bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pediatric Long COVID Subphenotypes: An EHR-based study from the RECOVER program
Authors: Lorman Vitaly , Bailey L. Charles , Song Xing , Rao Suchitra , Hornig Mady , Utidjian Levon , Razzaghi Hanieh , Mejias Asuncion , Leikauf John Erik , Brill Seuli Bose , Allen Andrea , Bunnell H Timothy , Reedy Cara , Mosa Abu Saleh Mohammad , Horne Benjamin D , Geary Carol Reynolds , Chuang Cynthia H. , Williams David A , Christakis Dimitri A , Chrischilles Elizabeth A , Mendonca Eneida A , Cowell Lindsay G. , McCorkell Lisa , Liu Mei , Cummins Mollie R , Jhaveri Ravi , Blecker Saul , Forrest Christopher B. 
Published: September 2024

ABSTRACTPediatric Long COVID has been associated with a wide variety of symptoms, conditions, and organ systems, but distinct clinical presentations, or subphenotypes, are still being elucidated. In this exploratory analysis, we identified a cohort of pediatric (age <21) patients with evidence of Long COVID and no pre-existing complex chronic conditions using electronic health record data from 38 institutions and used an unsupervised machine learning-based approach to identify subphenotypes. Our method, an extension of the Phe2Vec algorithm, uses tens of thousands of clinical concepts from multiple domains to represent patients’ clinical histories to then identify groups of patients with similar presentations. The results indicate that cardiorespiratory presentations are most common (present in 54% of patients) followed by subphenotypes marked (in decreasing order of frequency) by musculoskeletal pain, neuropsychiatric conditions, gastrointestinal symptoms, headache, and fatigue.
Subcallosal Cingulate structural connectivity as biomarker for chronic low back pain
Authors: Tsolaki Evangelia , Wei Wenxin , Ward Michael , Bari Ausaf , Pouratian Nader 
Published: September 2024

AbstractBackgroundChronic low back pain (CLBP) poses a significant challenge, contributing significantly to the ongoing opioid crisis while also being a leading cause of disability. Although spinal cord stimulation (SCS) stands as the primary FDA-endorsed method for neuromodulatory therapy in CLBP, there remains a subset of patients unresponsive to SCS and others who experience insufficient pain relief over time. In view of the evidence suggesting the critical role of subcallosal cingulate cortex (SCC) connectivity in pain processing, in the current study we investigated the role of the baseline SCC structural as a potential neuroimaging predictive biomarker to identify patients that are likely to benefit from SCS.MethodsDiffusion magnetic resonance imaging scans were acquired in 8 patients with CLBP (mean (SD) age = 70 (10) years; 6 female/2 male, 6 UCLA site, 2 UTSW) before their initial SCS trial. Probabilistic tractography from subject-specific anatomically defined SCC seed regions to the ventral striatum (VS), anterior cingulate cortex (ACC), uncinate fasciculus (UCF) and bilateral medial prefrontal cortex (mPFC) was used to calculate FSL structural probabilistic connectivity in the target network. To explore cross-sectional variations in SCC connectivity related to SCS trial response, we employed a general linear model (GLM) using the SCC probability of connectivity as dependent variable, and the response to the SCS trial as independent variable. We used Pearson correlation to evaluate further the relationships between the critical SCC probability of connectivity and the change in VAS score after the SCS trial. Finally, the role of depression in the treatment outcome was evaluated.ResultsResponders to SCS had significantly lower ipsilateral SCC connectivity to mPFC (F1,8 =8.19, p = 0.03) and VS (F1,8 =17.48, p=0.01) on the left hemisphere compared to non-responders. Pearson correlation analysis showed that decreased ipsilateral SCC baseline connectivity to left mPFC (p=0.03) and VS (p=0.01) was correlated with higher improvement in VAS scores. The baseline depression severity did not significantly influence the change in VAS score following the SCS trial. On the other hand, baseline SCC-VS connectivity on the left hemisphere was a significant predictor of change in VAS score (p=0.02).ConclusionsOur study highlights the important role of SCC connectivity that can serve as a potential biomarker for CLBP stratification and prediction to SCS treatment. These results can reshape our perspective on CLBP management and can serve as early indicator of response to the treatment providing a personalized approach based on the individual’s underlying SCC connectivity.
Gaps in protection toAnophelesexposure in high malaria endemic regencies of Papua Province, Indonesia
Authors: Rozi Ismail E , Syahrani Lepa , Permana Dendi H , Asih Puji B S , Sumiwi Maria E , Lobo Neil F , Hawley William A , Syafruddin Din 
Published: September 2024

