bluuebunny/crossref_metadata_2025_split huggingface dataset:
Changes in population immunity to omicron SARS-CoV-2 variants and selected Sarbecoviruses from 2020 to 2023 in urban Colombo, Sri Lanka
Authors: Bary Farha , Karunananda Maneshka Vindesh , Jeewandara Chandima , Danasekara Saubhagya , Guruge Dinuka , Rizan Rizna , Aberathna Inoka Sepali , Ranasinghe Thushali , Kuruppu Heshan , Jayamali Jeewantha , Perera Lahiru , Chathurangika Harshani , Gunaratne Amaya , Dasanthi Naduni , Ranatunga Chathura , Ishara A.W. Shashini , Yatiwelle Sathsara , Wijayamuni Ruwan , Tan Tiong Kit , Townsend Alain , Ogg Graham S. , Malavige Gathsaurie Neelika 
Published: October 2024

AbstractBackgroundTo understand how the population immunity evolved over time and possible susceptibility of the Sri Lankan population to emerging SARS-CoV-2 variants, we proceeded to evaluate the changes in antibody positivity rates to omicron variants BA.2.75 and XBB.1.5 and for selected sarbecoviruses.MethodsThe haemagglutination test (HAT) was carried out to determine the presence of antibodies against the RBD of the SARS-CoV-2 omicron variants XBB.1.5 and BA.2.75 and the RBD of the Sabecoviruses RaTG13, WIV1, Khosta-2 and SARS-CoV-1, in individuals aged 5 to 80 years of age in years 2020 (n=381), 2022 (n=432) and 2023 (n=382).ResultsThe highest positivity rates for BA.2.75, RaTG13, WIV1, Khosta-2 and SARS-CoV-1 were seen in 2022, with positivity rates significantly declining to many of the viruses except XBB.1.5 and Khosta-2 by 2023. The positivity rates for Khosta-2 (p<0.001) and WIVI (p<0.001) were significantly lower in children <14 years age, but not for XBB.1.5, BA.2.75 and RaTG13. Children <14 years who were SARS-CoV-2 unvaccinated had the lowest positivity rates for all tested viruses except BA.2.75. <20% of individuals in all age groups had antibody titres equivalent to 1:80, which correspond to neutralising antibody titres by 2023.ConclusionsPopulation immunity to omicron SARS-CoV-2 variants and selected sarbecoviruses had significantly declined in Colombo, Sri Lanka by 2023. Therefore, although T cells might still offer some protection against severe disease, immunizing vulnerable individuals in the community with protective vaccine designs, might be important to consider at this stage.
Sex-specific Metabolic Signatures of Insulin Resistance, Body Mass Index, and Visceral Adiposity in Fasting and Postprandial States
Authors: Shojaeifard Zahra , Chahibakhsh Negar , Horner David , Schoos Ann-Marie M , Thorsen Jonathan , Stokholm Jakob , Vinding Rebecca , Bønnelykke Klaus , Rasmussen Morten A. , Ebrahimi Parvaneh 
Published: October 2024

AbstractThe rising prevalence of obesity and insulin resistance, a risk factor for type 2 diabetes (T2D), among adolescents is a growing public health concern. Understanding the metabolic underpinnings of adiposity and insulin resistance in adolescence can provide insights into the development of metabolic dysfunction, and potentially facilitate early intervention strategies to prevent the progression of these conditions into more severe metabolic disorders in adulthood. We explored the metabolic signatures of insulin resistance, Body Mass Index (BMI), and visceral adiposity in adolescents, in both fasting and postprandial states. A meal challenge was undertaken on 18-year-olds (154 females; 144 males), and their blood metabolites were profiled using Nuclear Magnetic Resonance spectroscopy (NMR). Least Absolute Shrinkage and Selection Operator (LASSO) regression was used for modeling and variable selection, in a sex-stratified manner. The results show distinct metabolic patterns between sexes, with males showing more pronounced postprandial responses and stronger associations between blood metabolome and insulin resistance, BMI, and visceral adiposity. Key metabolites such as lipid metabolites, Branched-Chain Amino Acids (BCAAs), glucose, and Glycoprotein Acetylation (GlycA) were selected as important metabolic entities in predicting insulin resistance and adiposity in adolescence. The findings underscore the complex interplay of metabolites with metabolic health and sex, and can pave the way for developing targeted interventions and preventive strategies specifically tailored to adolescents. Such interventions can potentially mitigate the risk of progression to more severe metabolic disorders.
Analysis of clinical characteristics of invasive non-typhoidalSalmonellainfections in children: a 5-year dual-center retrospective study
Authors: Lu Chenggang , Xie Yongping , Li Yan , Cheng Fangfang , Huang Lisu , Hua Wang 
Published: October 2024

