bluuebunny/crossref_metadata_2025_split huggingface dataset:
Subcortical brain volumes in neonatal hypoxic-ischemic encephalopathy
Authors: Kebaya Lilian M N , Kapoor Bhavya , Mayorga Paula Camila , Meyerink Paige , Foglton Kathryn , Altamimi Talal , Nichols Emily S. , de Ribaupierre Sandrine , Bhattacharya Soume , Tristao Leandro , Jurkiewicz Michael T , Duerden Emma G. 
Published: December 2022

AbstractBackgroundHypoxic ischemic encephalopathy (HIE) is a severe brain injury impacting term-born neonates. Despite treatment with therapeutic hypothermia (TH), HIE is associated with myriad adverse developmental outcomes suggesting the involvement of subcortical structures, including the thalamus and basal ganglia, which may be vulnerable to perinatal asphyxia, particularly during the acute period.Aims1) To examine subcortical macrostructure in the first few days of life in neonates with HIE compared to age- and sex-matched healthy neonates. 2) To determine whether subcortical volumetric maturation is associated with HIE severity.MethodsA cohort of 28 neonates (19 males [67.9%], median gestational age [GA]=38.6 weeks, interquartile range [IQR]=36.8-39.6) with HIE (mild=4, moderate=21, severe=3 based on Sarnat Staging) were scanned with MRI within the first four days of life (median postmenstrual age [PMA]=39.2, IQR=37.6-40.3), with the majority of scans occurring in the post-cooling period (n=23[82%]). The control group included 28 healthy neonates matched for GA, birth weight and PMA at the scan. Subcortical volumes (thalamus, basal ganglia, hippocampus, cerebellum) were automatically extracted from T1-weighted images. General linear models assessed between-group differences in subcortical volumes, adjusting for sex, GA, PMA, and total cerebral volumes. Within-group analyses evaluated the association between subcortical volumes and HIE severity.ResultsNeonates with HIE had significantly smaller bilateral thalamic, basal ganglia and right hippocampal and cerebellar volumes compared to healthy neonates (all, p<0.02). Within the HIE group, milder HIE severity was associated with smaller volumes of the left and right basal ganglia (both, p<0.007) and the left hippocampus and thalamus (both, p<0.04) when adjusting for TH, days of mechanical ventilation and other clinical and demographic factors.ConclusionsConsistent with findings from childhood survivors of HIE, newborns with HIE, scanned with MRI within the first days of life, had smaller subcortical volumes impacting sensory and motor regions, including the thalamus, basal ganglia and cerebellum compared to healthy newborns. Additionally, HIE severity was associated with subcortical volumes, particularly impacting the basal ganglia, suggesting these regions may be important brain-based biomarkers in newborns impacted by the hypoxic-ischaemic injury. Findings suggest that despite advances in neonatal care, HIE is associated with significant alterations in brain macrostructure.
Production and Characterization of Monoclonal antibodies to Xenopus proteins
Authors: Horr Brett , Kurtz Ryan , Pandey Ankit , Hoffstrom Benjamin G , Schock Elizabeth , LaBonne Carole , Alfandari Dominique 
Published: December 2022

AbstractMonoclonal antibodies are powerful and versatile tools that enable the study of proteins in diverse contexts. They are often utilized to assist with identifying subcellular localization and characterizing the function of target proteins of interest. However, because there can be considerable sequence diversity between orthologous proteins in Xenopus and mammals, antibodies produced against mouse or human proteins often do not recognize Xenopus counterparts. To address this issue, we refined existing protocols to produce mouse monoclonal antibodies directed against Xenopus proteins of interest. Here we describe several approaches for the generation of useful mouse anti-Xenopus antibodies to multiple Xenopus proteins and their validation in various experimental approaches. These novel antibodies are now available to the research community through theDevelopmentalStudyHybridomaBank (DSHB).Summary statementThe manuscript describes the generation and characterization of novel monoclonal antibodies toXenopus laevisproteins using refined hybridoma production methods suitable for basic science research labs.
Genetic Mapping of Progressive Ethanol Consumption in the Diversity Outbred Mouse
Authors: Tatom Zachary , Mignogna Kristin M. , Sergi Zachary , Nguyen Jeremy , Michenkova Marie , Smith Maren L. , Miles Michael F. 
Published: December 2022

