the whole week.

Conclusions
Adequately powered studies are important to evidence effective physical activity strategies. Our estimates of the ICC, CAC and IAC may be used to plan future school-based physical activity evaluations and were fairly consistent across a range of ages and settings, suggesting that results may be applied to other high income countries with similar school physical activity provision. It is important to use estimates appropriate to the study design, and that match the intended study population as closely as possible.
Prevalence of dermatoses in geriatric singaporeans in the community - a cross-sectional study
Authors: Juay Lester , Bhupendrabhai Monil Nagad , Ahmad Siti Hafizah Binte , Wong Hung Chew , Chong Justin Wee-Min , Tan Wee Hian , Chandran Nisha Suyien 
Published: August 2024

Abstract
Background
Little is known about the prevalence of dermatoses in “skin-well” geriatric Singaporeans. We aim to identify the prevalence of dermatoses and their associations within the geriatric population in Singapore, and to understand the distribution of dermatological encounters presenting to primary care physicians, and the resultant referral behaviour.

Methods
A joint quantitative-qualitative study was performed across 8 months. Patients aged 65 years and above who visited a local polyclinic for management of non-dermatological chronic diseases were recruited. They were administered questionnaires, and underwent full skin examinations. Online surveys were disseminated to polyclinic physicians under the same healthcare cluster.

Results
201 patients and 53 physicians were recruited. The most common dermatoses identified in patients were benign tumours and cysts (97.5%), and asteatosis (81.6%). For every 1-year increase in age, the odds of having asteatosis increased by 13.5% (95% CI 3.4–24.7%, p = 0.008), and urticarial disorders by 14.6% (95% CI 0.3–30.9%, p = 0.045). Patients who used any form of topical preparations on a daily basis had higher odds of having eczema and inflammatory dermatoses (OR 2.51, 95% CI 1.38 to 4.56, p = 0.003). Physicians reported dermatological conditions involving 20% of all clinical encounters. Eczema represented the most commonly reported dermatosis within the first visit. 50% of dermatology referrals were done solely at the patient’s own request.

Conclusion
The prevalence of dermatoses in the elderly in Singapore is high, especially asteatosis. Prompt recognition by the primary healthcare provider potentially prevents future morbidity. Outreach education for both primary care physicians and the general public will be key.

Ethics approval
National Healthcare group (NHG) Domain Specific Review Board (DSRB), Singapore, under Trial Registration Number 2020/00239, dated 11 August 2020.
Biomarkers of Airway Disease, Barrett’s and Underdiagnosed Reflux Noninvasively (BAD-BURN) in World Trade Center exposed firefighters: a case–control observational study protocol
Authors: Javed Urooj , Podury Sanjiti , Kwon Sophia , Liu Mengling , Kim Daniel H. , Fallahzadeh Aida , Li Yiwei , Khan Abraham R. , Francois Fritz , Schwartz Theresa , Zeig-Owens Rachel , Grunig Gabriele , Veerappan Arul , Zhou Joanna , Crowley George , Prezant David J. , Nolan Anna 
Published: August 2024

Abstract
Background
Particulate matter exposure (PM) is a cause of aerodigestive disease globally. The destruction of the World Trade Center (WTC) exposed first responders and inhabitants of New York City to WTC-PM and caused obstructive airways disease (OAD), gastroesophageal reflux disease (GERD) and Barrett’s Esophagus (BE). GERD not only diminishes health-related quality of life but also gives rise to complications that extend beyond the scope of BE. GERD can incite or exacerbate allergies, sinusitis, bronchitis, and asthma. Disease features of the aerodigestive axis can overlap, often necessitating more invasive diagnostic testing and treatment modalities. This presents a need to develop novel non-invasive biomarkers of GERD, BE, airway hyperreactivity (AHR), treatment efficacy, and severity of symptoms.

Methods
Our observational case-cohort study will leverage the longitudinally phenotyped Fire Department of New York (FDNY)-WTC exposed cohort to identify Biomarkers of Airway Disease, Barrett’s and Underdiagnosed Reflux Noninvasively (BAD-BURN). Our study population consists of n = 4,192 individuals from which we have randomly selected a sub-cohort control group (n = 837). We will then recruit subgroups of i. AHR only ii. GERD only iii. BE iv. GERD/BE and AHR overlap or v. No GERD or AHR, from the sub-cohort control group. We will then phenotype and examine non-invasive biomarkers of these subgroups to identify under-diagnosis and/or treatment efficacy. The findings may further contribute to the development of future biologically plausible therapies, ultimately enhance patient care and quality of life.