AbstractObjectiveTo investigate the incidence, microbiological characteristics, clinical manifestations, and antibiotic resistance of invasive non-typhoidalSalmonella(iNTS) infections in children.MethodsA retrospective study was conducted from January 2018 to December 2022 at two large teaching hospitals: Zhejiang University School of Medicine Children’s Hospital (ZCH) and Children’s Hospital of Soochow University (SCH). Medical records of culture-confirmed iNTS cases were reviewed, and a standardized case report form was used to collect demographic, clinical, and microbiological data.ResultsA total of 109 cases of iNTS infection were included, with 40 cases from SCH and 69 cases from ZCH. 71 cases (65.1%) were boys.. Infants under 1 year old accounted for 30.3% of the cases. Among the cases, 38 cases (34.9%) had underlying diseases, mainly tumors (55.3%,21/38). The most common sites of infection were the bloodstream (84.4%) and bones and joints (12.8%). The most common serogroups were B (36.8%), C (44.7%) and D (38.2%). The overall resistance rate of ampicillin was 53.6%, ceftriaxone resistance rate was 17.8%, and carbapenem resistance rate was 0%. Seasonal trends indicated higher incidence rates during the summer.ConclusioniNTS infections in children primarily affect the bloodstream and bones/joints, with a significant proportion of cases in those with underlying medical conditions. Ceftriaxone remains the first-line antibiotic, but increasing resistance highlights the need for vigilant antimicrobial stewardship. Carbapenems can be considered as second-line antibiotics in severe cases. Further studies are needed to understand the molecular characteristics and improve treatment strategies for iNTS infections in pediatric patients.
The Viability, Necessity, and Acceptability of Text Message Group Therapy Among Low-Income Racial-Ethnic Minority Mothers: A Qualitative Study
Authors: Guiroy Ilang M. , Caicedo Brianna I. , Nouri Roya , Kuhn Eric , Semple Randye J. 
Published: October 2024

AbstractPurposeThis qualitative focus group study conceptually explored the viability, necessity, and acceptability of a proposed text message group therapy (TMGT) intervention as a psychotherapy delivery format among racial-ethnic minority, low-income peripartum mothers.MethodThree semi-structured, virtual focus groups facilitated in-depth interviews with 12 adults who gave birth in the previous 24 months, self-identified as a racial-ethnic minority, had at least mild depression (PHQ-9 >5), participated in a government program requiring low-income (e.g. Special Supplemental Nutrition Program for Women, Infants, and Children [WIC]), and were fluent in English. Recruitment, data collection, and analyses were performed concurrently. This allowed theme saturation (no emergence of new themes) to determine the sample size of 12 participants. The qualitative analysis framework was Grounded Theory. Krippendorff’s alpha was set to > 0.8 for interrater reliability.ResultsTen of the 12 participants were willing to engage in the proposed TMGT. Participants reported a need for psychotherapy tailored to motherhood that was not met by their current support system or healthcare providers, which the proposed TMGT could meet. While all participants communicated via text messaging about motherhood and baby care, they varied in terms of how much. Text messaging has the unique strength of being resilient to interruptions by young children and allowing for multitasking. Text messaging can be a less emotionally stimulating form of communication for an often overstimulated parent. Some mothers found it easier to share their emotions via text message, whereas others found it more difficult. Drawbacks include that information could be lost (increasing frustration or making it possible to hide their true feelings), conversational turns could take too long, and keeping track of the conversation and mobile devices could increase the mental load.ConclusionThese racial-ethnic minority, low-income mothers with peripartum depression expressed a strong need for a safe space to share their lived experiences of motherhood, receive emotional support, and obtain high-quality information about motherhood and baby care tailored to their situation. The proposed text message group therapy is viable, acceptable, and necessary and could meet the needs of many women and increase access to group psychotherapy for this important, underserved population.
Advancing maternal and newborn health care measurement: Developing quality of care indices for postnatal and small and/or sick newborn care in low- and middle-income countries
Authors: Sheffel Ashley , King Shannon , Day Louise Tina , Marchant Tanya , Muzigaba Moise , Requejo Jennifer , Carter Emily , Munos Melinda K. 
Published: October 2024