ABSTRACTBackgroundMalaria in eastern Indonesia remains high despite significant reductions and local elimination in other parts of the country. Malaria control activities that have been implemented include early diagnosis and prompt treatment, provision of Long-lasting insecticide-treated nets (LLINs), and indoor residual spraying (IRS). To expedite malaria elimination in this region, a rapid entomological assessment combined with human behaviour observations (HBOs) were conducted in eight high malaria endemic regencies in Papua Province, Indonesia. The present study focuses on identifying gaps in protection against mosquito biting indoors and outdoors that may contribute to the sustained transmission and persistently high endemicity.MethodsThis study was conducted alongside a rapid entomologic assessment, including human landing catches (HLCs) of adult mosquitoes. Human behavior was documented by direct observations during HLCs. HBO data focused on temporal (over the night) and spatial (domestic or peri-domestic) presence, alongside bed net usage and sleeping patterns. Household questionnaires, also conducted during entomological collections, documented data on house structure materials, practices against mosquito bites, livestock presence, as well as intervention usage.ResultsAnalysis of human behaviors in each regency identified several indoor and outdoor gaps in protection against mosquito biting. Human exposure to mosquito bites was driven by ITN usage, IRS coverage, indoor presence without protection prior to sleeping, absence of mosquito house screens, and outdoor presence without protection.ConclusionsData demonstrates multiple gaps in protection against mosquito exposure in all eight regencies of Papua evaluated. Indoor interventions require optimization, while current vector control activities do not presently address outdoor exposure. Measured spatial and temporal exposure may be utilized to understand protective vector interventions that may function in these spaces while also pointing to continued exposure. Additional interventions, such as community-based larval source management, may reduce exposure overall, while novel interventions like spatial repellents may fill some gaps in protection – alongside optimized case detection and treatment. Results suggest that the present strategy may be insufficient to eliminate malaria in the region, and a rethought evidence-based and adaptive strategy is required.
Executive Function and Adherence in Children and Adolescents Living with HIV: Evidence from the HIV-associated Neurocognitive Disorders in Zambia (HANDZ) Study
Authors: Mwanza-Kabaghe Sylvia , Sportiello Kristen , Shah Mina , Adams Heather R. , Mbewe Esau G. , Kabundula Pelekelo P. , Schneider Colleen , Mweemba Milimo , Birbeck Gretchen L. , Bearden David R. 
Published: September 2024

AbstractIntroductionExecutive function (EF) may be impaired in people with human immunodeficiency virus (HIV) infection, and poor EF may affect medication adherence. However, there is little data on EF in children with HIV in sub-Saharan Africa.Methods208 children/adolescents with perinatally acquired HIV and 208 HIV-exposed uninfected controls were recruited in Zambia for this prospective cohort study. EF was measured using performance-based, self-report, and parental report measures. Adherence over one year of follow-up was assessed through questionnaires and viral load measurement.ResultsChildren with HIV performed significantly worse on all three measures of EF. Lower parental rating of EF was associated with poorer antiretroviral therapy adherence (OR: 1.5, 95% CI = 1.02 – 2.2, p = 0.04).ConclusionChildren with HIV have EF impairments which may lead to consequences like poor medication adherence and treatment failure. Interventions to improve EF or compensate for impaired EF may be necessary in this population.
Socio-medical Factors Associated with Neurodevelopmental Disorders on the Kenyan Coast
Authors: Kipkemoi Patricia , Savage Jeanne E. , Gona Joseph , Rimba Kenneth , Kombe Martha , Mwangi Paul , Kipkoech Collins , Chepkemoi Eunice , Ngombo Alfred , Mkubwa Beatrice , Rehema Constance , Kariuki Symon M. , Posthuma Danielle , Donald Kirsten A. , Robinson Elise , Abubakar Amina , Newton Charles R 
Published: September 2024

