bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ancestral genomes and population sequencing data reveal strand- and context-specificity of polymorphic G4 sites
Authors: Lobo Thamar Jessurun , Guryev Victor 
Published: September 2023

AbstractRecent studies highlight the important functional roles of non-canonical DNA conformations. One of such structures, G-quadruplex (G4), was shown to be involved in multiple processes within a cell such as telomere maintenance, gene regulation, protein translation and alternative splicing. On the other hand, DNA in non-double stranded context can hinder replication and repair processes and, indeed, a higher rate of polymorphisms was reported at G4 sites. However, strand-specificity, positional and nucleotide contexts of nucleotide substitutions at G4 sites are under-investigated.Here, we combine ancestral genome data and DNA variants from large populational sequencing project to investigate substitution patterns within putative DNA quadruplexes. We confirm the overall elevated rate of base replacement except transitions at CpG sites, which are less likely than in the rest of the genome potentially due to hypomethylated status of G4s. Within G4 loops, there is a trend of replacing weak bases (A, T) with strong bases (G, C) that could promote DNA duplex stabilization. However, this trend is less pronounced when derived allele is rare in the human population. The most over-represented thymine to guanine replacement is about order of magnitude more frequent within G4 than in non-G4 regions. The analysis of nucleotide context of the substitutions shows clear difference between G-rich and C-rich of DNA quadruplexes implying that the strands of the quadruplex might have different mutation dynamics. Finally, we show that the observed deviations from random mutation accumulation result in a biased nucleotide composition of G4 loops rich in adenines. Future studies should reveal specific mutation and selection processes that shape the content of G4-associated DNA polymorphisms.
The geometry of admixture in population genetics: the blessing of dimensionality
Authors: Oteo José-Angel , Oteo-García Gonzalo 
Published: September 2023

AbstractWe present a geometry-based interpretation of thef-statistics framework, commonly used to determine phylogenetic relationships from genetic data. The focus is on the determination of the mixing coefficients in population admixture events subject to post-admixture drift. The interpretation takes advantage of the high dimension of the dataset and analyzes the problem as a dimensional reduction issue. We show that it is possible to think of thef-statistics technique as an implicit transformation of the genetic data from a phase space into a subspace where the mapped data structure is more similar to the ancestral admixture configuration. The positive effect of the map can be explicitly assessed. The overarching geometric framework provides slightly more general formulas than thef-formalism by using a different rationale as a starting point. Explicitly addressed are two- and three-way admixtures. The mixture proportions are provided by suitable linear fits in two or three dimensions that can be easily visualized. The developments and findings are illustrated with numerical simulations from real world datasets.
Effect ofSargassumon the Behavior and Survival of the EarthwormEisenia fetida
Authors: Martínez-Cano Mayela , Dorantes-Acosta Ana E. , Lara-González Rogelio , Salgado-Hernández Enrique , Ortiz-Ceballos Angel I. 
Published: September 2023

AbstractIn the past decade,Sargassum natansandS. fluitanshave massively reached the Mexican Caribbean shores. As a result,Sargassumconfinement sites may be affecting the soil quality and health in coastal ecosystems and agroecosystems. The impact ofSargassum(e.g., polyphenols) on soil biodiversity has not yet been evaluated. Terrestrial ecotoxicological tests use the epigean earthwormEisenia fetidaas a model organism to assess the function of soil habitats. This study evaluated the behavior and survival of the earthwormE. fetidaexposed to fiveSargassumconcentrations (0, 25, 50, 75, and 100 %) using two toxicological tests. The avoidance test showed thatE. fetidarepelled (>80 %) a diet with 100 %Sargassum. In contrast, the acute test recorded a low mortality; however, the growth ofE. fetidawas lower with increasingSargassumconcentrations. It is concluded that the ability to repel andE. fetidabiomass are early warning bioindicators to predict the environmental risk ofSargassumin soil. Therefore, it is relevant to determine the potential risk of using earthworm compost andSargassumleachates as biofertilizers in agroecosystems.
Escalating High-dimensional Imaging using Combinatorial Channel Multiplexing and Deep Learning
Authors: Ben-Uri Raz , Ben Shabat Lior , Shainshein Dana , Bar-Tal Omer , Bussi Yuval , Maimon Noa , Keidar Haran Tal , Milo Idan , Goliand Inna , Addadi Yoseph , Salame Tomer-Meir , Rochwarger Alexander , Schürch Christian M. , Bagon Shai , Elhanani Ofer , Keren Leeat 
Published: September 2023

