bluuebunny/crossref_metadata_2025_split huggingface dataset:
The ABCs of Subarachnoid Hemorrhage Blood Volume Measurement: A Simplified Quantitative Method Predicts Outcomes and Delayed Cerebral Ischemia
Authors: Foettinger Fabian , Sharma Rohan , Salman Saif , Weston Alexander D. , Erickson Bradley J. , Huynh Thien , Tawk Rabih G. , Freeman William D. 
Published: September 2023

AbstractBackgroundWe sought to develop an easy-to-use quantifiable and more precise method to estimate total blood volume in patients with aneurysmal subarachnoid hemorrhage (SAH) and explore its volumetric extent on incidence of delayed cerebral ischemia (DCI) and poor outcomes by modified Rankin Scale by hospital discharge.MethodsIn this retrospective observational cohort study, we analyzed 277 patients with SAH admitted at our Comprehensive Stroke Center between 2012 and 2022. We derived a mathematical model (Model 1) by measuring SAH basal cisternal blood volume using a ABC/2-derived ellipsoid formula (A=width/thickness, B=length, C=vertical extension) on noncontrast computed tomography (NCCT) in 5 major SAH cisternal compartments. We compared Model 1 (M1) against a manual segmentation method (Model 2) on noncontrast head CT (NCCT). Data were analyzed using logistic regression analysis,ttest, receiver operator characteristic curves (ROC), and area under curve (AUC) analysis.ResultsThere was no significant difference in cisternal SAH volume (SAHV) analysis between the two models (p=.14). Average SAHV by M1 was 7.0 mL (95% CI, 5,89-8,09) and lower for good outcome at discharge and 16.6 mL (95% CI, 13.49-19.77) for poor outcome. Volumetric analysis showed that patients with DCI had higher SAHV with 10 mL as a cutoff value (JABC-SAHV-outcome=10.0855 mL and JABC-SAHV-DCI=10.117 mL).ConclusionsA simplified ABC/2-derived method of SAH blood volume measurement is comparable to manual segmentation, and more importantly, can be performed in low-resource settings. Higher total SAH volumes by ABC/2-derived method were associated with worse outcomes and higher risk of DCI in this study population. A potential dose-response relationship of SAHV blood greater than 10mL appeared to predict worse outcomes and higher risk for DCI. A future larger prospective trial is being planned to validate these results.Subject codes[50] Cerebral Aneurysm, AVM, & Subarachnoid hemorrhage; [58] Computerized tomography and Magnetic Resonance Imaging
Exploring the Relationship Between Household Income and Healthcare Travel Patterns
Authors: Bemanian Amin , Mosser Jonathan F 
Published: September 2023

AbstractIntroductionTransportation is a social determinant of health which affects how easily individuals attend clinic appointments, obtain medications, or seek emergency care. Despite the importance of transportation, there are few large-scale studies characterizing typical transportation behaviors related to seeking healthcare. This study investigates demographic differences in travel times and transportation mode for healthcare/medical related trips using the National Household Travel Survey (NHTS) dataset and identifies potential access inequities.MethodsMedical trip data was obtained from the 2017 NHTS dataset. All analysis was adjusted by survey weights. Multiple linear regression models were developed to investigate the relationships between demographic variables, transportation mode, and travel time. Additionally, a logistic regression model was used to investigate the relationship between demographics and transportation mode.ResultsMedical trips using public transportation were found to be significantly longer relative to personal automobile trips. Higher household income was found to be associated with shorter travel times, but the effect size decreased with the inclusion of transportation mode. Higher household income respondents were also likely to use public transportation. Respondent race was not significantly associated with any differences in travel times, but there were significant differences across races in public transportation use.ConclusionsThis study demonstrates that individuals with lower household incomes tended to have longer medical trips. Additionally, it identifies public transit to be a potential mediating factor for this difference, as lower-income residents were significantly more likely to use public transit. This analysis highlights the importance of maintaining accessible and efficient public transportation for access to healthcare, especially for populations which have traditionally been at-risk for health disparities.
Single-cell atlas of ABCA7 loss-of-function reveals impaired neuronal respiration via choline-dependent lipid imbalances
Authors: von Maydell Djuna , Wright Shannon , Bonner Julia Maeve , Staab Colin , Spitaleri Andrea , Liu Liwang , Pao Ping-Chieh , Yu Chung Jong , Scannail Aine Ni , Li Mingpei , Boix Carles A. , Mathys Hansruedi , Leclerc Guillaume , Menchaca Gloria Suella , Welch Gwyneth , Graziosi Agnese , Leary Noelle , Samaan George , Kellis Manolis , Tsai Li-Huei 
Published: September 2023

