bluuebunny/crossref_metadata_2025_split huggingface dataset:
Establishing a HOPE Program in a Real-life Setting: A Brazilian Case Series
Authors: Boteon Amanda P.C.S. , Lima Marisa R.D. , Della Guardia Bianca , Carvalho Mauricio F. , Schlegel Andrea , Boteon Yuri L. 
Published: November 2023

Background.Although hypothermic oxygenated perfusion (HOPE) improves posttransplant outcomes, setting up machine perfusion programs may be subjected to specific obstacles under different conditions. This study aims to describe the establishment of HOPE in a real-life setting in Brazil.Methods.Extended criteria donors in donation after brain death organs preserved by HOPE were accepted for higher-risk candidates needing expedited transplantation, perceived as those who would benefit most from the technique because of its limited availability. Extended criteria donors was defined by the Eurotransplant criteria. High-risk transplant candidates were characterized by suboptimal surgical conditions related to the recipient or the procedure.Results.Six HOPE-preserved grafts were transplanted from February 2022 to August 2022. The mean donor risk index was 1.7 (SD 0.5). One organ was severely steatotic, and 3 had an anticipated cold ischemia time above 12 h. Recipients’ mean model for end-stage liver disease was 28.67 (SD 6.79), with 1 case of retransplant, 1 of refractory ascites, and 1 of acute-on-chronic liver failure. The mean cold ischemia time was 5 h 42 min (SD 82 min), HOPE 6 h 3 min (SD 150 min), and total preservation time 11 h 46 min (SD 184 min). No case had early allograft dysfunction. The mean length of hospital stay was 10 d with 100% graft and patient survival and no ischemic cholangiopathies at a median follow-up of 15 mo (min 12, max 18). Costs and country-specific legal regulations for device utilization were the major hurdles to implementing the program.Conclusion.We presented a pathway to introduce and rationalize the use of HOPE in a scenario of challenging donor-recipient matching with good results. These findings may aid in implementing machine perfusion programs, especially in settings with limited resources or complex transplant logistics.
A Rapid, Portable, and Electricity-Free Sample Extraction Method for Enhanced Molecular Diagnostics in Resource-Limited Settings
Authors: Pennisi Ivana , Cavuto Mathew L. , Miglietta Luca , Malpartida-Cardenans Kenny , Stringer Oliver W , Mantikas Katerina-Theresa , Reid Ruth , Frise Rebecca , Moser Nicolas , Randell Paul , Davies Frances , Bolt Frances , Barclay Wendy , Holmes Alison , Georgiou Pantelis , Rodriguez-Manzano Jesus 
Published: November 2023

ABSTRACTThe COVID-19 pandemic has highlighted the need for rapid and reliable diagnostics that are accessible in resource-limited settings. To address this pressing issue, we have developed a rapid, portable, and electricity-free method for extracting nucleic acids from respiratory swabs (i.e.nasal, nasopharyngeal and buccal swabs),successfully demonstrating its effectiveness for the detection of SARS-CoV-2 in residual clinical specimens. Unlike traditional approaches, our solution eliminates the need for micropipettes or electrical equipment, making it user-friendly and requiring little to no training. Our method builds upon the principles of magnetic bead extraction and revolves around a low-cost plastic magnetic lid, called SmartLid, in combination with a simple disposable kit containing all required reagents conveniently pre-aliquoted. Here, we clinically validated the SmartLid sample preparation method in comparison to the gold standard QIAamp Viral RNA Mini Kit from QIAGEN, using 406 clinical isolates, including 161 SARS-CoV-2 positives, using the SARS-CoV-2 RT-qPCR assays developed by the US Centers for Disease Control and Prevention (CDC). The SmartLid method showed an overall sensitivity of 95.03% (95% CI: 90.44%–97.83%) and a specificity of 99.59% (95% CI: 97.76%–99.99%), with a positive agreement of 97.79% (95% CI: 95.84%–98.98%) when compared to QIAGEN’s column-based extraction method. There are clear benefits to using the SmartLid sample preparation kit: it enables swift extraction of viral nucleic acids, taking less than 5 minutes, without sacrificing significant accuracy when compared against more expensive and time-consuming alternatives currently available on the market. Moreover, its simplicity makes it particularly well-suited for the point-of-care where rapid results and portability are crucial. By providing an efficient and accessible means of nucleic acid extraction, our approach aims to introduce a step-change in diagnostic capabilities for resource-limited settings.
A Genomics England haplotype reference panel and the imputation of the UK Biobank
Authors: Shi Sinan , Rubinacci Simone , Hu Sile , Moutsianas Loukas , Stuckey Alex , Need Anna C ,   The Genomics England Research Consortium, Caulfield Mark , Marchini Jonathan , Myers Simon 
Published: November 2023

