bluuebunny/crossref_metadata_2025_split huggingface dataset:
A need for standardized reporting of introgression: Insights from studies across eukaryotes
Authors: Dagilis Andrius J. , Peede David , Coughlan Jenn M. , Jofre Gaston I. , D'Agostino Emmanuel R. R. , Mavengere Heidi , Tate Alexander D. , Matute Daniel R. 
Published: July 2022

AbstractWith the rise of affordable next-generation sequencing technology, introgression—or the exchange of genetic materials between taxa—has become widely perceived to be a ubiquitous phenomenon in nature. Although this claim is supported by several keystone studies, no thorough assessment of the frequency of introgression across eukaryotes in nature has been performed to date. In this manuscript, we aim to address this knowledge gap by examining patterns of introgression across eukaryotes. We collated a single statistic, Patterson's D, which can be used as a test for introgression across 123 studies to further assess how taxonomic group, divergence time, and sequencing technology influence reports of introgression. Overall, introgression has mostly been measured in plants and vertebrates, with less attention given to the rest of the Eukaryotes. We find that the most frequently used metrics to detect introgression are difficult to compare across studies and even more so across biological systems due to differences in study effort, reporting standards, and methodology. Nonetheless, our analyses reveal several intriguing patterns, including the observation that differences in sequencing technologies may bias values of Patterson's D and that introgression may differ throughout the course of the speciation process. Together, these results suggest the need for a unified approach to quantifying introgression in natural communities and highlight important areas of future research that can be better assessed once this unified approach is met.
Joule heating effect on radiating MHD mixed convection stagnation point flow along vertical stretching sheet embedded in a permeable medium and heat generation/absorption
Authors: Mehta Ruchika , Kumar Ravindra , Rathore Himanshu , Singh Jagdev 
Published: July 2022

AbstractThe goal of this study is to investigate magnetohydrodynamics varied convective stagnation point stream with a vertically extended sheet embedded in a permeable material. Warmth generation/absorption, radiation impacts, and viscous dissipation are all considered. Using the process of likeness change, the principal boundary layer equations are written and turned into nonlinear ordinary joined differential equations, and the numerical result is produced using the Runge–Kutta fourth‐order approach via shooting technique. Varied physical limits have different effects, such as velocity fraction restriction, mixed convection restriction, Hartmann numeral, Prandtl numeral, permeability restriction, warm air radiation restriction, hotness generation/absorption restriction, and so on, over velocity and temperature scatterings are introduced graphically and then mathematically. The skin friction constant, in addition to Nusselt numerals, over the sheet is determined, expressed mathematically as well as introduced through tables. Fluid velocity and temperature increase with radiation restriction Ra. Skin friction and Nusselt numeral are increasing functions of Hartmann numeral Ha, and decreasing ones of permeability restriction K.
The Effects of Acute High‐Intensity Interval Exercise and Hyperinsulinemic‐Euglycemic Clamp on Osteoglycin Levels in Young and Middle‐Aged Men
Authors: Bauer Carlie , Tacey Alexander , Garnham Andrew , Smith Cassandra , Woessner Mary N , Lin Xuzhu , Zarekookandeh Navabeh , Hare David L , Lewis Joshua R , Parker Lewan , Levinger Itamar 
Published: July 2022

