bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chikungunya virus infection disrupts lymph node lymphatic endothelial cell composition and function via MARCO
Authors: Lucas Cormac J. , Sheridan Ryan M. , Reynoso Glennys V. , Davenport Bennett J. , McCarthy Mary K , Martin Aspen , Hesselberth Jay R. , Hickman Heather D. , Tamburini Beth A. J. , Morrison Thomas E. 
Published: October 2023

ABSTRACTInfection with chikungunya virus (CHIKV) causes disruption of draining lymph node (dLN) organization, including paracortical relocalization of B cells, loss of the B cell-T cell border, and lymphocyte depletion that is associated with infiltration of the LN with inflammatory myeloid cells. Here, we find that during the first 24 h of infection, CHIKV RNA accumulates in MARCO-expressing lymphatic endothelial cells (LECs) in both the floor and medullary LN sinuses. The accumulation of viral RNA in the LN was associated with a switch to an antiviral and inflammatory gene expression program across LN stromal cells, and this inflammatory response, including recruitment of myeloid cells to the LN, was accelerated by CHIKV-MARCO interactions. As CHIKV infection progressed, both floor and medullary LECs diminished in number, suggesting further functional impairment of the LN by infection. Consistent with this idea, we find that antigen acquisition by LECs, a key function of LN LECs during infection and immunization, was reduced during pathogenic CHIKV infection.
Diversity of visual inputs to Kenyon cells of theDrosophilamushroom body
Authors: Ganguly Ishani , Heckman Emily L. , Litwin-Kumar Ashok , Josephine Clowney E. , Behnia Rudy 
Published: October 2023

AbstractThe arthropod mushroom body is well-studied as an expansion layer that represents olfactory stimuli and links them to contingent events. However, 8% of mushroom body Kenyon cells inDrosophila melanogasterreceive predominantly visual input, and their tuning and function are poorly understood. Here, we use the FlyWire adult whole-brain connectome to identify inputs to visual Kenyon cells. The types of visual neurons we identify are similar across hemispheres and connectomes with certain inputs highly overrepresented. Many visual projection neurons presynaptic to Kenyon cells receive input from large swathes of visual space, while local visual interneurons, providing smaller fractions of input, receive more spatially restricted signals that may be tuned to specific features of the visual scene. Like olfactory Kenyon cells, visual Kenyon cells receive sparse inputs from different combinations of visual channels, including inputs from multiple optic lobe neuropils. The sets of inputs to individual visual Kenyon cells are consistent with random sampling of available inputs. These connectivity patterns suggest that visual coding in the mushroom body, like olfactory coding, is sparse, distributed, and combinatorial. However, the expansion coding properties appear different, with a specific repertoire of visual inputs projecting onto a relatively small number of visual Kenyon cells.
Akaluc bioluminescence offers superior sensitivity to trackin vivodynamics of SARS-CoV-2 infection
Authors: Tamura Tomokazu , Ito Hayato , Torii Shiho , Wang Lei , Suzuki Rigel , Tusjino Shuhei , Kamiyama Akifumi , Oda Yoshitaka , Morioka Yuhei , Suzuki Saori , Shirakawa Kotaro , Sato Kei , Yoshimatsu Kumiko , Matsuura Yoshiharu , Iwano Satoshi , Tanaka Shinya , Fukuhara Takasuke 
Published: October 2023

SummaryMonitoringin vivoviral dynamics can improve our understanding of pathogenicity and tissue tropism. For positive-sense, single-stranded RNA viruses, several studies have attempted to monitor viral kineticsin vivousing reporter genomes. The application of such recombinant viruses can be limited by challenges in accommodating bioluminescent reporter genes in the viral genome. Conventional luminescence also exhibits relatively low tissue permeability and thus less sensitivity for visualizationin vivo. Here we show that unlike NanoLuc bioluminescence, the improved method, termed AkaBLI, allows visualization of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in Syrian hamsters. By successfully incorporating a codon-optimized Akaluc luciferase gene into the SARS-CoV-2 genome, we visualizedin vivoinfection, including the tissue-specific differences associated with particular variants. Additionally, we could evaluate the efficacy of neutralizing antibodies and mRNA vaccination by monitoring changes in Akaluc signals. Overall, AkaBLI is an effective technology for monitoring viral dynamics in live animals.
THI1Gene Evolutionary Trends: A Comprehensive Plant-Focused Assessment via Data Mining and Large-Scale Analysis
Authors: Dias Henrique Moura , de Toledo Naiara Almeida , Mural Ravi V. , Schnable James C. , Van Sluys Marie-Anne 
Published: October 2023