AbstractLoss-of-function (LoF) variants in the lipid transporter ABCA7 significantly increase the risk of Alzheimer’s disease (odds ratio ∼2), yet the pathogenic mechanisms and the neural cell types affected by these variants remain largely unknown. Here, we performed single-nuclear RNA sequencing of 36 humanpost-mortemsamples from the prefrontal cortex of 12 ABCA7 LoF carriers and 24 matched non-carrier control individuals. ABCA7 LoF was associated with gene expression changes in all major cell types. Excitatory neurons, which expressed the highest levels of ABCA7, showed transcriptional changes related to lipid metabolism, mitochondrial function, cell cycle-related pathways, and synaptic signaling. ABCA7 LoF-associated transcriptional changes in neurons were similarly perturbed in carriers of the common AD missense variant ABCA7 p.Ala1527Gly (n = 240 controls, 135 carriers), indicating that findings from our study may extend to large portions of the at-risk population. Consistent with ABCA7’s function as a lipid exporter, lipidomic analysis of isogenic iPSC-derived neurons (iNs) revealed profound intracellular triglyceride accumulation in ABCA7 LoF, which was accompanied by a relative decrease in phosphatidylcholine abundance. Metabolomic and biochemical analyses of iNs further indicated that ABCA7 LoF was associated with disrupted mitochondrial bioenergetics that suggested impaired lipid breakdown by uncoupled respiration. Treatment of ABCA7 LoF iNs with CDP-choline (a rate-limiting precursor of phosphatidylcholine synthesis) reduced triglyceride accumulation and restored mitochondrial function, indicating that ABCA7 LoF-induced phosphatidylcholine dyshomeostasis may directly disrupt mitochondrial metabolism of lipids. Treatment with CDP-choline also rescued intracellular amyloidβ-42 levels in ABCA7 LoF iNs, further suggesting a link between ABCA7 LoF metabolic disruptions in neurons and AD pathology. This study provides a detailed transcriptomic atlas of ABCA7 LoF in the human brain and mechanistically links ABCA7 LoF-induced lipid perturbations to neuronal energy dyshomeostasis. In line with a growing body of evidence, our study highlights the central role of lipid metabolism in the etiology of Alzheimer’s disease.
Automated detection and classification of polioviruses from nanopore sequencing reads using piranha
Authors: O’Toole Áine , Colquhoun Rachel , Ansley Corey , Troman Catherine , Maloney Daniel , Vance Zoe , Akello Joyce , Bujaki Erika , Majumdar Manasi , Khurshid Adnan , Arshad Yasir , Alam Muhammad Masroor , Martin Javier , Shaw Alexander G , Grassly Nicholas C , Rambaut Andrew 
Published: September 2023

AbstractWidespread surveillance, rapid detection and appropriate intervention will be critical for successful eradication of poliovirus. With deployable next-generation sequencing (NGS) approaches, such as Oxford Nanopore Technologies’ MinION, the time from sample to result can be significantly reduced compared to cell culture and Sanger sequencing. We developed piranha (poliovirus investigation resource automating nanopore haplotype analysis) to aid routine poliovirus testing of both stool and environmental samples and alleviate the bioinformatic bottleneck that often exists for labs adopting novel NGS approaches. Piranha can be used for efficient intratypic differentiation of poliovirus serotypes, for classification of Sabin-like polioviruses and for detection of wild-type and vaccine derived polioviruses. It produces interactive, distributable html reports, as well as summary csv files and consensus poliovirus FASTA sequences. The reports describe each nanopore sequencing run with interpretable plots enabling researchers to easily detect the presence of poliovirus in samples and quickly disseminate their results.
Kisspeptin fiber and receptor distribution analysis suggests its potential role in central sensorial processing and behavioral state control
Authors: Zhang Limei , Hernández Vito S. , Zetter Mario A. , Hernández-Pérez Oscar R. , Hernández-González Rafael , Camacho-Arroyo Ignacio , Eiden Lee E. , Millar Robert P. 
Published: September 2023