Discussion
Although many studies have suggested interdependence between airway and digestive diseases, the causative factors and specific mechanisms remain unclear. The detection of the disease is further complicated by the invasiveness of conventional GERD diagnosis procedures and the limited availability of disease-specific biomarkers. The management of reflux is important, as it directly increases risk of cancer and negatively impacts quality of life. Therefore, it is vital to develop novel noninvasive disease markers that can effectively phenotype, facilitate early diagnosis of premalignant disease and identify potential therapeutic targets to improve patient care.

Trial registration
Name of Primary Registry: “Biomarkers of Airway Disease, Barrett's and Underdiagnosed Reflux Noninvasively (BADBURN)”. Trial Identifying Number: NCT05216133. Date of Registration: January 31, 2022.
Field-applicable simultaneous multiplex LAMP assay for screening HBV and HCV co-infection in a single tube
Authors: Agel Esra , Altın Kevser Hanne 
Published: August 2024

Abstract
Background
Globally, around 7 to 20 million people are believed to be suffering from coinfection with both hepatitis B virus (HBV) and hepatitis C virus (HCV). The loop-mediated isothermal amplification (LAMP) approach, introduced by Notomi and colleagues, has undergone substantial advancements as an effective molecular tool that enables the simultaneous analysis of multiple samples in a single tube.

Methods
The present study examined the simultaneous detection of HBV and HCV in a single tube using melt curve analysis multiplex LAMP (mLAMP), which is based on the identification of unique melting peak temperatures. Selected regions for primer design including the S gene of HBV and the UTR gene of HCV. Primer optimization is initially performed through individual HBV and HCV LAMP analysis. Following the optimization process, the mLAMP assay was evaluated by optimizing the multiplex reaction mixture, determining the reaction time, and analyzing the limit of detection (LOD). The results are also analyzed using lateral flow dipsticks (LFD), which enable the visual detection of HBV and HCV by adding 20 pmol FITC-labeled LF primers into the reaction mixture prior the mLAMP.

Results
The LOD for the mLAMP assay was determined as 10 copies/µl, and no cross-reactivity with other microorganisms was detected. The detection results obtained from patient plasma were also visually demonstrated using LFD, and displayed significant concordance with those obtained from Real-Time Polymerase Chain Assay. The mLAMP assay revealed a diagnostic sensitivity of 95% for detecting the HBV, and LOD is 90% for HCV. The overall diagnostic sensitivity of the mLAMP assay for both viruses was 85%. The assay confirmed a specificity of 100%.

Conclusion
The mLAMP assay displays significant promise for analyzing coinfected samples by simultaneously detecting the dual targets HBV and HCV within a set temperature of 62 °C, all within a time frame of 1 h. Additionally, when paired with disposable LFD, the mLAMP assay enables rapid visual detection of assay results in a matter of minutes. The result contributes to the mLAMP assay being highly suitable for coinfection screening, particularly in field conditions.
Virus and viral components transmitted through surgical smoke; a silent danger in operating room: a systematic review
Authors: Mahdood Bahareh , Merajikhah Amirmohammad , Mirzaiee Mina , Bastami Maryam , Banoueizadeh Sara 
Published: August 2024

Abstract
Background
During surgical procedures, heat-generating devices are widely used producing surgical smoke (SS). Since the SS can transmit infectious viruses, this systematic review was designed to investigate the potential viruses transmitted through SS.

Methods
PubMed, Scopus, Web of Science, ProQuest, and Embase databases, along with Cochran Library, and Google Scholar search engine were searched systematically (by April 21, 2024). No language, place, and time restrictions were considered. All studies evaluating the SS and virus transmission, and whole investigations regarding the viral infections transmitted through SS were totally considered inclusion criteria. Besides, non-original, qualitative, case reports, case series, letters to the editor, editorial, and review studies were excluded from the analysis. This study was conducted in accordance with the PRISMA 2020 statement.

Results
Twenty-six eligible studies were selected and reviewed for data extraction. The results showed that the SS contains virus and associated components. Six types of viruses or viral components were identified in SS including papillomavirus (HPV, BPV), Human Immunodeficiency Virus (HIV), varicella zoster, Hepatitis B (HBV), SARS-CoV-2, and Oral poliovirus (OPV), which are spread to surgical team through smoke-producing devices.