ABSTRACTMolecular evolution analysis typically involves identifying selection pressure and reconstructing evolutionary trends. This process usually necessitates access to specific data related to a target gene or gene family within a particular group of organisms. While recent advancements in high-throughput sequencing techniques have resulted in the rapid accumulation of extensive genomics and transcriptomics data and the creation of new databases in public repositories, extracting valuable insights from such vast datasets remains a significant challenge for researchers. Here, we elucidated the evolutionary history ofTHI1, a gene responsible for encoding thiamine thiazole synthase. The thiazole ring is a precursor for vitamin B1 and crucial cofactor in primary metabolic pathways. We conducted a comprehensive search forTHI1information within public repositories with careful curation to achieve this. Our searches reveal an evolutionary trend of 702THI1homologs of Archaea and Eukarya, with a detailed focus on plants. The green lineage of these organisms preserved the THI4 protein domain throughout its diversification by incorporating the N-terminus and targeting chloroplasts. Furthermore, evolutionary pressures and lifestyle appear to be associated with retention of TPP-riboswitch sites and consequent dual post-transcriptional regulation of thede novobiosynthesis pathway in basal groups. Multicopy retention ofTHI1is not a typical plant pattern, even successive rounds of genome duplications. Additionally, we identified the diversification of cis-regulatory sites in plants with the conservation of biological processes associated with the initial stages of seed development and preservation of the transcriptional pattern during the diurnal cycle. Our data mining of 484 transcriptome datasets supports this finding and brings a new look at public repositories and evolutionary trends toTHI1.
Assessing the quality ofde novoparasite genomes assembled using only Oxford Nanopore Technologies MinION data
Authors: Herzog Kaylee S. , Wu Rachel , Hawdon John M. , Nejsum Peter , Fauver Joseph R. 
Published: October 2023

SummaryParasitic nematode infections represent a significant burden of disease in impoverished populations. Genomic studies of parasitic nematodes have revealed novel drug and vaccine targets and provided unprecedented insights into parasite biology. A key component of these studies is the availability of high-quality reference genomes (i.e., genomes that are contiguous, complete, and accurate) that capture the biological diversity contained within species. However, relatively few genomic resources exist for parasitic nematodes and few species are represented by more than a single reference genome. Streamlined laboratory and computational workflows to generate high-quality reference genomes from individual specimens using a single data source have the potential to increase the availability of genomic data from parasitic nematodes. The Oxford Nanopore Technologies (ONT) MinION is an accessible sequencing platform capable of generating ultra-long read data ideal for assembling genomes. However, lower read-level accuracy of ONT data has previously required assemblies to be error-corrected with more accurate short-read data. In this study, we assessed the quality ofde novogenome assemblies for three species of parasitic nematodes (Brugia malayi, Trichuris trichiura,andAncylostoma caninum) generated using only ONT MinION data. Assemblies were benchmarked against current reference genomes and against additional assemblies that were supplemented with short-read Illumina data through polishing or hybrid assembly approaches. For each species, assemblies generated using only MinION data had similar or superior measures of contiguity, completeness, and gene content. In terms of gene composition, depending on the species, between 88.9–97.6% of complete coding sequences predicted in MinION data only assemblies were identical to those predicted in assemblies polished with Illumina data. Polishing MinION data only assemblies with Illumina data therefore improved gene-level accuracy to a degree. Furthermore, modified DNA extraction and library preparation protocols produced sufficient genomic DNA fromB. malayiandT. trichiurato generatede novoassemblies from individual specimens.Data Availability StatementQuality-controlled MinION and Illumina data for each species are deposited in the NCBI Sequence Read Archive (SRA) under the BioProject accession ID PRJNA1074771 under BioSample accession nos. SAMN39888962 (Brugia malayi), SAMN39888963 (Trichuris trichiura) and SAMN39888964 (Ancylostoma caninum). Final assemblies for each species are publicly available on GenBank.
Staphylococcus epidermidisenablesCutibacterium acnesto form biofilms under aerobic conditions
Authors: Kaplan Jeffrey B. 
Published: October 2023