AbstractThe choice of reference panels significantly impacts phasing, imputation and GWAS results. In this study, we built a haplotype reference panel using the Genomics England (GEL) high-coverage sequencing dataset, one of the largest genetic variation resources ever collected in the UK. The resulting reference panel consists of 156,390 haplotypes and 342 million autosomal variants. The GEL reference panel demonstrates reliable imputation of variants as rare as 1 in 10,000 within the White British population, with an imputation r2value of 0.75. The resulting imputed UKB data (GEL-UKB) contains three times more variants, predominantly rare variants, compared to the UKB data previously imputed using the HRC and UK10K reference panel. The GEL-UKB presents a unique opportunity for the reliable discovery of rare associations across the whole genome, especially within the regions not covered by the exome sequencing data. Rare variant signals with high confidence are predominantly from rare coding variants, implying firstly, a probable tendency for existing rare non-coding mutations to not reach a disruptive level comparable to that of coding variants. Secondly, it raises the possibility that the current sample size of UK Biobank may be insufficient for detecting rare variants with a moderate effect size, even with the whole genome sequencing. The resulting GEL phased haplotype reference panel has been made available on the GEL platform and widely used by GEL users. Our GEL imputed UKB data has been adopted as one of the UKB official imputed data resources (Data Field 21008).
Triglyceride and Glucose Index and Sex Differences in Relation to Cognitive Impairment in Hypertensive Patients without Diabetes
Authors: Liu Rufei , Cheng Wenli 
Published: November 2023

BackgroundPrevious observational studies in patients with diabetes have examined the relationship between insulin resistance (IR) and cognitive outcomes and failed to find that IR is associated with cognitive function. And the triglyceride-glucose (TyG) index, which measured serum triglyceride (TG) and fasting blood glucose (FBG), has been suggested as a surrogate reliable marker of IR and widely used due to its convenience and cost-effectiveness.However, to the best of our knowledge, the relationship between IR and intensive blood pressure control in specific cognitive outcomes has never been investigated.MethodsTo fill this knowledge gap, we analyzed the relationship between TYG levels and cognitive outcomes in hypertensive patients within the Systolic Blood Pressure Intervention Trial (SPRINT). The SPRINT evaluated the impact of intensive blood pressure control (systolic blood pressure < 120 mmHg) versus standard blood pressure control (systolic blood pressure < 140 mmHg). The Cox proportional risk regression was used to investigate the association between different TYG status and clinical outcomes. Additional stratified analyzes were performed to evaluate the robustness of gender difference.ResultsA total of 9,323 participants (6016 [64.53%] males and 3307 [35.47%] females) with hypertension from the SPRINT research were included in the analysis. The median follow-up period was 3.26 years. Our population was divided into three groups according to the size of the TyG index. The low TyG group was the reference. Sensitivity analyzes showed that in the SPRINT, the TyG index was significantly associated with the risk of cognitive outcomes across various subgroups. There was no significant interaction in the confounders.ConclusionsIn this cohort study, results suggest that patients with TyG levels higher had lower risk of probable dementia, but this study tested association, not causation. Our results demonstrated that in patients with hypertension, the association between TyG and risk of probable dementia is L-shaped.
Exploring Access to Social Protection for People with Disabilities in Bangladesh
Authors: Rahman Mizanur , Rana Md Shohel , Rahman Md Mostafizur , Khan Md Nuruzzaman 
Published: November 2023