ABSTRACTOsteoglycin (OGN) is a leucine‐rich proteoglycan that has been implicated in the regulation of glucose in animal models. However, its relationship with glucose control in humans is unclear. We examined the effect of high‐intensity interval exercise (HIIE) and hyperinsulinemic‐euglycemic clamp on circulating levels of OGN as well as whether circulating OGN levels are associated with markers of glycemic control and cardio‐metabolic health. Serum was analyzed for OGN (ELISA) levels from 9 middle‐aged obese men (58.1 ± 2.2 years, body mass index [BMI] = 33.1 ± 1.4 kg∙m−2, mean ± SEM) and 9 young men (27.8 ± 1.6 years, BMI = 24.4 ± 0.08 kg∙m−2) who previously completed a study involving a euglycemic‐hyperinsulinemic clamp at rest and after HIIE (4x4 minutes cycling at approximately 95% peak heart rate (HRpeak), interspersed with 2 minutes of active recovery). Blood pressure, body composition (dual‐energy X‐ray absorptiometry), and insulin sensitivity (hyperinsulinemic‐euglycemic clamp) were assessed. Serum OGN was higher in the young cohort compared with the middle‐aged cohort (65.2 ± 10.1 ng/mL versus 36.5 ± 4. 5 ng/mL, p ≤ 0.05). Serum OGN was unaffected by acute HIIE but decreased after the insulin clamp compared with baseline (~−27%, p = 0.01), post‐exercise (~−35%, p = 0.01), and pre‐clamp (~−32%, p = 0.02) time points, irrespective of age. At baseline, lower circulating OGN levels were associated with increased age, BMI, and fat mass, whereas higher OGN levels were related to lower fasting glucose. Higher OGN levels were associated with a higher glucose infusion rate. Exercise had a limited effect on circulating OGN. The mechanisms by which OGN affects glucose regulation should be explored in the future. © 2022 The Authors. JBMR Plus published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research.
Foldscope microscope, an inexpensive alternative tool to conventional microscopy—Applications in research and education: A review
Authors: Ganesan Mijithra , Selvan Christyraj Johnson Retnaraj Samuel , Venkatachalam Saravanakumar , Yesudhason Beryl Vedha , Chelladurai Karthikeyan Subbiahanadar , Mohan Manikandan , Kalimuthu Kalishwaralal , Narkhede Yogesh B. , Christyraj Jackson Durairaj Selvan 
Published: July 2022

AbstractMicroscope is a device used for the visualization of tiny objects which are not visible to the naked eye. Traditional microscopes have been crucial for the advancement of contemporary science and medicine. Recent advancements in the field of microscopy have fueled its exponential growth rate. However, due to their expensive cost and complicated structure, modern microscopes remain inaccessible to the majority of the public. Nonetheless, the foldscope paper microscope has made it possible for anyone to explore and understand the world of microbes and organisms. In this review, we have listed foldscope‐based research projects in various domains, as well as their key properties when compared to traditional research microscopes. In addition, we have briefly explored the impact of a foldscope microscope on public health, clinical diagnostics, forensic science, agriculture, basic science, developmental biology, and education. Moreover, the major drawbacks of paper microscopes and the current steps being taken to upgrade foldscope and its features are discussed in this review. Finally, we have concluded with our perspective that the microscope may be updated to imitate the advancement of a conventional microscope.Research Highlights
The foldscope, a low‐cost instrument for studying the microscopic world.
Foldscope applications were compared to conventional microscopes in many sectors.
The foldscope microscope's existing limitations and potential prospects are highlighted.
Automatic skin lesions detection from images through microscopic hybrid features set and machine learning classifiers
Authors: Alyami Jaber , Rehman Amjad , Sadad Tariq , Alruwaythi Maryam , Saba Tanzila , Bahaj Saeed Ali 
Published: July 2022

AbstractSkin cancer occurrences increase exponentially worldwide due to the lack of awareness of significant populations and skin specialists. Medical imaging can help with early detection and more accurate diagnosis of skin cancer. The physicians usually follow the manual diagnosis method in their clinics but nonprofessional dermatologists sometimes affect the accuracy of the results. Thus, the automated system is required to assist physicians in diagnosing skin cancer at early stage precisely to decrease the mortality rate. This article presents an automatic skin lesions detection through a microscopic hybrid feature set and machine learning‐based classification. The employment of deep features through AlexNet architecture with local optimal‐oriented pattern can accurately predict skin lesions. The proposed model is tested on two open‐access datasets PAD‐UFES‐20 and MED‐NODE comprising melanoma and nevus images. Experimental results on both datasets exhibit the efficacy of hybrid features with the help of machine learning. Finally, the proposed model achieved 94.7% accuracy using an ensemble classifier.Research highlights
The deep features accurately predicted skin lesions through AlexNet architecture with local optimal‐oriented pattern.
Proposed model is tested on two datasets PAD‐UFES‐20, MED‐NODE comprising melanoma, nevus images and exhibited high accuracy.
A qualitative study of unaffected ATM and CHEK2 carriers: How participants make meaning of ‘moderate risk’ genetic results in a population breast cancer screening trial
Authors: James Jennifer Elyse , Riddle Leslie , Caruncho Mikaella , Koenig Barbara Ann , Joseph Galen 
Published: July 2022