AbstractBackgroundNeurodevelopmental disorders (NDDs) are a group of conditions with their onset during the early developmental period and include conditions such as autism, intellectual disability and attention deficit hyperactivity disorder (ADHD). Occurrence of NDDs is thought to be determined by both genetic and environmental factors, but data on the role of environmental risk factors for NDD in Africa is limited. This study investigates environmental influences on NDDs in children from Kenya. This case-control study compared children with NDDs and typically developing children from two studies on the Kenyan coast that did not overlap.Methods and FindingsWe included 172 of the study participants from the Kilifi Autism Study and 151 from the NeuroDev Study who had a diagnosis of at least one NDD and 112 and 73 with no NDD diagnosis from each study, respectively. Potential risk factors were identified using unadjusted univariable analysis and adjusted multivariable logistic regression analysis. Univariable analysis in the Kilifi Autism Study sample revealed hypoxic-ischaemic encephalopathy conferred the largest odds ratio (OR) 10.52 (95%CI 4.04 – 27.41) for NDDs, followed by medical complications during pregnancy (gestational hypertension & diabetes, eclampsia, and maternal bleeding) OR: 3.17 (95%CI 1.61 – 6.23). In the NeuroDev study sample, labour and birth complications (OR: 7.30 (2.17 – 24.61)), neonatal jaundice (OR: 5.49 (95%CI 1.61 – 18.72)) and infection during pregnancy (OR: 5.31 (1.56 – 18.11)) conferred the largest risk associated with NDDs. In the adjusted analysis, seizures before age 3 years in the Kilifi Autism study and labour and birth complications in the NeuroDev study conferred the largest increased risk. Higher parity, the child being older and delivery at home were associated with a reduced risk for NDDs.ConclusionRecognition of important risk factors such as labour and birth complications could guide preventative interventions, developmental screening of at-risk children and monitoring progress. Further studies examining the aetiology of NDDs in population-based samples, including investigating the interaction between genetic and environmental factors, are needed.
Inositol polyphosphates regulate resilient mechanisms in the green algaChlamydomonas reinhardtiito adapt to extreme nutrient conditions
Authors: Bedera-García Rodrigo , García-Gómez María Elena , Personat José María , Couso Inmaculada 
Published: September 2024

AbstractIn the actual context of climate changing environments, photosynthetic organisms need to adapt to more extreme conditions. Microalgae can be excellent organisms to understand molecular mechanisms that activate survival strategies under stress.Chlamydomonas reinhardtiisignaling mutants are extremely useful to decipher which strategies they use to cope with changeable environments. In this study, we conducted prolonged starvation in wild type andvip1-1 Chlamydomonascells. The mutantvip1-1has an altered profile of pyroinositol polyphosphates (PP-InsPs) which are signaling molecules present in all eukaryotes. These molecules have been connected to P signaling in other organisms including plants but their implications in other nutrient signaling is still under evaluation. After prolonged starvation, WT andvip1-1showed important differences in the levels of chlorophyll and photosystem II (PSII) activity. We also performed a metabolomic analysis under these conditions and found an overall decrease in different organic compounds such as amino acids including arginine and its precursors and tryptophan which is considered as a signaling molecule itself in plants. In addition, we observed significant differences in RNA levels of genes related to nitrogen assimilation that are under the control of NIT2 transcription factor. Overall our data indicate an important role of PP-InsPs in the regulation of nutrient starvation especially regarding N assimilation and C distribution. These data are of great importance for the generation of resilient strains to be used in open ponds and high capacity bioreactors.
The mechanism of peptidoglycan O-acetylation in Gram-negative bacteria typifies bacterial MBOAT-SGNH acyltransferases
Authors: Anderson Alexander C. , Schultz Bailey J. , Snow Eric D. , Brott Ashley S. , Stangherlin Stefen , Malloch Tyler , London Jalen R. , Walker Suzanne , Clarke Anthony J. 
Published: September 2024