PurposeThis study aimed to assess the accessibility of social protection programs for individuals with disabilities in Bangladesh and identify factors at the individual, household, and community levels influencing this accessibility.MethodsWe analyzed data from 4,293 respondents in the 2021 National Survey on Persons with Disabilities. We categorized participation in social protection programs as follows: no assistance (0), support received within six months (1), and support received beyond six months (2). Explanatory variables were considered at individual, household, and community levels. A multilevel multinomial logistic regression model assessed associations, with two age groups: 0-17 and 18+.ResultsOnly 38% reported inclusion in social protection programs within six months, rising to 48% for support beyond six months. Disability allowances were the most common, followed by old age allowances and VGD/VGF assistance. Inclusion was likelier for older, unmarried, widowed, divorced, or separated individuals with disabilities. Conversely, those with higher education, wealthier households, and residing in Dhaka division were less likely to be included. Among children aged 0-17, multiple disabilities increased the likelihood of inclusion.ConclusionThese findings underscore the urgent need for more comprehensive and inclusive social protection policies and programs to support the well-being of individuals with disabilities in Bangladesh.
Single-cell analysis reveals an active and heterotrophic microbiome in the Guaymas Basin deep subsurface with significant heterotrophic inorganic carbon fixation
Authors: Meyer Nicolette R. , Morono Yuki , Dekas Anne E 
Published: November 2023

AbstractThe marine subsurface is a long-term sink of atmospheric carbon dioxide with significant implications for climate on geologic timescales. Subsurface microbial cells can either enhance or reduce the potential for the subsurface to sequester carbon, depending on their metabolic activity. However, the activity of subsurface microbes is rarely measured, leaving their role in biogeochemical cycling poorly characterized. Here, we used nanoscale secondary ion mass spectrometry to quantify anabolic activity in 3,203 individual cells from the thermally altered deep subsurface in the Guaymas Basin, Mexico (3–75 m below the seafloor, 0-14 C). We observed that a large majority of cells were active (83–100%), although rates of biomass generation were low, suggesting cellular maintenance rather than doubling. Mean single-cell activity decreased with increasing sediment depth and temperature, and was most strongly correlated with porewater sulfate concentrations. Intracommunity heterogeneity in cell-specific activity decreased with increasing sediment depth and age. Using a dual-isotope labelling approach we determined that all active cells analyzed at all depths were heterotrophic. We detected and quantified inorganic carbon assimilation by heterotrophs and found that it contributes on average at least 5% of total heterotrophic biomass carbon in this community. Our results therefore suggest that the deep marine biosphere at Guaymas Basin is largely active and contributes to subsurface carbon cycling primarily by assimilating organic carbon but also by mediating heterotrophic inorganic carbon fixation. Heterotrophic assimilation of inorganic carbon may be a small yet significant and widespread underappreciated source of labile carbon in the global subsurface.ImportanceThe global subsurface is the largest reservoir of microbial life on the planet yet remains poorly characterized. The activity of life in this realm has implications for long-term elemental cycling, particularly of carbon, as well as how life survives in extreme environments. Here, we recovered cells from the deep subsurface of the Guaymas Basin and investigated the level and distribution of activity, the physicochemical drivers of activity, and the relative significance of organic versus inorganic carbon to subsurface biomass. Using a sensitive single-cell assay we find that the majority of cells are active, that activity is likely driven by availability of energy, and that while organic carbon supplies most cellular carbon, inorganic carbon also contributes. We additionally find that the inorganic carbon assimilation observed was mediated by heterotrophs, not autotrophs, highlighting the importance of this often overlooked mode of carbon assimilation in the subsurface and beyond.
Factors affecting macromolecule orientations in thin films formed in cryo-EM
Authors: Yadav Swati , Vinothkumar Kutti R. 
Published: November 2023