AbstractRelatively little is known about experiences of individuals with a pathogenic variant in a moderately penetrant breast cancer gene, particularly those without a personal history of cancer. The WISDOM trial is testing a model of risk‐based breast cancer screening that integrates genomic (nine genes and polygenic risk) and other risk factors. In the context of an embedded Ethical, Legal, and Social Implications (ELSI) study of WISDOM, we conducted qualitative interviews at two timepoints post‐result disclosure with 22 ATM and CHEK2 carriers. Results disclosure and interview recordings were transcribed and analyzed using a grounded theory analysis framework. We found that participants minimized the significance of their results in comparison to BRCA; were surprised but not alarmed by the results in the absence of family history; did not fundamentally change their perception of their breast cancer risk despite the new genomic information; exhibited variable responses to WISDOM’s screening and risk reduction recommendations; and shared test results with family but did not strongly encourage cascade testing. Participants viewed the results as having limited utility and responded accordingly. Our study offers important insights into how genetic test results for moderate‐risk genes are received, understood, and acted upon in population screening context.
High rates of treatment stage migration for early hepatocellular carcinoma and association with adverse outcomes: An Australian multicenter study
Authors: Loo Kee Fong , Woodman Richard J , Bogatic Damjana , Chandran Vidyaleha , Muller Kate , Chinnaratha Mohamed Asif , Bate John , Campbell Kirsty , Maddison Matthew , Narayana Sumudu , Le Hien , Pryor David , Wigg Alan 
Published: July 2022

AbstractBackground and AimThe rate of contraindications to percutaneous ablation (PA) for inoperable early hepatocellular carcinoma (HCC) and subsequent outcomes is not well described. We investigated the prevalence and outcomes of inoperable early HCC patients with contraindications to PA, resulting in treatment stage migration (TSM).MethodsBarcelona Clinic Liver Cancer (BCLC) 0/A patients diagnosed between September 2013 and September 2019 across five hospitals were identified. Primary endpoint was proportion of BCLC 0/A HCCs with contraindications to PA. Secondary endpoints included overall survival (OS), local tumor control (LTC), and recurrence‐free survival (RFS). The causal effects of PA versus TSM were assessed using a potential outcome means (POM) framework in which the average treatment effects (ATEs) of PA were estimated after accounting for potential selection bias and confounding.ResultsTwo hundred twenty patients with inoperable BCLC 0/A HCC were identified. One hundred twenty‐two patients (55.5%) had contraindications to PA and received TSM therapy, 98 patients (44.5%) received PA. The main contraindication to PA was difficult tumor location (51%). Patients who received TSM therapy had lower median OS (2.4 vs 5.3 years), LTC (1.0 vs 4.8 years), and RFS (0.8 vs 2.9 years); P < 0.001, respectively, compared with PA. The ATE for PA versus TSM yielded an additional 1.11 years (P = 0.019), 2.45 years (P < 0.001), and 1.64 years (P < 0.001) for OS, LTC, and RFS, respectively. Three‐year LTC after PA was suboptimal (65%).ConclusionOur study highlights high rates of contraindication to PA in early HCCs, resulting in TSM and poorer outcomes. The LTC rate for PA appears suboptimal despite being considered as curative therapy. Both findings support the exploration of improved treatment options for early HCCs.
Acceptability and feasibility of leveraging community‐based HIV counselling and testing platforms for same‐day oral PrEP initiation among adolescent girls and young women in Eastern Cape, South Africa
Authors: Medina‐Marino Andrew , Bezuidenhout Dana , Ngwepe Phuti , Bezuidenhout Charl , Facente Shelley N. , Mabandla Selly , Hosek Sybil , Little Francesca , Celum Connie L. , Bekker Linda‐Gail 
Published: July 2022