ABSTRACTBackgroundHigh-quality healthcare for pregnant women and newborns, particularly postnatal care (PNC) and small and/or sick newborn care (SSNC), is essential to reducing maternal and newborn morbidity and mortality in low- and middle-income countries (LMICs). Poor quality of care is a major contributor to preventable morbidity and mortality, emphasizing the need for improvements in health service delivery, which requires measuring and monitoring quality of care (QoC). Although indicators measuring QoC have been identified, there is a current gap in the availability of composite indicators that can summarize the complex, multidimensional nature of QoC. This study systematically developed three composite QoC indices for maternal PNC, newborn PNC, and SSNC feasible to measure using existing data in LMICs.MethodsA four-step process was used to define the indices: (1) Intervention selection: Key interventions were identified by reviewing global clinical guidelines and QoC frameworks; (2) Guideline review and item identification: Discrete items recommended for delivery of each of the selected interventions were extracted from intervention-specific guidelines; (3) Data mapping: These items were mapped to health facility survey data to assess their alignment with standardized tools; and (4) Final index development: A quality readiness index (QRI) was developed for each service area based on QoC frameworks, available data, and clinical guidelines.ResultsThe maternal PNC-QRI includes 12 interventions and contains 24 items. The newborn PNC-QRI includes 3 interventions and contains 16 items. The SSNC-QRI includes 8 interventions and contains 48 items. Data gaps for maternal PNC, newborn PNC, and SSNC led to the exclusion of some evidence-based interventions and limited item inclusion. No data on provision/experience of care were available for PNC or SSNC, thus the indices reflect only facility readiness.ConclusionsThe three QRIs developed provide composite measures for PNC and SSNC readiness and can be adapted at country level and operationalized using health facility assessment survey data, facilitating their use by decision-makers for planning and resource allocation. Revision of existing health facility assessments to address gaps in readiness and provision/experience of care measurement for PNC and SSNC would bolster efforts to monitor and improve QoC for mothers and newborns.
Segmentation of leukoaraiosis on noncontrast head CTs using CT-MRI paired data without human annotation
Authors: Ryu Wi-Sun , Song Jae W. , Lim Jae-Sung , Lee Ju Hyung , Sunwoo Leonard , Kim Dongmin , Lee Myungjae , Kim Beom Joon 
Published: October 2024