AbstractUnderstanding tissue structure and function requires tools that quantify the expression of multiple proteins at single-cell resolution while preserving spatial information. Current imaging technologies use a separate channel for each individual protein, inherently limiting their throughput and scalability. Here, we present CombPlex (COMBinatorial multiPLEXing), a combinatorial staining platform coupled with an algorithmic framework to exponentially increase the number of proteins that can be measured fromCup to 2c− 1. In CombPlex, every protein can be imaged in several channels, and every channel contains agglomerated images of several proteins. These combinatorically-compressed images are then decompressed to individual protein-images using deep learning. We achieve accurate reconstruction when compressing the stains of twenty-two proteins to five imaging channels and demonstrate that the approach works in both fluorescence microscopy and in mass-based imaging. Combinatorial staining coupled with deep-learning decompression can escalate the number of proteins measured using any imaging modality, without the need for specialized instrumentation. Coupling CombPlex with instruments for high-dimensional imaging could pave the way to image hundreds of proteins at single-cell resolution in intact tissue sections.
Autism Caregiver Coaching in Africa (ACACIA): Protocol for a type 1-hybrid effectiveness-implementation trial
Authors: Franz Lauren , Viljoen Marisa , Askew Sandy , Brown Musaddiqah , Dawson Geraldine , Di Martino J Matias , Sapiro Guillermo , Sebolai Katlego , Seris Noleen , Shabalala Nokuthula , Stahmer Aubyn , Turner Elizabeth L , de Vries Petrus J 
Published: September 2023

AbstractBackgroundWhile early autism intervention can significantly improve outcomes, gaps in implementation exist globally. These gaps are clearest in Africa, where forty percent of the world’s children will live by 2050. Task-sharing early intervention to non-specialists is a key implementation strategy, given the lack of specialists in Africa. Naturalistic Developmental Behavioral Interventions (NDBI) are a class of early autism intervention that can be delivered by caregivers. As a foundational step to address the early autism intervention gap, we adapted a non-specialist delivered caregiver coaching NDBI for the South African context, and pre-piloted this cascaded task-sharing approach in an existing system of care.ObjectivesFirst, we will test the effectiveness of the caregiver coaching NDBI compared to usual care. Second, we will describe coaching implementation factors within the Western Cape Department of Education in South Africa.MethodsThis is a type 1 effectiveness-implementation hybrid design; assessor-blinded, group randomized controlled trial. Participants include 150 autistic children (18-72 months) and their caregivers who live in Cape Town, South Africa, and those involved in intervention implementation. Early Childhood Development practitioners, employed by the Department of Education, will deliver 12, one hour, coaching sessions to the intervention group. The control group will receive usual care. Distal co-primary outcomes include the Communication Domain Standard Score (Vineland Adaptive Behavior Scales, Third Edition) and the Language and Communication Developmental Quotient (Griffiths Scales of Child Development, Third Edition). Proximal secondary outcome include caregiver strategies measured by the sum of five items from the Joint Engagement Rating Inventory. We will describe key implementation determinants.ResultsParticipant enrolment started in April 2023. Estimated primary completion date is March 2027.ConclusionThe ACACIA trial will determine whether a cascaded task-sharing intervention delivered in an educational setting leads to meaningful improvements in communication abilities of autistic children, and identify implementation barriers and facilitators.Trial registrationNCT05551728 in Clinical Trial Registry (https://clinicaltrials.gov)
Relationship between Dietary Patterns with Closure Growth Plate in 12-13 Years Old Girls in Kermanshah
Authors: mirian Mahsa , Rafiei Mohammadreza , Khosravy Tina , Moradinazar Mehdi , Samadi Mehnoosh 
Published: September 2023