AbstractThe formation of a vitrified thin film embedded with randomly oriented macromolecules is an essential prerequisite for cryogenic sample electron microscopy. Most commonly, this is achieved using the plunge freeze method described nearly 40 years ago. Although this is a robust method, the behaviour of different macromolecules shows great variation upon freezing and often needs to be optimized to obtain an isotropic, high-resolution reconstruction. For a macromolecule in such a film, the probability of encountering the air-water interface in the time between blotting and freezing and adopting preferred orientations is very high. 3D reconstruction using preferentially oriented particles often leads to anisotropic and uninterpretable maps. Currently, there are no general solutions to this prevalent issue, but several approaches largely focusing on sample preparation with the use of additives and novel grid modifications have been attempted. In this study, the effect of physical and chemical factors on the orientations of macromolecules was investigated through an analysis of select well-studied macromolecules and important parameters that determine the behaviour of proteins on cryo-EM grids were revealed. These insights highlight the nature of interactions that cause preferred orientations and can be utilized to systematically address orientation bias for any given macromolecule and provide a framework to design small-molecule additives to enhance sample stability and behaviour.
Real-world effectiveness of non-pharmaceutical interventions in containing COVID-19 pandemic after the roll-out of coronavirus vaccines: A systematic review
Authors: He Xiaona , Chen Huiting , Zhu Xinyu , Gao Wei 
Published: November 2023

AbstractBackgroundNon-pharmaceutical interventions (NPIs) have been widely used to control the transmission of infectious diseases. However, the current research evidence on the policy mechanisms of NPIs is still limited. This study aims to systematically identify, describe, and evaluate the existing literature for the real-world effectiveness of NPIs in containing COVID-19 pandemic after the roll-out of coronavirus vaccines, in order to search for optimal strategies for implementing NPIs.MethodsWe conducted a comprehensive search of relevant studies from January 1, 2021, to June 4, 2023 in PubMed, Embase, Web of science and MedRxiv. Two authors independently assessed eligibility and extracted data. Risk of bias assessment tool was used to evaluate the study design, statistical methodology, and quality of reporting. Data were collected, synthesised and analyzed through quantitative and qualitative approaches. The findings were presented using summary tables and figures, including information on the target countries and regions of the study, types of NPIs, and evidence quality.ResultsThe review included a total of seventeen studies that examined the real-world effectiveness of NPIs in containing the COVID-19 pandemic after the vaccine roll-out. These studies used five composite indicator that combined multiple NPIs and fourteen individual NPIs. The studies had an average quality assessment score of 13 (range: 10-16), indicating moderately high quality. Among the included studies, nine assessed the effectiveness of the composite indicator, with four of them also evaluating individual NPIs. Additionally, twelve studies investigated the effectiveness of individual NPIs. The most frequently evaluated individual NPIs were testing policy, restrictions on gathering, facial covering, and school closure. Workplace closures and stay-at-home requirements were also assessed. The effectiveness of NPIs varied depending on time frames, countries and regions.ConclusionIn summary, the research evidence suggests that NPIs remain effective in curbing the spread of COVID-19 even after the roll-out of vaccines. Studies based on different contexts had different viewpoints or conclusions regarding the effectiveness of NPIs in containing the COVID-19 pandemic. Further research is needed to understand the policy mechanisms and address potential future challenges.
Childhood adverse life events and skeletal muscle mitochondrial function
Authors: Duchowny Kate A. , Mau Theresa , Diaz-Ramierz L. Grisell , Lui Li-Yung , Marcinek David J. , Toledo Frederico G. S. , Cawthon Peggy M. , Hepple Russell T. , Kramer Philip A. , Newman Anne B. , Kritchevsky Stephen B. , Cummings Steven R. , Coen Paul M. , Molina Anthony J. A. 
Published: November 2023

ABSTRACTSocial stress experienced in childhood is associated with adverse health later in life. Mitochondrial function has been implicated as a mechanism for how stressful life events “get under the skin” to influence physical wellbeing. Using data from the Study of Muscle, Mobility and Aging (n=879, 59% women), linear models examined whether adverse childhood events (i.e., physical abuse) were associated with two measures of skeletal muscle mitochondrial energetics in older adults: (1) maximal adenosine triphosphate production (ATPmax) and (2) maximal state 3 respiration (Max OXPHOS). Forty-five percent of the sample reported experiencing 1+ adverse childhood event. After adjustment, each additional event was associated with -0.07 SD (95% CI= - 0.12, -0.01) lower ATPmax. No association was observed with Max OXPHOS. Adverse childhood events are associated with lower ATP production in later life. Findings indicate that mitochondrial function may be a mechanism in understanding how early social stress influences health in later life.
Water fluoridation : A bibliometric study from 1950 to 2020
Authors: Liu Anqi , Yuan Changyong , Xu Ling , Zhao Li 
Published: November 2023