AbstractBackgroundCompared to white matter hyperintensity (WMH) on MRI, evaluating leukoaraiosis (LA) on CT can be challenging due to its low contrast-to-noise ratio against white matter and similar attenuation to parenchymal gliosis and edema. We aimed to develop and validate a deep learning algorithm that segments LA using CT-MRIFLAIRpaired data from a multicenter, multi-vendor registry from Korea and from a head CT dataset from a US population.MethodsWe retrospectively identified CT-MRIFLAIRpairs from a nationwide ischemic stroke registry for training and internal validation (n=482), external testing (n=390), and clinical validation (n=867). Additionally, 100 scans from a US population were collected. WMH on MRI were segmented using previously validated software and the segmentation mask was registered onto the CT scan. Performance was assessed using Dice similarity coefficient (DSC), concordance correlation coefficient (ρ), and Pearson correlation. Predicted LA volumes were analyzed for associations with clinical outcomes.ResultsMean age (SD) for training and external testing datasets were 68.1 (SD 12.7) and 69.2 (SD 13.5) years and 33.2% and 47.9% were female, respectively. External test showed a DSC of 0.527, with ρ values of 0.919 and 0.760 for predicted LA volumes compared to registered LA and WMH volumes on MRI, respectively. In external testing and US datasets, the predicted LA volumes were significantly correlated with Fazekas grade (Pearson correlation coefficient=0.832 and 0.891, respectively). Subgroup analysis demonstrated consistent performance across different CT vendors (ρ ranged from 0.875 to 0.950) and infarct volumes (≤10 mL vs >10 mL; ρ=0.912 and ρ=0.922). In an independent clinical dataset, the predicted LA volumes correlated with age and clinical outcomes after ischemic stroke.ConclusionOur deep learning algorithm offers a reproducible method for LA segmentation on CT, bridging the gap between CT and MRI assessments in patients with ischemic stroke.
A bifunctional snoRNA with separable activities in guiding rRNA 2’-O-methylation and scaffolding gametogenesis effectors
Authors: Leroy Estelle , Challal Drice , Pelletier Stéphane , Goncalves Coralie , Menant Alexandra , Marchand Virginie , Jaszczyszyn Yan , van Dijk Erwin , Naquin Delphine , Andreani Jessica , Motorin Yuri , Palancade Benoit , Rougemaille Mathieu 
Published: October 2024

AbstractSmall nucleolar RNAs are non-coding transcripts that guide chemical modifications of RNA substrates and modulate gene expression at the epigenetic and post-transcriptional levels. However, the extent of their regulatory potential and the underlying molecular mechanisms remain poorly understood. Here, we identify a conserved, previously unannotated intronic C/D-box snoRNA, termedsnR107, hosted in the fission yeast long non-coding RNAmamRNAand carrying two independent cellular functions. On the one hand,snR107guides site-specific 25S rRNA 2’-O-methylation and promotes pre-rRNA processing and 60S subunit biogenesis. On the other hand,snR107associates with the gametogenic RNA-binding proteins Mmi1 and Mei2, mediating their reciprocal inhibition and restricting meiotic gene expression during sexual differentiation. Both functions require distinctcis-motifs withinsnR107, including a conserved 2’-O-methylation guiding sequence. Together, our results positionsnR107as a dual regulator of rRNA modification and gametogenesis effectors, expanding our vision on the non-canonical functions exerted by snoRNAs in cell fate decisions.
A triple serine motif in the intracellular domains of sortilin-related receptors SorCS1-3 regulates neurotrophic activity
Authors: Dalby Anders , Kaas Mathias , Meinertz-Byg Lars , Christiansen Signe Bundgaard , Bøggild Simon , Qvist Per , Nyengaard Jens R. , Madsen Peder , Mølgaard Simon , Glerup Simon 
Published: October 2024

AbstractThe Vps10p-domain receptors SorCS1-3 have been repeatedly associated with the development of neurological and psychiatric disorders. They have emerged as key regulators of synaptic activity and neurotrophic signaling, but the underlying molecular mechanism remains poorly understood. Here we report that the SorCS1-3 intracellular domains (ICDs) contain a conserved triple serine motif that potentially functions as a signaling switch to induce neurotrophic signaling in hippocampal neurons. We demonstrate that phosphorylation mimicking mutations of the SorCS1-3 triple serine motifs display neurotrophic activity independently of both their extracellular domains (ECDs) and BDNF, and that the substitution of serines to alanines renders neurons less responsive to BDNF. Hence, we develop triple serine motif-based cell-penetrating peptides that modulate downstream signaling kinases of the BDNF pathway, ultimately activating the transcription factor CREB. Taken together, we provide the first mechanistic insights into SorCS1-3 mediated neurotrophic signaling and use this knowledge to develop pharmacologically active modulators.
Ancestral complexity and constrained diversification of the ant olfactory system
Authors: Marty Simon , Couto Antoine , Dawson Erika H. , Brard Neven , d’Ettorre Patrizia , Montgomery Stephen H. , Sandoz Jean-Christophe 
Published: October 2024