Conclusions
Since the studies confirm the presence of viruses, and viral components in SS, the potential risk to the healthcare workers, especially in operating room (OR), seems possible. Thus, the adoption of protective strategies against SS is critical. Despite the use of personal protective equipment (PPE), these viruses could affect OR personnel in surgical procedures.
Association between COVID-19 and the incidence of type 1 diabetes in Portugal – a registry study
Authors: Bjerregaard-Andersen Morten , Da Silva Jessica , Diogo Rui , Claro Ana Raquel , Ferro Inês , Romana Andreia , Rocha Patrícia , Sá Beatriz , Lobarinhas Goreti , Rolim Sara , Juhl Claus Bogh , Højlund Kurt , Fernandes Isabel , Antunes Sónia , Félix Calha Maria Manuela , Gama Guida , Amálio Sofia , Figueiras Mariana , Silva Teresa , Rosado Margarida , Ferrão Estela , Arez Luísa , Baptista Ana , Martins Ferreira Adriana , Alba Diana , Godinho Carlos , Leite Ana Luísa , Afonso Lopes Maria de Lurdes , Sampaio Maria Lurdes , Serra-Caetano Joana , Carvalho Eugenia 
Published: August 2024

Abstract
Background
Viral respiratory infections may precipitate type 1 diabetes (T1D). A possible association between the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for COVID-19, and the incidence of T1D is being determined. This study was carried out using Portuguese registries, aiming at examining temporal trends between COVID-19 and T1D.

Methods
Hospital data, comparing the incidence before and during the COVID-19 pandemic, from children and young adults diagnosed with new-onset T1D, was acquired beginning in 2017 and until the end of 2022. Data was obtained from nine different Portuguese hospital units. The impact of the COVID-19 pandemic, beginning in March 2020, was assessed comparing the annual numbers of new-onset T1D cases. The annual median levels of glucose, glycated hemoglobin (HbA1c) and fasting C-peptide at T1D diagnosis were compared. The annual number of diabetic ketoacidosis (DKA) episodes among new T1D cases was also assessed at two centers.

Results
In total, data from 574 newly diagnosed T1D patients was analyzed, including 530 (92.3%) children. The mean ages for child and adult patients were 9.1 (SD 4.4) and 32.8 (SD 13.6) years, respectively. 57.8% (331/573) were male, one patient had unknown sex. The overall median (25–75 percentiles) levels of glucose, HbA1c and fasting C-peptide at diagnosis were 454 mg/dL (356–568), 11.8% (10.1–13.4) and 0.50 µg/L (0.30–0.79), respectively. DKA at T1D diagnosis was present in 48.4% (76/157). For eight centers with complete 2018 to 2021 data (all calendar months), no overall significant increase in T1D cases was observed during the COVID-19 pandemic, i.e. 90 cases in 2018, 90 cases in 2019, 112 in 2020 and 100 in 2021 (P for trend = 0.36). Two of the centers, Faro (CHUA) and Dona Estefânia (CHULC) hospitals, did however see an increase in T1D from 2019 to 2020. No significant changes in glucose (P = 0.32), HbA1c (P = 0.68), fasting C-peptide (P = 0.20) or DKA frequency (P = 0.68) at the time of T1D diagnosis were observed over the entire study period.

Conclusion
The T1D incidence did not increase significantly, when comparing the years before and during the COVID-19 pandemic, nor did key metabolic parameters or number of DKA episodes change.
Modelling timelines to elimination of sleeping sickness in the Democratic Republic of Congo, accounting for possible cryptic human and animal transmission
Authors: Crump Ronald E. , Aliee Maryam , Sutherland Samuel A. , Huang Ching-I , Crowley Emily H. , Spencer Simon E. F. , Keeling Matt J. , Shampa Chansy , Mwamba Miaka Erick , Rock Kat S. 
Published: August 2024

Abstract
Background
Sleeping sickness (gambiense human African trypanosomiasis, gHAT) is a vector-borne disease targeted for global elimination of transmission (EoT) by 2030. There are, however, unknowns that have the potential to hinder the achievement and measurement of this goal. These include asymptomatic gHAT infections (inclusive of the potential to self-cure or harbour skin-only infections) and whether gHAT infection in animals can contribute to the transmission cycle in humans.

Methods
Using modelling, we explore how cryptic (undetected) transmission impacts the monitoring of progress towards and the achievement of the EoT goal. We have developed gHAT models that include either asymptomatic or animal transmission, and compare these to a baseline gHAT model without either of these transmission routes, to explore the potential role of cryptic infections on the EoT goal. Each model was independently calibrated to five different health zones in the Democratic Republic of the Congo (DRC) using available historical human case data for 2000–2020 (obtained from the World Health Organization’s HAT Atlas). We applied a novel Bayesian sequential updating approach for the asymptomatic model to enable us to combine statistical information about this type of transmission from each health zone.