AbstractIntroductionCommunity‐based delivery of HIV pre‐exposure prophylaxis (PrEP) to South African adolescent girls and young women's (AGYW) could increase access but needs evaluation. We integrated PrEP services via home‐based services and pop‐up tents into existing community‐based HIV testing services (CB‐HTS) in Eastern Cape Province, South Africa.MethodsAfter accessing CB‐HTS via a “pop‐up” tent or home‐based services, HIV‐negative AGYW aged 16–25 years were invited to complete a baseline questionnaire and referred for PrEP services at a community‐based PrEP site co‐located with pop‐up HTS tents. A 30‐day supply of PrEP was dispensed. PrEP uptake, time‐to‐initiation, cohort characteristics and first medication refill within 90 days were measured using descriptive statistics.ResultsOf the 1164 AGYW who tested for HIV, 825 (74.3%) completed a questionnaire and 806 (97.7%) were referred for community‐based PrEP. Of those, 624 (77.4%) presented for PrEP (482/483 [99.8%] from pop‐up HTS and 142/323 [44.0%] from home‐based HTS), of which 603 (96.6%) initiated PrEP. Of those initiating PrEP following home‐based HTS, 59.1% initiated within 0–3 days, 25.6% within 4–14 days and 15.3% took ≥15 days to initiate; 100% of AGYW who used pop‐up HTS initiated PrEP the same day. Among AGWY initiating PrEP, 37.5% had a detectable sexually transmitted infection (STI). Although AGYW reported a low self‐perception of HIV risk, post‐hoc application of HIV risk assessment measures to available data classified most study participants as high risk for HIV acquisition. Cumulatively, 329 (54.6%) AGYW presented for a first medication refill within 90 days of accepting their first bottle of PrEP.ConclusionsLeveraging CB‐HTS platforms to provide same‐day PrEP initiation and refill services was acceptable to AGYW. A higher proportion of AGYW initiated PrEP when co‐located with CB‐HTS sites compared to those referred following home‐based HTS, suggesting that proximity of CB‐HTS and PrEP services facilitates PrEP uptake among AGYW. The high prevalence of STIs among those initiating PrEP necessitates the integration of STI and HIV prevention programs for AGYW. Eligibility for PrEP initiation should not be required among AHYW in high HIV burden communities. Community‐based service delivery will be crucial to maintaining access to PrEP services during the COVID‐19 pandemic and future health and humanitarian emergencies.
Aging Effect, Reproducibility, and Test–Retest Reliability of a New Cerebral Amyloid Angiopathy MRI Severity Marker—Cerebrovascular Reactivity to Visual Stimulation
Authors: van Dijk Suzanne E. , Lak Jessie , Drenth Nadieh , Hafkemeijer Anne , Rombouts Serge A.R.B. , van der Grond Jeroen , van Rooden Sanneke 
Published: July 2022

BackgroundDecreased cerebrovascular reactivity, measured as changes in blood‐oxygen‐level‐dependent (BOLD) signal, is a potential new cerebral amyloid angiopathy (CAA) severity marker. Before clinical application, the effect of aging on BOLD parameters, and reproducibility and test–retest reliability of these parameters should be assessed.PurposeAssess the effect of healthy aging on cerebrovascular reactivity (BOLD amplitude, time to peak, and time to baseline). And determine reproducibility and test–retest reliability of these parameters.Study TypeProspective‐observational.PopulationEighty‐six healthy adults (mean age 56 years, 55% female), 10 presymptomatic D‐CAA mutation carriers (mean age 34 years, 70% female), and 10 symptomatic D‐CAA mutation carriers (mean age 54 years, 70% female).Field Strength/Sequence3‐T, three‐dimensional (3D) T1‐weighted MRI and gradient echo BOLD fMRI.AssessmentTo assess test–retest reliability of BOLD parameters, i.e. BOLD amplitude, time to peak, and time to baseline, BOLD fMRI scans were repeated three times immediately after each other, in both controls and mutation carriers. To assess reproducibility, BOLD fMRI scans were repeated with a 3‐week interval for each subject.Statistical TestsLinear regression analyses and two‐way mixed absolute agreement intra‐class correlation approach.ResultsHealthy aging was associated with decreased BOLD amplitude (β = −0.711) and prolonged time to baseline (β = 0.236) in the visual cortex after visual stimulation Reproducibility of BOLD amplitude was excellent (ICC 0.940) in the subgroup of healthy adults. Test–retest reliability for BOLD amplitude was excellent in healthy adults (ICC 0.856–0.910) and presymptomatic D‐CAA mutation carriers (ICC 0.959–0.981). In symptomatic D‐CAA mutation carriers, test–retest reliability was poor for all parameters (ICCs < 0.5).Data ConclusionHealthy aging is associated with decreased cerebrovascular reactivity, measured by changes in BOLD response to visual stimulation. The BOLD amplitude appears to be a robust measurement in healthy adults and presymptomatic D‐CAA mutation carriers, but not in symptomatic D‐CAA mutation carriers.
Epidemiology and genetic characterization of human metapneumovirus in pediatric patients from Hangzhou China
Authors: Du Yun , Li Wei , Guo Yajun , Li Lin , Chen Qiang , He Lin , Shang Shiqiang 
Published: July 2022