AbstractTraditional genetic mapping studies using inbred crosses are a powerful tool for identifying chromosomal regions associated with ethanol-related traits, but typically have very large confidence intervals which make identification of specific and potentially causal candidate genes difficult. Diversity Outbred (DO) mice offer the ability to map quantitative trait loci (QTLs) associated with ethanol-drinking behaviors at a high resolution that allows for easier identification of candidate genes. Here, we exposed a population of 636 male DO mice to four weeks of intermittent ethanol access via a three-bottle choice paradigm, identifying 3 significant (Chrs 3, 4, and 12) and 12 suggestive loci for ethanol-drinking behaviors. The confidence intervals for these loci were narrow (1-4 Mbp for significant QTLs). We then further analyzed positional candidate genes using transcriptomics data from prefrontal cortex samples taken from 220 of these animals, as well as human GWAS data and prior gene set data for ethanol or other drugs of abuse. These results represent the highest-resolution genetic mapping of ethanol consumption behaviors in mice to date, providing for the identification of novel loci and candidate genes for progressive ethanol consumption, includingCar8--the lone gene with a significantcis-eQTL in strong linkage disequilibrium with our QTL for last week ethanol consumption on Chr 4.
Evaluation of EV Storage Buffer for Efficient Preservation of Engineered Extracellular Vesicles
Authors: Kawai-Harada Yuki , Itawi Hanine El , Komuro Hiroaki , Harada Masako 
Published: December 2022

AbstractExtracellular vesicles (EVs), detectable in all bodily fluids, mediate intercellular communication by transporting molecules between cells. The capacity of EVs to transport molecules between distant organs has drawn interest for clinical applications in diagnostics and therapeutics. Although EVs hold potential for nucleic acid-based and other molecular therapeutics, the lack of standardized technologies, including isolation, characterization, and storage, leaves many challenges for clinical applications, potentially resulting in misinterpretation of crucial findings. Previously, several groups demonstrated the problems of commonly used storage methods that distort EV integrity. This work aims to evaluate the process to optimize the storage conditions of EVs and then characterize them according to the experimental conditions and the models used previously. Our study reports a highly efficient EV storage condition, focusing on EVs’ capacity to protect their molecular cargo from biological, chemical, and mechanical damage. Compared with commonly used EV storage conditions, our EV storage buffer leads to less size and particle number variation at both 4°C and -80 °C, enhancing the ability to protect EVs while maintaining targeting functionality.
Aging Fly Cell Atlas Identifies Exhaustive Aging Features at Cellular Resolution
Authors: Lu Tzu-Chiao , Brbić Maria , Park Ye-Jin , Jackson Tyler , Chen Jiaye , Kolluru Sai Saroja , Qi Yanyan , Katheder Nadja Sandra , Cai Xiaoyu Tracy , Lee Seungjae , Chen Yen- Chung , Auld Niccole , Liang Chung-Yi , Ding Sophia H. , Welsch Doug , D’Souza Samuel , Pisco Angela Oliveira , Jones Robert C. , Leskovec Jure , Lai Eric C. , Bellen Hugo J. , Luo Liqun , Jasper Heinrich , Quake Stephen R. , Li Hongjie 
Published: December 2022

AbstractAging is characterized by a decline in tissue function, but the underlying changes at cellular resolution across the organism remain unclear. Here, we present the Aging Fly Cell Atlas, a single-nucleus transcriptomic map of the whole agingDrosophila. We characterize 163 distinct cell types and perform an in-depth analysis of changes in tissue cell composition, gene expression, and cell identities. We further develop aging clock models to predict the fly age and show that ribosomal gene expression is a conserved predictive factor for age. Combining all aging features, we find unique cell type-specific aging patterns. This atlas provides a valuable resource for studying fundamental principles of aging in complex organisms.
The effectiveness of acellular nerve allografts compared to autografts in animal models: a systematic review and meta-analysis
Authors: Broeren Berend O. , Hundepool Caroline A. , Kumas Ali H. , Duraku Liron S. , Walbeehm Erik T. , Hooijmans Carlijn R. , Power Dominic M. , Zuidam J. Michiel , De Jong Tim 
Published: December 2022