AbstractBackgroundKisspeptin (KP) signaling in the brain is defined by the anatomical distribution of KP-producing neurons, their fibers, receptors, and connectivity. Technological advances have prompted a re-evaluation of these chemoanatomical aspects, originally studied in the early years after the discovery of KP and its receptorKiss1r.We have previously characterized(1) seven KP neuronal populations in the mouse brain at the mRNA level, including two novel populations, and examined their short-term response to gonadectomy.MethodsIn this study, we mapped KP fiber distribution in rats and mice using immunohistochemistry under intact and short- and long-term post-gonadectomy conditions.Kiss1rmRNA expression was examined via RNAscope, in relation to vesicular GABA transporter (Slc32a1) in whole mouse brain and to KP and vesicular glutamate transporter 2 (Kiss1andSlc17a6) in hypothalamic RP3V and arcuate regions.ResultsWe identified KP fibers in 118 brain regions, primarily in extra-hypothalamic areas associated with sensorial processing and behavioral state control. KP-immunoreactive fiber density and distribution were largely unchanged by gonadectomy.Kiss1rwas expressed prominently in sensorial and state control regions such as septal nuclei, the suprachiasmatic nucleus, locus coeruleus, hippocampal layers, thalamic nuclei, and cerebellar structures. Co-expression ofKiss1randKiss1was observed in hypothalamic neurons, suggesting both autocrine and paracrine KP signaling mechanisms.ConclusionThese findings enhance our understanding of KP signaling beyond reproductive functions, particularly in sensorial and behavioral state regulation. This study opens new avenues for investigating KP’s role in controlling complex physiological processes, including those not related to reproduction.
Differing effects of alcohol use on epigenetic and brain age in adult children of alcoholic parents
Authors: Scholl Jamie L. , Pearson Kami , Fercho Kelene A. , Van Asselt Austin J. , Kallsen Noah A. , Ehli Erik. A. , Potter Kari N. , Brown-Rice Kathleen A. , Forster Gina L. , Baugh Lee A. 
Published: September 2023

AbstractIt is known that being the adult child of an alcoholic (ACoA) can confer a wide variety of increased health and psychological risks, including higher rates of anxiety, depression, and posttraumatic stress disorder symptoms. Additionally, ACoAs are at greater risk of developing substance use disorders than individuals from non-alcoholic families. To better understand the psychobiological factors underlying these risks, ACoA individuals with risky hazardous alcohol use (n=14) and those not engaged in hazardous use (n=14) were compared to a group of healthy controls. We examined structural brain differences and applied machine learning algorithms to predict biological brain and DNA methylation ages to investigate differences between these groups. Contrary to our hypothesis, we found that hazardous and non-hazardous ACoA groups had lower predicted brain ages than the healthy control group (n=100), which may result from neuro-developmental differences between ACoA groups and controls. When examining specific brain regions, we observed decreased cortical volume within bilateral pars orbitalis and frontal poles, as well as the left middle temporal gyrus and entorhinal cortex within the hazardous alcohol ACoA group, all areas consistent with previous research examining how alcohol use affects brain structure. When looking at the epigenetic aging data, the hazardous ACoA participants had increased predicted epigenetic age difference scores compared to the control group (n=34) and the non-hazardous ACoA participant groups. In summary, the results demonstrate a decreased brain age in the ACoAs compared to control, concurrent with increased epigenetic age specifically in the hazardous ACoA group, laying the foundation for future research to identify individuals that may have an increased susceptibility to developing hazardous alcohol use. Together, these results provide a better understanding of the associations between epigenetic factors, brain structure, and alcohol use disorders.
Photoemission electron microscopy for connectomics
Authors: Boergens Kevin M. , Wildenberg Gregg , Li Ruiyu , Lambert Lola , Moradi Amin , Stam Guido , Tromp Rudolf , van der Molen Sense Jan , King Sarah B. , Kasthuri Narayanan 
Published: September 2023