AbstractHuman metapneumovirus (HMPV), which is distributed worldwide, is a significant viral respiratory pathogen responsible for causing acute respiratory tract infections (ARTIs) in children. The aim of the present study was to investigate the epidemiological and genetic characteristics of HMPV in pediatric patients in Hangzhou China following the peak of onset of coronavirus disease 2019 (COVID‐19). A total of 1442 throat swabs were collected from the pediatric patients with a diagnosis of ARTI from November 2020 to March 2021. The following viruses were detected by real‐time polymerase chain reaction analysis: HMPV, RSV, adenovirus, hPIV1‐3, influenza A, and influenza B. A two‐step method was used to amplify the F genes of the HMPV‐positive samples. Following sequencing, phylogenetic analyses were conducted using the MEGA version 7 software package. Among the 1442 samples, 103 (7.14%) were positive for HMPV. No significant differences were observed in the gender distribution. The highest incidence of HMPV occurred in children older than 6 years and the lowest was noted in children younger than 6 months. Lower respiratory tract infections were diagnosed at a higher rate than upper respiratory tract infections in HMPV‐infected children. Only 10 HMPV‐infected children (5.41%) were inpatients compared with 93 outpatients (7.39%). Co‐infection was observed in 31 HMPV‐positive samples including 24 samples of double infection and seven samples of triple infection. A total of 61F gene fragments of HMPV, which were approximately 727 bp in length were successfully sequenced. All the HMPVs belonged to the genotype B and were clustered into subgenotypes B1 (1.6%, 1/61) and B2 (98.4%, 60/61). A total of four specific amino acid substitutions were noted as follows: aa280, aa296, aa392, and aa396. These substitutions were present between sequences derived from the subgenotypes B1 and B2 in the fusion open reading frame from position 244 to 429. In conclusion, the present study provided significant information regarding the epidemiological and genetic characteristics of HMPV in children living in Hangzhou. Following the first peak of the COVID‐19 pandemic, HMPV was considered an important viral respiratory pathogen present in children with ARTI.
Smectic C Self‐Assembly in Mesogen‐Free Liquid Crystalline Chiral Polyethers with Sulfonylated Methyl‐Branched Side Chains
Authors: Bohannon Caleb A. , Kwok Man‐Hin , Huang Jiahao , Rui Guanchun , Li Ruipeng , Zhu Lei , Zhao Bin 
Published: July 2022

AbstractTo realize advanced electrical applications for ferroelectric liquid crystalline polymers, high spontaneous polarization (Ps) is highly desired. However, current ferroelectric liquid crystalline polymers usually exhibit a low Ps. In this work, mesogen‐free, chiral polyethers containing sulfonylated methyl‐branched alkyl side chains with a (CH2)3O spacer between the sulfonyl and the branched alkyl groups are designed and synthesized. In contrast to the linear n‐alkyl side chains, the methyl‐branched alkyl side chains induce chain tilting in the smectic layers. When double chirality exists in both the main chain and the side chains, a crystalline structure is observed after mechanical stretching. Intriguingly, when single chirality exists in either the backbone or the side chains, a liquid crystalline smectic C phase is obtained. The electric displacement–electric field study, however, does not show typical ferroelectric switching, although the dielectric constants are relatively high for these liquid crystalline polymers. This is likely because the dipole–dipole interactions among neighboring sulfonyl groups along the main chain are so strong that the ferroelectric switching is hindered in the samples. For the future work, it is desired to weaken the dipole–dipole interaction to achieve ferroelectricity in these mesogen‐free liquid crystalline polymers.