AbstractBackgroundTreatment of nerve injuries proves to be a worldwide clinical challenge. Acellular nerve allografts are suggested to be a promising alternative for bridging a nerve gap to the current gold standard, an autologous nerve graft.ObjectiveTo systematically review the efficacy of the acellular nerve allograft, its difference from the gold standard (the nerve autograft) and to discuss its possible indications.Material and methodsPubMed, Embase and Web of Science were systematically searched until the 4th of January 2022. Original peer reviewed paper that presented 1) distinctive data; 2) a clear comparison between not immunologically processed acellular allografts and autologous nerve transfers; 3) was performed in laboratory animals of all species and sex. Meta analyses and subgroup analyses (for graft length and species) were conducted for muscle weight, sciatic function index, ankle angle, nerve conduction velocity, axon count diameter, tetanic contraction and amplitude using a Random effects model. Subgroup analyses were conducted on graft length and species.ResultsFifty articles were included in this review and all were included in the meta-analyses. An acellular allograft resulted in a significantly lower muscle weight, sciatic function index, ankle angle, nerve conduction velocity, axon count and smaller diameter, tetanic contraction compared to an autologous nerve graft. No difference was found in amplitude between acellular allografts and autologous nerve transfers. Post hoc subgroup analyses of graft length showed a significant reduced muscle weight in long grafts versus small and medium length grafts. All included studies showed a large variance in methodological design.ConclusionOur review shows that the included studies, investigating the use of acellular allografts, showed a large variance in methodological design and are as a consequence difficult to compare. Nevertheless, our results indicate that treating a nerve gap with an allograft results in an inferior nerve recovery compared to an autograft in seven out of eight outcomes assessed in experimental animals. In addition, based on our preliminary post hoc subgroup analyses we suggest that when an allograft is being used an allograft in short and medium (0-1cm, > 1-2cm) nerve gaps is preferred over an allograft in long (> 2cm) nerve gaps.
Pynapple, a toolbox for data analysis in neuroscience
Authors: Viejo Guillaume , Levenstein Daniel , Carrasco Sofia Skromne , Mehrotra Dhruv , Mahallati Sara , Vite Gilberto R , Denny Henry , Sjulson Lucas , Battaglia Francesco P , Peyrache Adrien 
Published: December 2022

AbstractDatasets collected in neuroscientific studies are of ever-growing complexity, often combining high dimensional time series data from multiple data acquisition modalities. Handling and manipulating these various data streams in an adequate programming environment is crucial to ensure reliable analysis, and to facilitate sharing of reproducible analysis pipelines. Here, we present Pynapple, the PYthon Neural Analysis Package, a lightweight python package designed to process a broad range of time-resolved data in systems neuroscience. The core feature of this package is a small number of versatile objects that support the manipulation of any data streams and task parameters. The package includes a set of methods to read common data formats and allows users to easily write their own. The resulting code is easy to read and write, avoids low-level data processing and other error-prone steps, and is open source. Libraries for higher-level analyses are developed within the Pynapple framework but are contained within in a collaborative repository of specialized and continuously updated analysis routines. This provides flexibility while ensuring long-term stability of the core package. In conclusion, Pynapple provides a common framework for data analysis in neuroscience.HighlightsAn open-source framework for data analysis in systems neuroscience.Easy-to-use object-oriented programming for data manipulation.A lightweight and standalone package ensuring long-term backward compatibility.
Characterization of a novel botybirnavirus with a unique dsRNA infectingDidymella theifoliafrom tea plants
Authors: Ye Liangchao , Shi Xinyu , He Yunqiang , Chen Jiao , Xu Qingeng , Shafik Karim , Xu Wenxing 
Published: December 2022