AbstractBackground & ObjectiveBone linear growth during puberty depends on several factors, including nutrition. In addition, malnutrition in children and adolescents can affect both linear growth and growth plate chondrocytes. This study was conducted to determine the association between dietary patterns, bone age status, and closure growth plate in adolescent girls.Methods and MaterialsIn this study, a validated semi-quantitative 167-items food frequency questionnaire was used to determine major dietary patterns. Major dietary patterns were also identified by the component analysis method. Furthermore, anthropometric data and information about physical activity were collected from participants.ResultsIn the present study, 70.3% of participants had bone age less than chronological age, and the findings related to 3 main dietary patterns were identified (healthy diet, high salt and sugar diet, and western/mixed diets). Among the 3 main dietary patterns, a healthy dietary pattern showed a significant correlation with the difference between chronological age and bone age (B=-0.106). This research reveals that adherence to a healthy diet was associated with an increase in bone age (P=0.02).ConclusionThe current study showed a significant association between healthy dietary patterns and the bone age of participants. Based on the results, it can be claimed that a lack of components in dietary patterns can have a negative effect on chondrocytes of growth plates. The present findings confirm that children and adolescents who followed suitable dietary patterns were less likely to be stunted.
Abnormal breathlessness during cardiopulmonary exercise testing - validation in people with chronic airflow limitation
Authors: Ekström Magnus , Li Pei Zhi , Lewthwaite Hayley , Bourbeau Jean , Tan Wan C. , Jensen Dennis 
Published: September 2023

ABSTRACTBackgroundExertional breathlessness is the cardinal symptom in cardiorespiratory disease. We aimed to validate recently developed normative reference equations to evaluate breathlessness abnormality during cardiopulmonary exercise testing (CPET) in people with chronic airflow limitation.MethodsAnalysis of people aged ≥40 years with chronic airflow limitation undergoing CPET in the Canadian Cohort Obstructive Lung Disease (CanCOLD) study. Breathlessness intensity ratings (Borg 0-10 category ratio scale [CR10]) were evaluated in relation to power output (W), rate of oxygen uptake (V’O2), and minute ventilation (V’E) at peak exercise using normative reference equations as: 1) probability of breathlessness normality, defined as the predicted probability of the Borg CR10 rating among healthy references, with lower probability reflecting more severe breathlessness; and 2) presence of abnormal breathlessness, defined as a Borg CR10 intensity rating above the upper limit of normal (ULN). Validity of breathlessness severity (lower probability of normality) and abnormality (>ULN) was evaluated as correlations with relevant participant-reported and physiologic outcomes.ResultsWe included 330 participants (44% women): mean±SD age 64±10 years (range 40– 89), FEV1/FVC 57.3±8.2%, FEV175.6±17.9%predicted. Relative to peak W, V’O2and V’E, abnormal breathlessness was present in 22.7%, 21.5%, and 15.2% of participants, respectively. For all equations, people with abnormal breathlessness had worse lung function, exercise capacity, self-reported symptom burden, physical activity, health-related quality of life, and physiological abnormalities during CPET.ConclusionEvaluation of breathlessness abnormality using CPET normative reference equations was valid in people with chronic airflow limitation.
Use of ChatGPT in Pediatric Urology and its Relevance in Clinical Practice: Is it useful?
Authors: Martinelli Braga Antonio Vitor Nascimento , Nunes Noel Charlles , Santos Emanoel Nascimento , Veiga Maria Luiza , Martinelli Braga Ana Aparecida Nascimento , de Abreu Glicia Estevam , Bessa Jose , Braga Luis Henrique , Kirsch Andrew J , Barroso Ubirajara 
Published: September 2023