AbstractAnts are a monophyletic but diverse group of social insects whose heightened olfactory ability has been crucial to their evolutionary success. Their complex olfactory system is believed to have evolved due to the expansion of a specialized olfactory subsystem and the associated clade of olfactory receptors. Specifically, ants exhibit specialized antennal hairs known as basiconic sensilla, whose neurons project to a distinctive cluster of numerous, small glomeruli in their antennal lobes. This adaptation is believed to be linked to their social lifestyle, enabling the detection of recognition cues like cuticular hydrocarbons (CHCs), which are essential for nestmate recognition and maintaining colony cohesion. However, our understanding of the ant olfactory system remains incomplete, lacking evolutionary context and phylogenetic breadth, which leaves the complexity in their most recent common ancestor uncertain. We thus conducted a comparative study of neuroanatomical traits across the phylogeny of the Formicidae. Our findings reveal a common blueprint for the ant olfactory pathway, alongside lineage-specific adaptations. This highlights a dynamic evolution, particularly for the CHC-related subsystem. Ancestral trait reconstructions indicate that olfactory sophistication predates the most recent common ancestor of ants. Additionally, we found that the chemical complexity of species-specific recognition cues is associated with neuronal investment within the olfactory system. Lastly, behavioral experiments on anatomically divergent ant species show that, despite variation in neuroanatomical traits, ants consistently discriminate nestmates from non-nestmates. This suggests that the evolution of ants’ olfactory system integrates sensory adaptations to diverse chemical environments, facilitating communication, a key to social behaviors.
PoreMeth2: decoding the evolution of methylome alterations with Nanopore sequencing
Authors: Mattei Gianluca , Baragli Marta , Gega Barbara , Mingrino Alessandra , Chieca Martina , Ducci Tommaso , Frigè Gianmaria , Mazzarella Luca , D’Aurizio Romina , De Logu Francesco , Nassini Romina , Pelicci Pier Giuseppe , Magi Alberto 
Published: October 2024

AbstractIn epigenetic analysis, identifying differentially methylated regions (DMRs) typically involves detecting groups of consecutive CpGs that show significant changes in their average methylation levels. However, the methylation state of a genomic region can also be characterized by a mixture of patterns (epialleles) with variable frequencies, and the relative proportions of such patterns can provide insights into its mechanisms of formation.Traditional methods based on bisulfite conversion and NGS, due to the read size (150 bp), allow epiallele frequency analysis only in high-CpG-density regions, limiting differential methylation studies to just 50% of the human methylome. Nanopore sequencing, with its long reads, enables the analysis of epiallele frequency across both high- and low-CpG-density regions.We introduce a novel computational approach, PoreMeth2, an R library that integrates epiallelic diversity and methylation frequency changes from Nanopore data to identify DMRs, assess their formation mechanisms, and annotate them to genic and regulatory elements. We applied PoreMeth2 to cancer and glial cell datasets, demonstrating its ability to distinguish epigenomic changes with a strong effect on gene expression from those with a weaker impact on transcriptional activity.PoreMeth2 is publicly available athttps://github.com/Lab-CoMBINE/PoreMeth2.
PUNCH2: explore the strategy for Intrinsically Disordered Protein predictor
Authors: Meng Di , Pollastri Gianluca 
Published: October 2024

AbstractIntrinsically disordered proteins (IDPs) lack stable three-dimensional structures, which poses significant challenges for their computational prediction. This study introduces PUNCH2, a novel approach for predicting intrinsically disordered regions (IDRs) in proteins. We address key issues such as the scarcity of comprehensive IDR databases, effective feature extraction, and robust model architecture. By integrating sequences from experimental PDB datasets and fully disordered DisProt sequences for training, PUNCH2 achieves superior prediction accuracy. Various sequence embeddings, including One-Hot, MSA-based, and PLM-based methods, were evaluated, with ProtTrans-based embeddings showing the best performance. The optimal model architecture features multiple convolutional layers, enhancing predictive confidence. PUNCH2 and its lighter variant, PUNCH2-light, demonstrate high efficiency and accuracy in benchmarking against top predictors on the CAID2 dataset, offering promising tools for advancing IDP research and understanding.