1AbstractDetailing the physical basis of neural circuits with large-volume serial electron microscopy (EM), ‘connectomics’, has emerged as an invaluable tool in the neuroscience armamentarium. However, imaging synaptic resolution connectomes is currently limited to either transmission electron microscopy (TEM) or scanning electron microscopy (SEM). Here, we describe a third way, using photoemission electron microscopy (PEEM) which illuminates ultra-thin brain slices collected on solid substrates with UV light and images the photoelectron emission pattern with a wide-field electron microscope. PEEM works with existing sample preparations for EM and routinely provides sufficient resolution and contrast to reveal myelinated axons, somata, dendrites, and sub-cellular organelles. Under optimized conditions, PEEM provides synaptic resolution; and simulation and experiments show that PEEM can be transformatively fast, at Gigahertz pixel rates. We conclude that PEEM imaging leverages attractive aspects of SEM and TEM, namely reliable sample collection on robust substrates combined with fast wide-field imaging, and could enable faster data acquisition for next-generation circuit mapping.
Utilizing ChatGPT to select literature for meta-analysis shows workload reduction while maintaining a similar recall level as manual curation
Authors: Cai Xiangming , Geng Yuanming , Du Yiming , Westerman Bart , Wang Duolao , Ma Chiyuan , Garcia Vallejo Juan J. 
Published: September 2023

AbstractBackgroundLarge language models (LLMs) like ChatGPT showed great potential in aiding medical research. A heavy workload in filtering records is needed during the research process of evidence-based medicine, especially meta-analysis. However, no study tried to use LLMs to help screen records in meta-analysis.ObjectiveIn this research, we aimed to explore the possibility of incorporating ChatGPT to facilitate the screening step based on the title and abstract of records during meta-analysis.MethodsTo assess our strategy, we selected three meta-analyses from the literature, together with a glioma meta-analysis embedded in the study, as additional validation. For the automatic selection of records from curated meta-analyses, a four-step strategy called LARS-GPT was developed, consisting of (1) criteria selection and single-prompt (prompt with one criterion) creation, (2) best combination identification, (3) combined-prompt (prompt with one or more criteria) creation, and (4) request sending and answer summary. Recall, workload reduction, precision, and F1 score were calculated to assess the performance of LARS-GPT.ResultsA variable performance was found between different single-prompts with a mean recall of 0.841. Based on these single-prompts, we were able to find combinations with performance better than the pre-set threshold. Finally, with a best combination of criteria identified, LARS-GPT showed a 39.5% workload reduction on average with a recall greater than 0.9.ConclusionsWe show here the groundbreaking finding that automatic selection of literature for meta-analysis is possible with ChatGPT. We provide it here as a pipeline, LARS-GPT, which showed a great workload reduction while maintaining a pre-set recall.
Developmental pathways of physical aggression from infancy to early school age
Authors: Nærde Ane , Janson Harald Tage , Stoolmiller Mike 
Published: September 2023

AbstractThis study identified latent trajectories of physical aggression from infancy to preschool age and tested for (a) early parent, parenting and child predictor effects on trajectory membership and (b) trajectory-effects net of parent, parenting, and child predictor effects on Grade 2 social, behavioral and academic functioning. We used data from the Behavior Outlook Norwegian Developmental Study (BONDS), comprising 1,159 children (559 girls). Parents reported on risk and protective factors, and on physical aggression from 1 to 5 years; teachers reported on Grade 2 outcomes. We employed latent class growth curve analyses to identify nine aggression trajectories. In fully adjusted models testing simultaneously all associations among predictors, trajectories, and outcomes, maternal and paternal harsh parenting, child gender, and sibling presence predicted trajectory membership, which significantly predicted Grade 2 externalizing. Child gender had a pervasive influence on all outcomes as well as on trajectory membership. This is the first trajectory study that attempts to sort out which predictors are most proximal, more distal, or just confounded, with their relative direct effect sizes, and to link early paternal as well as maternal harsh parenting with children’s development of physical aggression from infancy to preschool age. Our findings underscore the need to include fathers in developmental research and early prevention and intervention efforts.
Multi-Generation Ecosystem Selection Of Rhizosphere Microbial Communities Associated With Plant Genotype and Biomass InArabidopsis thaliana
Authors: Shankar Nachiket , Shetty Prateek , Melo Tatiana C , Kesseli Rick 
Published: September 2023