AbstractWater fluoridation (WF) is considered by the Centers for Disease Control and Prevention (CDC)to be one of the top ten public health achievements of the 20th century. However, discussions about WF have been ongoing. The purpose of this study is to collect and analyze the scientific literature for WF and understand the keyword network of the entire field, important articles, high-yield countries, institutions and authors, and the mutual cooperation between them. The data of this research are extracted from the Web of Science (WoS) from 1950 to 2020. In total, 1,008 articles were published. The United States published the largest number of papers. Australia’s University of Adelaide ranks first among the top 20 institutions. Seven scholars, including AJ Spencer, constitute the largest author collaboration network. Community Dentistry and Oral Epidemiology had the most publications, with 107 articles. Keywords density map found that the main keywords were dental caries, fluoride, children, drinking water, prevalence, and dental fluorosis. Keywords clusters mainly related to dental caries, fluoride, epidemiology research, and dental fluorosis. In the highly cited literature, we found that the research also focused on the relationship between stopping WF and caries and the systemic effects of WF.
Risky Sexual Behavior and its Determinants among Undergraduate Hostellers of Kathmandu Metropolitan City
Authors: Chaudhary Ram Kumar , Chalise Anisha , Pandey Saloni , Paudel Shishir 
Published: November 2023

ABSTRACTBackgroundRisky sexual behavior (RSB) includes practices of unprotected sex, sex with multiple partners, and/or sex under substance abuse, increasing vulnerability to reproductive health problems. This study explored the risky sexual behavior and its associated factors among Nepalese undergraduates.MethodsA cross-sectional study was executed among 361 undergraduates residing in hostels of Kathmandu Metropolitan. The data was collected through a self-administered questionnaire. Pearson’s chi-square test and multivariable logistic regression analysis was performed to determine factors associated with risky sexual behavior at 5% level of significance.ResultThe prevalence of risky sexual behavior among undergraduates was found to be 64.3% (95% CI: 59.8-69.8%). Risky sexual behavior was found to be associated with higher age (aOR: 3.938; 95% CI: 1.707-8.673), male gender (aOR: 3.233; 95% CI: 1.623-6.439), being in past/current relationship (aOR: 3.914, 95% CI: 2.099-7.012), lower education of mother (aOR: 3.655; 95% CI: 1.189-9.237), and peer pressure to have a sexual relationship (aOR: 2.356; 95% CI: 1.260-4.349). Notably, bivariate analysis illustrated problematic pornographic consumption to have a statistical relation with risky sexual behavior. However, this association weakened and became non-significant after accounting for other factors in the adjusted model (aOR:1.213, 95% CI: 0.331-4.442).ConclusionThe study highlights a significant prevalence of risky sexual behaviour among undergraduate students, linked to the factors such as age, gender, relationship status, parental education, and peer pressure. These findings suggest the need for comprehensive sex education programs that equip students with the knowledge and skills to navigate healthy relationships, make safe choices, and embrace responsible sexual practices.Key MessagesWhat is already known on this topicNepalese adolescents and youth have scant knowledge about sexual and reproductive health.Despite Nepal’s commitments to adolescent health, a gap persisted in the utilization of sexual and reproductive health services among youths and very little is known about their sexual practice.What this study addsIssues such as early sexual engagement, unprotected sex, multiple partners, and engagement in commercial sex work are prominent concerns among Nepalese youths.Despite existing laws and programs, risky sexual behaviors persist, emphasizing the urgency for effective interventions tailored to Nepalese adolescents.How this study might affect research, practice or policyThe findings underscore urgent necessity for targeted interventions such as comprehensive sex education to address the concerning prevalence of RSB among Nepalese undergraduates.