AbstractDidymella theifoliaspecifically infects some local varieties ofCamellia sinensisin China, representing a unique fungal species, and characterization of the mycoviruses related to this fungal species is attractive. Three double-stranded RNAs (dsRNAs; dsRNAs 1, 2 and 3 with sizes of 6338, 5910 and 727 bp, respectively) were identified in an avirulent strain CJP4-1 ofD. theifoliaexhibiting normal growth and morphologies. Characterization of the dsRNAs 1 and 2 revealed that they are genomic components of a novel botybirnavirus, tentatively named Didymella theifolia botybirnavirus 1 (DtBRV1), and encapsidated in isometric virions with a size of ∼39.8 nm in diameter. It is worth noting that dsRNA3 shares no detectable identity with those sequences deposited in NCBI database, while a high identity (36.58% and 40.93%) with the left regions of dsRNAs 1 and 2, but is not encapsidated in DtBRV1 particles, suggesting it is a unique dsRNA unit that is not a DtBRV1 component or a satellite and its taxonomic classification remains unclear. SDS-polyacrylamide gel electrophoresis in combination with peptide mass fingerprint analysis revealed that DtBRV1 capsid protein consisting of polypeptides encoded by the left regions of both genomic components. DtBRV1 is efficiently vertically transmitted through conidia while difficult in horizontal transmission from strain CJP4-1 to other strains. DtBRV1 has no effects on fungal growth and virulence as accessed with the transfectants of virulent strain JYC1-6 ofD. theifoliainfected by DtBRV1. DtBRV1 with specific molecular traits contributes useful information for a better understanding of the mycoviral community.ImportanceTea plants represent an ancient and unique plant species community cultured in China, while the mycoviruses related to the phytopathogenetic fungi infecting tea remain limited. Here, we characterized a novel botybirnavirus (tentatively named Didymella theifolia botybirnavirus1 (DtBRV1), and a specific dsRNA infectingDidymella theifoliaresponsible for a noticeable disease of tea plants. DtBRV1 contains two dsRNAs (1 and 2) encapsidated in isometric virions in size of ∼39.8 nm, while dsRNA3 is not encapsidated in the viral particles although it has a high identity with the mycoviral genomic components. Additionally, DtBRV1 coat proteins are composed of fused proteins encoded by both dsRNA-coding open reading frames most likely after cleave and fuse processing progress, which is striking unlike most mycoviruses. With some specific molecular traits, DtBRV1 and the related specific dsRNA unit expand our understanding of virus diversity, taxonomy, and evolution.
Continence problems and mental health in adolescents from a UK cohort
Authors: Gordon Katie , Warne Naomi , Heron Jon , Gontard Alexander von , Joinson Carol 
Published: December 2022

AbstractBackgroundAdolescents with continence problems experience a unique range of threats to their psychological wellbeing including perceived stigma, social isolation, and poor self-image. Despite this, the long-term mental health sequelae of adolescent continence problems are unknown.MethodsWe used data from the Avon Longitudinal Study of Parents and Children (n=7,332: 3,639 males, 3,693 females) to examine prospective relationships between self-reported incontinence/lower urinary tract symptoms (LUTS) at 14 years (daytime wetting, bedwetting, soiling, urgency, frequent urination, low voided volume, voiding postponement, and nocturia) and common mental health problems at 18 years (any common mental disorder, depression, anxiety, self-harm, and disordered eating). We estimated multivariable regression models adjusted for sex, socioeconomic position, developmental level, IQ, stressful life events, maternal psychopathology, body mass index, and earlier emotional/behavioural problems.FindingsDaytime wetting and voiding postponement showed the greatest number of associations with mental health problems. All incontinence subtypes/LUTS were associated with increased odds of generalised anxiety disorder symptoms [e.g., odds ratio for daytime wetting= 3.01, 95% confidence interval (1.78, 5.09), p<0.001] and/or higher anxiety scores. There was also evidence of associations with common mental disorder [e.g., voiding postponement: 1.88 (1.46, 2.41), p<0.001], depression [e.g., urgency: 1.94 (1.19, 3.14), p=0.008], depressive symptoms [e.g., daytime wetting: 1.70 (1.13, 2.56), p=0.011], self-harm thoughts [e.g., voiding postponement: 1.52 (1.16, 1.99), p=0.003], and disordered eating [e.g., nocturia 1.72 (1.27, 2.34), p=0.001].InterpretationIncontinence/LUTS at age 14 are associated with increased vulnerability to mental health problems in late adolescence. Treatment of incontinence/LUTS should be integrated with psychological support to mitigate long-term sequelae.
Effective tree-based classification for automated flow cytometry data analysis on samples with suspected haematological malignancy
Authors: Rothwell Alex , Carter Anthony , Green Peter , Jones Andrew R 
Published: December 2022