AbstractThe role of the microbiome in shaping the host phenotype has emerged as a critical area of investigation, with implications in ecology, evolution, and host health. The complex and dynamic interactions involving plants and their diverse rhizosphere microbial communities are influenced by a multitude of factors, including but not limited to soil type, environment, and plant genotype. Understanding the impact of these factors on microbial community assembly is key to yielding host-specific and robust benefits for plants, yet remains challenging. Here we ran an artificial ecosystem selection experiment, over eight generations, inArabidopsis thalianaLerand Cvi to select soil microbiomes associated with higher or lower biomass of the host. This resulted in divergent microbial communities, shaped by a complex interplay between random environmental variations, plant genotypes, and biomass selection pressures. In the initial phases of the experiment, the genotype and the biomass selection treatment have modest but significant impacts. Over time, the plant genotype and biomass treatments gain more influence, explaining ∼40% of the variation in the microbial community composition. Furthermore, a genotype-specific association of a plant growth-promoting rhizobacterial taxa,Labraceaewith LerandRhizobiaceaewith Cvi, is observed under selection for high biomass.
Partial alopecia area retains bulge hair follicle progenitor cells in Indian androgenetic alopecia patients
Authors: Hegde Akshay , Saha Dyuti , Somaiah Savitha , Jamora Colin 
Published: September 2023

AbstractAndrogenic alopecia (AGA) is a pathological condition characterized by the progressive decrease of scalp hair follicle density. Completely bald areas of AGA scalp still retain hair follicle stem cells but the progenitor cells are drastically decreased in number. However, it is unknown when the progenitor cells begin to diminish in number during the progression of AGA. Despite the prevalence of AGA in 58% of the Indian male population, no study to date has characterized the hair follicle stem and progenitor cell populations in AGA patients in this ethnic group. We observed that the partially bald area retains progenitor cells expressing CD34 and Sox9 but they are not present in the hair follicles in the completely bald area. Our study sheds light on the timeframe for effective therapeutic interventions based on modulating regulatory mechanisms to reinitiate the existing inactive follicle stem cells.
Genome of the endangered eastern quoll (Dasyurus viverrinus) reveals signatures of historical decline and pelage color evolution
Authors: Hartley Gabrielle A. , Frankenberg Stephen R. , Robinson Natasha M. , MacDonald Anna J. , Hamede Rodrigo K. , Burridge Christopher P. , Jones Menna E. , Faulkner Tim , Shute Hayley , Rose Karrie , Brewster Robert , O’Neill Rachel , Renfree Marilyn B. , Pask Andrew J. , Feigin Charles Y. 
Published: September 2023

AbstractThe eastern quoll (Dasyurus viverrinus) is an endangered marsupial mesopredator native to Australia. Since the extirpation of the last mainland Australian populations in the late 20th century, wild populations of this species have been restricted to two islands at the far southern end of its historical range. Eastern quolls are the subject of captive breeding programs and attempts have recently been made to re-establish a population in mainland Australia through translocations. However, few resources currently exist to guide the genetic management of this species. Here, we generated a chromosome-scale reference genome for the eastern quoll, along with gene annotations supported by multi-tissue transcriptomes. Through comparisons with related species, we find that our reference genome is among the most complete marsupial assemblies currently available. Using this assembly, we infer the species’ demographic history and identify potential evidence of a long-term decline beginning in the late Pleistocene. Finally, we identify a deletion at theASIPlocus that likely drives differences in pelage color between the eastern quoll and the closely related Tasmanian devil (Sarcophilus harrisii). The genomic resources we present are valuable new tools for evolutionary and conservation genomic studies.