AbstractBacterial cell envelope polymers are commonly modified with acyl groups that provide fitness advantages. Many polymer acylation pathways involve pairs of membrane-boundO-acyltransferase (MBOAT) and SGNH family proteins. As an example, the MBOAT protein PatA and the SGNH protein PatB are required in Gram-negative bacteria for peptidoglycan O-acetylation. The mechanism for how MBOAT-SGNH transferases move acyl groups from acyl-CoA donors made in the cytoplasm to extracellular polymers is unclear. Using the peptidoglycanO-acetyltransferase proteins PatAB, we explore the mechanism of MBOAT-SGNH pairs. We find that the MBOAT protein PatA catalyzes auto-acetylation of an invariant Tyr residue in its conserved C-terminal hexapeptide motif. We also show that PatB can use a synthetic hexapeptide containing an acetylated tyrosine to donate an acetyl group to a peptidoglycan mimetic. Finally, we report the structure of PatB, finding that it has structural features that shape its activity as anO-acetyltransferase and distinguish it from other SGNH esterases and hydrolases. Taken together, our results support a model for peptidoglycan acylation in which a tyrosine-containing peptide at the MBOAT’s C-terminus shuttles an acyl group from the MBOAT active site to the SGNH active site, where it is transferred to peptidoglycan. This model likely applies to other systems containing MBOAT-SGNH pairs, such as those that O-acetylate alginate, cellulose, and secondary cell wall polysaccharides. The use of an acyl-tyrosine intermediate for MBOAT-SGNH acyl transfer is also shared with AT3-SGNH proteins, a second major group of acyltransferases that modify cell envelope polymers.
RIPK1 is essential for Herpes Simplex Virus-triggered ZBP1-dependent necroptosis in human cells
Authors: Amusan Oluwamuyiwa T. , Wang Shuqi , Yin Chaoran , Koehler Heather S. , Li Yixun , Tenev Tencho , Wilson Rebecca , Bellenie Benjamin , Zhang Ting , Wang Jian , Liu Chang , Seong Kim , Poorbaghi Seyedeh L. , Yates Joseph , Shen Yuchen , Upton Jason W. , Meier Pascal , Balachandran Siddharth , Guo Hongyan 
Published: September 2024

AbstractNecroptosis initiated by the host sensor Z-NA Binding Protein-1 (ZBP1) is essential for host defense against a growing number of viruses, including Herpes Simplex Virus-1 (HSV-1). Studies with HSV-1 and other necroptogenic stimuli in murine settings have suggested that ZBP1 triggers necroptosis by directly complexing with the kinase RIPK3. Whether this is also the case in human cells, or whether additional co-factors are needed for ZBP1-mediated necroptosis, is unclear. Here, we show that ZBP1-induced necroptosis in human cells requires RIPK1. We have found that RIPK1 is essential for forming a stable and functional ZBP1-RIPK3 complex in human cells, but is dispensable for the formation of the equivalent murine complex. The RIP Homology Interaction Motif (RHIM) in RIPK3 is responsible for this difference between the two species, because replacing the RHIM in human RIPK3 with the RHIM from murine RIPK3 is sufficient to overcome the requirement for RIPK1 in human cells. These observations describe a critical mechanistic difference between mice and humans in how ZBP1 engages in necroptosis, with important implications for treating human diseases.
Brain plasticity for visual words: Elementary school teachers can drive changes in weeks that rival those formed over years
Authors: Wang Fang , Toomarian Elizabeth Y. , Gosavi Radhika S. , Kaneshiro Blair , Norcia Anthony M. , McCandliss Bruce D. 
Published: September 2024

AbstractThis study aims to investigate the impact of vocabulary acquisition through short-term classroom learning and its relation to broader forms of vocabulary learning through long-term exposure in daily life. Through a two week of “learning sprint” in collaboration with a local elementary school and EEG-Steady State Visual Evoked Potentials (EEG-SSVEP) paradigm, we assessed new vocabulary learning in first and second graders within their pedagogical environment. We then compared the results with the word frequency effect, a well-established phenonmenon that reflects long-term vocabulary learning. After two weeks of classroom instruction, newly acquired words elicited neural responses similar to those of high-frequency words, with the effect significantly correlated with children’s phonological decoding skills. Additionally, we successfully replicated the word frequency effect using the SSVEP paradigm for the first time. These findings highlight the potential of the “learning sprint” model for conducting neuroscience research in authentic educational settings, thereby fostering a stronger connection between education and neuroscience.
Core splicing architecture and early spliceosomal recognition determine microexon sensitivity to SRRM3/4
Authors: Bonnal Sophie , Bajew Simon , Corral Rosa Martinez , Irimia Manuel 
Published: September 2024