AbstractIntroductionArtificial intelligence (AI) can be described as the combination of computer sciences and linguistics, objective building machines capable of performing various tasks that otherwise would need Human Intelligence. One of the many AI based tools that has gained popularity is the Chat-Generative Pre-Trained Transformer (ChatGPT). Due to the popularity and its massive media coverage, incorrect and misleading information provided by ChatGPT will have a profound impact on patient misinformation. Furthermore, it may cause mistreatment and misdiagnosis as ChatGPT can mislead physicians on the decision-making pathway.ObjectiveEevaluate and assess the accuracy and reproducibility of ChatGPT answers regarding common pediatric urological diagnoses.MethodsChatGPT 3.5 version was used. The questions asked for the program involved Primary Megaureter (pMU), Enuresis and Vesicoureteral Reflux (VUR). There were three queries for each topic, adding up to 9 in total. The queries were inserted into ChatGPT twice, and both responses were recorded to examine the reproducibility of ChatGPT’s answers. After that analysis, both questions were combined, forming a single answer. Afterwards, those responses were evaluated qualitatively by a board of three specialists with a deep expertise in the field. A descriptive analysis was performed.ResultsChatGPT demonstrated general knowledge on the researched topics, including the definition, diagnosis, and treatment of Enuresis, VUR and pMU. Regarding Enuresis, the provided definition was partially correct, as the generic response allowed for misinterpretation. As for the definition of VUR, the response was considered appropriate. And for pMU it was partially correct, lacking essential aspects of its definition such as the diameter of the dilatation of the ureter. Unnecessary exams were suggested, for both Enuresis and pMU. Regarding the treatment of the conditions mentioned, it specified treatments to Enuresis that are known to be ineffective, such as bladder training.DiscussionAI has a wide potential to bring several benefits to medical knowledge, improving decision-making and patient education. However, following the reports on the literature, we found a lack of genuine clinical experience and judgment from ChatGPT, performing well in less complex questions, yet with a steep decrease on its performance as the complexity of the queries increase. Therefore, providing wrong answers to crucial topics.ConclusionChatGPT responses present a combination of accurate and relevant information, but also incomplete, ambiguous and, occasionally, misleading details, especially regarding the treatment of the investigated diseases. Because of that, it is not recommended to make clinical decisions based exclusively on ChatGPT.
Association of heavy menstrual bleeding with cardiovascular diseases in US female hospitalizations
Authors: Dubey Pallavi , Abdeldayem Jasmin , Singh Vishwajeet , Abdelrehman Yousif , Mada Sanjana , Reddy Sireesha , Dwivedi Alok 
Published: September 2023

AbstractBACKGROUNDHeavy menstrual bleeding (HMB) is a common type of menstrual disorder that causes social and mental distress leading to a variety of health problems. Although limited evidence highlights the links between HMB and metabolic abnormalities, the association between HMB and CVD outcomes is unknown in the presence or absence of comorbid irregular menstruation (IM).METHODSAll female hospitalizations between the ages of 12 to 40 years were identified using the National Inpatient Sample database in 2017 and grouped into HMB and no menstrual disorders. Outcomes including major adverse cardiovascular events (MACE), coronary heart disease (CHD), stroke/cerebrovascular accident (CVA), heart failure (HF), arterial fibrillation (AF) or arrhythmia, myocardial infarction (MI), and diabetes (DM) were extracted using ICD-10 codes. Adjusted logistic regression models were conducted to summarize associations with an odds ratio (OR) along with a 95% confidence interval (CI).RESULTSIn the entire cohort, 8,291 (0.69%) had an HMB diagnosis including 1623 (0.14%) with IM and 6668 (0.55%) without IM. In the fully adjusted analysis, HMB was significantly associated with most CVD outcomes, including MACE (OR=1.61; 95% CI: 1.38, 1.88, p<0.001), CHD (OR=1.88; 95% CI: 1.52, 2.31, p<0.001), Stroke/CVA (OR=1.51; 95% CI: 1.1, 2.07, p=0.011), HF (OR=1.60; 95% CI: 1.33, 1.92, p<0.001), AF/arrhythmia (OR=1.93; 95% CI: 1.16, 2.45, p=0.006), and DM (OR=1.45; 95% CI: 1.33, 1.58), p<0.001). HMB without IM was strongly associated with DM, HF, AF, and MACE outcomes while HMB with IM was strongly associated with CHD and AF outcomes.CONCLUSIONSHMB is independently and strongly associated with CVD events among US hospitalizations of young women. Our findings suggest promoting increased awareness, early detection, and optimum management of HMB to avoid adverse CVD outcomes.Clinical PerspectiveWhat Is New?Although menstruation dysfunction is associated with cardiovascular disease (CVD), the relationship between heavy menstrual bleeding (HMB) and CVD outcomes is not evaluated.In a US sample of 1,204,715 hospitalized women, HMB was independently and strongly associated with major adverse cardiovascular events and coronary heart disease.HMB without irregular menstruation was markedly associated with CVD outcomes than HMB with irregular menstruation.What Are the Clinical Implications?Our findings support that HMB as an early vital sign for CVD outcomes among young women. A routine investigation and screening of menstrual disorders, especially HMB, and its effective management is useful for the prevention of CVD risk in women.
The discriminative ability of ROTEM for Delayed Cerebral Ischemia and Poor Clinical Outcome following Aneurysmal Subarachnoid Haemorrhage
Authors: Tjerkstra Maud A. , Labib Homeyra , Coert Bert A. , Post René , Vandertop W. Peter , Verbaan Dagmar , Juffermans Nicole P. 
Published: September 2023