Results
Our results suggest that, when matched to past case data, we estimated similar numbers of new human infections between model variants, although human infections were slightly higher in the models with cryptic infections. We simulated the continuation of screen-confirm-and-treat interventions, and found that forward projections from the animal and asymptomatic transmission models produced lower probabilities of EoT than the baseline model; however, cryptic infections did not prevent EoT from being achieved eventually under this approach.

Conclusions
This study is the first to simulate an (as-yet-to-be available) screen-and-treat strategy and found that removing a parasitological confirmation step was predicted to have a more noticeable benefit to transmission reduction under the asymptomatic model compared with the others. Our simulations suggest vector control could greatly impact all transmission routes in all models, although this resource-intensive intervention should be carefully prioritised.

Graphical Abstract
Knockdown resistance mutations in Phlebotomus argentipes sand flies in Bihar, India
Authors: Kristan Mojca , Hazelgrove Carlamarita , Kumar Kundan , Kumar Ashish , Kumar Vijay , Das Pradeep , Collins Emma , Mark-Carew Miguella , Campino Susana , Cameron Mary 
Published: August 2024

Abstract
Background
Vector control based on indoor residual spraying (IRS) is one of the main components of the visceral leishmaniasis (VL) elimination programme in India. Dichlorodiphenyltrichloroethane (DDT) was used for IRS until 2015 and was later replaced by the synthetic pyrethroid alpha-cypermethrin. Both classes of insecticides share the same target site, the voltage-gated sodium channel (Vgsc). As high levels of resistance to DDT have been documented in the local sand fly vector, Phlebotomus argentipes, it is possible that mutations in the Vgsc gene could provide resistance to alpha-cypermethrin, affecting current IRS pyrethroid-based vector control.

Methods
This study aimed to compare frequencies of knockdown resistance (kdr) mutations in Vgsc between two sprayed and two unsprayed villages in Bihar state, India, which had the highest VL burden of the four endemic states. Across four villages, 350 female P. argentipes were collected as part of a 2019 molecular xenomonitoring study. DNA was extracted and used for sequence analysis of the IIS6 fragment of the Vgsc gene to assess the presence of kdr mutations.

Results
Mutations were identified at various positions, most frequently at codon 1014, a common site known to be associated with insecticide resistance in mosquitoes and sand flies. Significant inter-village variation was observed, with sand flies from Dharampur, an unsprayed village, showing a significantly higher proportion of wild-type alleles (55.8%) compared with the three other villages (8.5–14.3%). The allele differences observed across the four villages may result from selection pressure caused by previous exposure to DDT.

Conclusions
While DDT resistance has been reported in Bihar, P. argentipes is still susceptible to pyrethroids. However, the presence of kdr mutations in sand flies could present a threat to IRS used for VL control in endemic villages in India. Continuous surveillance of vector bionomics and insecticide resistance, using bioassays and target genotyping, is required to inform India’s vector control strategies and to ensure the VL elimination target is reached and sustained.

Graphical Abstract
Building shape-focused pharmacophore models for effective docking screening
Authors: Moyano-Gómez Paola , Lehtonen Jukka V. , Pentikäinen Olli T. , Postila Pekka A. 
Published: August 2024

Abstract
The performance of molecular docking can be improved by comparing the shape similarity of the flexibly sampled poses against the target proteins’ inverted binding cavities. The effectiveness of these pseudo-ligands or negative image-based models in docking rescoring is boosted further by performing enrichment-driven optimization. Here, we introduce a novel shape-focused pharmacophore modeling algorithm O-LAP that generates a new class of cavity-filling models by clumping together overlapping atomic content via pairwise distance graph clustering. Top-ranked poses of flexibly docked active ligands were used as the modeling input and multiple alternative clustering settings were benchmark-tested thoroughly with five demanding drug targets using random training/test divisions. In docking rescoring, the O-LAP modeling typically improved massively on the default docking enrichment; furthermore, the results indicate that the clustered models work well in rigid docking. The C+ +/Qt5-based algorithm O-LAP is released under the GNU General Public License v3.0 via GitHub (https://github.com/jvlehtonen/overlap-toolkit).

Scientific contribution
This study introduces O-LAP, a C++/Qt5-based graph clustering software for generating new type of shape-focused pharmacophore models. In the O-LAP modeling, the target protein cavity is filled with flexibly docked active ligands, the overlapping ligand atoms are clustered, and the shape/electrostatic potential of the resulting model is compared against the flexibly sampled molecular docking poses. The O-LAP modeling is shown to ensure high enrichment in both docking rescoring and rigid docking based on comprehensive benchmark-testing.

Graphical Abstract