ABSTRACTMicroexons are essential for proper functioning of neurons and pancreatic endocrine cells, where their inclusion depends on the splicing factors SRRM3/4. However, in pancreatic cells, lower expression of these regulators limits inclusion to only the most sensitive subset among all neuronal microexons. Although variouscis-acting elements can contribute to microexon regulation, how they determine this differential dose response and high or low sensitivity to SRRM3/4 remains unknown. Here, Massively Parallel Splicing Assays probing 28,535 variants show that sensitivity to SRRM4 is conserved across vertebrates and support a regulatory model whereby high or low microexon sensitivity is largely determined by an interplay between core splicing architecture and length constraints. This conclusion is further supported by distinct spliceosome activities in the absence of SRRM3/4 and by a mathematical model that assumes that the two types of microexons differ only in their efficiency to recruit early spliceosomal components.
Athene cunicularia hypugaeawintering in a central California urban setting arrive later, leave earlier, prefer sheltered micro-habitat, tolerate rain, and contend with diverse predators
Authors: Nicolaus Martin A 
Published: September 2024

AbstractThe wintering phase of the Western Burrowing Owl (Athene cunicularia hypugaea) life cycle has received little attention in the literature. Small numbers of Burrowing Owls have been observed and recorded since 2008 in the winter season in Cesar Chavez Park, a 36-ha peninsula that forms part of the waterfront of the City of Berkeley. The relative ease of observation in this setting allows study of their arrival and departure dates, selection of micro-habitats, tolerance of human presence, behavior in inclement weather, and response to avian and canine predator threats. Viewed over a decade, fewer owls arrived, arrived later, left earlier, and spent less time in residence. Most owls settled in shoreline rip-rap or in tall vegetation; only one fourth settled in short grass. Owls chose exposure to rain for as long as two days. Owls varied widely in tolerance to human proximity. Owls successfully dealt with avian predators, but displayed stress and in some cases became casualties of looseCanis lupus familiaris. Recommendations for habitat management follow.
Association of complex traits with common genetic variation across genomic regions containing pathogenic copy number variations
Authors: Snihirova Yelyzaveta , Breddels Esmee M. , Frei Oleksandr , Sønderby Ida E. , Andreassen Ole A , van Amelsvoort Therese , Linden David E.J. , van der Meer Dennis 
Published: September 2024

AbstractBackgroundCopy Number Variations (CNVs) are structural variation in the genome, which may impact complex human traits and diseases. The investigation of rare CNVs is impeded by low sample size. To understand the mechanisms through which CNVs influence human health, common variation in the genomic region of the CNV from large samples could be used as a proxy.MethodsUtilising genome-wide association study (GWAS) summary statistics of 20 traits, we assessed the cumulative effect of common genetic variants in eight genomic regions containing pathogenic CNVs, using MAGMA gene-based analysis. We used GSA-MiXeR to estimate the fold enrichment of these CNV regions for the specific phenotypes.ResultsThe distal and proximal regions of the 16p11.2 CNV exhibited the highest number of significant associations and were enriched for the highest number of traits: 12 of 27 significant MAGMA associations (44%) were enriched. These CNV regions also had the highest number of phenotype-associated genes related to ion transport, signalling, transcriptional regulation, development, and protein metabolism. We compared the significance of all the genomic regions and the genes in these regions and found two opposing patterns: 1) cumulative value of separate genes, resulting in the higher significance of the whole region than of the particular genes; 2) higher significance of the specific genes that drive the association of the whole region.ConclusionsCharting the features of genomic regions encompassing CNVs might aid in clarifying CNVs’ role in human disease, especially pinpointing candidate genes within these regions that are associated with complex traits.