ABSTRACTIntroductionAneurysmal subarachnoid haemorrhage (aSAH) and delayed cerebral ischemia (DCI) have been associated with hypercoagulability as detected by viscoelastic testing. In this study, we evaluate temporal alterations in rotational thromboelastography (ROTEM-) coagulation profiles and the discriminative ability of ROTEM-parameters for DCI and poor clinical outcome following aSAH.Materials and MethodsROTEM-parameters were measured on days 0, 3-5 and 9-11 after aSAH and compared between patients with and without DCI, radiological DCI and 6-months’ poor clinical outcome (modified Rankin Scale 4-6). ROC-curve analyses were used to calculate areas-under-the-curve (AUC) and to determine optimal cut-off values with a sensitivity of >90% and highest possible specificity for DCI and radiological DCI. For poor outcome, a specificity >90% with highest possible sensitivity was used.ResultsOf 160 aSAH patients, 31 (19%) had DCI, 16 (10%) radiological DCI and 68 (44%) had poor outcome at six months. DCI, radiological DCI and poor clinical outcome were associated with hypercoagulability. The ROTEM-parameter with the best discriminative ability for radiological DCI was INTEM CT (AUC: 0.75), with optimal cut-off value <153 seconds (sensitivity 94%, specificity 59%). For poor outcome, this was FIBTEM A10, (AUC: 0.85), with optimal cut-off value >27 mm (specificity 94%, sensitivity 49%).ConclusionsHypercoagulability, as detected by ROTEM-parameters, is an excellent marker of poor clinical outcome after aSAH and might be useful for stratifying patients for inclusion in future trials on therapeutic interventions. Conversely, the absence of hypercoagulability on ROTEM may be used to identify patients at low risk of DCI for early hospital discharge.
Sexual Gender-Based Violence among Adolescent Girls and Young Women during COVID-19 Pandemic, Mid-Eastern Uganda
Authors: Mwine Patience , Kwesiga Benon , Migisha Richard , Cheptoris Juliet , Kadobera Daniel , Bulage Lilian , Nsubuga Edirisa J. , Mudiope Peter , Ario Alex R. 
Published: September 2023

AbstractBackgroundGlobal studies indicate that sexual gender based violence (SGBV) may increase during pandemics including the COVID-19. The Mid-Eastern region in Uganda was of a concern due to high prevalence of intimate partner sexual violence among adolescent girls and young women (AGYW) (13% in 2016). Due to limited data, we investigated factors associated with SGBV among AGYW during the COVID-19 pandemic in Eastern Uganda, April 2022.MethodsWe line listed all AGYW 10-24 years who obtained SGBV services at ten high-volume health facilities from March 2020 to December 2021, the main COVID-19 period in Uganda. We conducted a case-control study among these AGYW. A case was ≥1 SGBV episode experienced by an AGYW aged 10-24 years residing in Tororo and Busia Districts. For every randomly-selected case from the health facility line list, we identified two neighbourhood-matched AGYW controls who reported no SGBV. We interviewed 108 and 216 controls on socio-demographics, socio-economics, and SGBV experiences during COVID-19. We conducted logistic regression to obtain adjusted odds ratios and confidence intervals.ResultsAmong 389 SGBV cases, the mean age was 16.4 (SD± 1.6: range 10-24) years, and 350 (90%) were 15-19 years. Among 108 cases interviewed, 79 (73%) reported forced sex. Most (73; 68%) knew the perpetrator. In multivariate analysis, self-reported SGBV before the COVID-19 period [aOR=5.8, 95%CI: 2.8-12] and having older siblings [aOR=1.9, 95%:CI 1.1-3.4] were associated with SGBV during the period. Living with a family that provided all the basic needs was protective [aOR=0.42, 95%: CI 0.23-0.78].ConclusionPrevious SGBV experiences and family dynamics, such as having older siblings, increased the odds of SGBV during the COVID-19 pandemic in Uganda. Conversely, a supportive family environment was protective. Identifying, supporting, and enacting protective interventions for existing SGBV victims and socioeconomically vulnerable AGYW could reduce the burden of SGBV during similar events.