AbstractFlow cytometry is a commonly used diagnostic technique for haematological malignancies. The gold standard method for analysis of flow cytometry data is manual gating, which is time consuming and requires a highly skilled operator, generating a bottleneck in the workflow and potentially increasing time to diagnose malignancy. For nearly 20 years attempts have been made at replacing manual analysis with automated algorithms, however these are not deemed accurate enough for clinical practice. Clustering methods have been the focus of previous automated attempts, though supervised methods have been shown to be more accurate and require less manual intervention. Tree-based classification algorithms make decisions using an analogous process to manual gating. One hundred and fifty-two flow cytometry files were generated from peripheral blood samples of patients with suspected haematological malignancies. A trained operator labelled events in these files as one of nine cell types. CART, Random Forest and XGBoost were trained on the labelled dataset and the performance was evaluated against previously published clustering methods. Classification algorithms showed higher mean F1 scores than clustering methods. There was no significant difference between CART, Random Forest and XGBoost mean F1 scores, and all three algorithms showed mean prediction times per sample of less than 25 seconds. Tree-based methods struggled to differentiate B cell subtypes, which show similar phenotypic signatures and present an area for future improvement. This work demonstrates the effectiveness of tree-based classification algorithms for flow cytometry analysis. Overall, CART may offer a solution to automated flow cytometry analysis for the purpose of haematological malignancies due to showing high agreement with manual analysis, and short prediction and training times.
Selection for insecticide resistance can promotePlasmodium falciparuminfection inAnopheles
Authors: Adams Kelsey L. , Selland Emily K. , Willett Bailey C. , Carew John W. , Vidoudez Charles , Singh Naresh , Catteruccia Flaminia 
Published: December 2022

AbstractInsecticide resistance is under strong selective pressure inAnophelesmosquitoes due to widespread usage of insecticides in vector control strategies. Resistance mechanisms likely cause changes that profoundly affect mosquito physiology, yet it remains poorly understood how selective pressures imposed by insecticides may alter the ability of the mosquito to host and transmit aPlasmodiuminfection. From pyrethroid-resistant field-derivedAnopheles gambiae s.l. mosquitoes, we performed selection experiments to establish resistant (RES) and susceptible (SUS) colonies by either selection for, or loss of, insecticide resistance. We show increased prevalence, intensity, and oocyst growth rate ofPlasmodium falciparuminfection in RES females compared to SUS. The increase in infection intensity in RES females was not associated with the presence of thekdrL1014F mutation, and was not impacted by inhibition of Cytochrome P450s. The lipid transporter lipophorin (Lp), which was upregulated in RES compared to SUS, was at least partly implicated in the increased intensity ofP. falciparumbut not directly in the insecticide resistance phenotype. Interestingly, we observed that althoughP. falciparuminfections were not affected when RES females were exposed to permethrin, these females had decreased lipid abundance in the fat body following exposure, pointing to a possible role for lipid mobilization in response to damage caused by insecticide challenge. The finding that selection for insecticide resistance can increaseP. falciparuminfection intensities and growth rate reinforces the need to assess the overall impact on malaria transmission dynamics of selective pressures mosquitoes experience during repeated insecticide challenge.Significance StatementInsecticide resistance poses a severe threat for malaria control. Resistance to pyrethroid insecticides, the active component of most insecticide-treated nets, is now widespread in sub-Saharan Africa, reducing the efficacy of these crucial tools. Despite significant research characterizing insecticide resistance mechanisms, it remains unknown how these traits influencePlasmodium falciparuminfections in malaria-transmittingAnophelesmosquitoes. We established a pyrethroid-resistant and pyrethroid-susceptible population ofAnopheles gambiaederived from the same genetic background and performed experimental infections withP. falciparum. We found that the pyrethroid-resistant population was more supportive of malaria parasites compared to the susceptible population. This was not caused by well-known insecticide resistance mechanisms, but linked with a lipid transporter, lipophorin, which may play an indirect role in resistance.