ABSTRACTStaphylococcus epidermidisandCutibacterium acnesare among the most abundant members of the human skin microbiome. Both species are associated with skin health and disease. Although skin microbes typically grow in surface-associated biofilms, few studies on the interaction betweenS. epidermidisandC. acnesin biofilms have been reported. In the present study we measured the ability ofS. epidermidisandC. acnes, either individually or jointly, to form biofilms in glass culture tubes. SinceS. epidermidisis a facultative anaerobe andC. acnesis an aerotolerant anaerobe, tubes were incubated both aerobically and anaerobically to assess the role of atmosphere in biofilm forma4on. When cultured individually, we found thatS. epidermidisformed biofilms under both aerobic and anaerobic conditions, whereasC. acnesformed biofilms only under aerobic conditions. When co-cultured, the presence ofC. acneshad no effect onS. epidermidisbiofilm formation under either aerobic or anaerobic conditions. However, the presence ofS. epidermidissignificantly enhanced the growth ofC. acnesbiofilms under anaerobic conditions and enabledC. acnesto form biofilms under aerobic condi2ons. This finding may be clinically relevant to the interaction betweenS. epidermidisandC. acneson human skin.
Liver size is predetermined in the neonate by adding lobules at the periphery
Authors: Azizoglu D. Berfin , Perez Karina , Zheng Sherry Li , Rahman Shahadat , Rim Ellen Youngsoo , Anbarchian Teni , Fish Matt , Loh Kyle M. , Red-Horse Kristy , Nusse Roel 
Published: October 2023

AbstractOrgans vary in size between and within species to match organismal needs1,2. Decades-old theoretical work has proposed that scaling of organs and body parts relative to the body relies on the features of energy-transport systems, the vascular system in mammals3. Yet, experimental studies on whether or how vascularization helps determine organ size have lagged behind. The mammalian liver is a remarkable example, as liver size scales proportionally with high precision between individuals4. Here, we use quantitative clonal mapping, volumetric imaging, and genetic perturbations combined with novel molecular and genetic tools to identify the temporal and spatial constraints that establish mouse liver size. We find that adult liver size is predetermined during a neonatal period when new functional units, termed lobules, are added to the organ. New lobules are vascularized by prominent sprouting angiogenesis of the hepatic vein, restricted to the periphery of the organ. When Wnt signals are ablated in the single cell-layered mesothelium at the periphery, lobule growth fails, and the organ adopts a compromised size set point. Remarkably, within a week after birth and well before hepatocyte division stops, vein sprouting rapidly declines and lobule addition concludes, setting a limit on the final liver size. These findings posit that vascularization in the neonate constrains and helps determine adult liver size. Together, these results propose a novel, vasculature-centric experimental framework for studying organ size control and scaling in mammals.
Age, sex, and cell type-resolved hypothalamic gene expression across the pubertal transition in mice
Authors: Sokolowski Dustin J. , Hou Huayun , Yuki Kyoko E. , Roy Anna , Chan Cadia , Faykoo-Martinez Mariela , Hudson Matt , Uusküla-Reimand Liis , Goldenberg Anna , Palmert Mark R. , Wilson Michael D. 
Published: October 2023

AbstractAlthough the hypothalamus plays a critical role in the regulation of puberty, more research is needed to identify the gene regulatory networks that control pubertal timing. Here, we investigate the age-, sex- and cell-type-specific gene regulation in the hypothalamus across the pubertal transition. We used RNA-seq to profile hypothalamic gene expression in male and female mice at five time points spanning the onset of puberty (postnatal days (PD) 12, 22, 27, 32, and 37). By combining this data with hypothalamic scRNA-seq data of pre- and post-pubertal mice, we were able to assign gene expression changes to their cell types of origin. In our colony, pubertal onset occurs earlier in male mice allowing us to focus on genes whose expression is dynamic across ages and offset between sexes and to explore bases of sex effects. Our age-by- sex pattern of expression enriched for biological pathways involved hormone production, neuronal activation, and glial maturation. Additionally, we found a dramatic expansion of oligodendrocytes precursor cells into mature oligodendrocytes spanning the pre-pubertal (PD12) to peri-pubertal (PD27) timepoints, and that genes driving this expansion enrich for genes involved in pubertal regulation. Together, by incorporating multiple biological timepoints with male and female mice simultaneously, our work furthers the understanding of gene and cell-type changes that accompany the development of secondary sex characteristics in both sexes.
Live soil ameliorated the negative effects of biodegradable but not non-biodegradable microplastics on the growth of plant communities
Authors: Fu Yanmei , Oduor Ayub M. O. , Jiang Ming , Liu Yanjie 
Published: October 2023

AbstractPlastic pollution has become a global environmental problem. Alternative use of biodegradable plastics has been proposed to mitigate the pollution problem caused by the traditional non-biodegradable plastics but the relative impacts of both types of microplastics on plant community productivity and diversity remain unknown. Microplastics can affect growth of individual plants directly by altering plant physiological processes and indirectly by altering soil biota that in turn influence plant growth. However, it remains unknown whether soil biota can mediate impact of biodegradable and non-biodegradable microplastics on plant community productivity and diversity due to a lack of studies on the topic.Here, we performed a greenhouse experiment with six plant communities and five biodegradable and five non-biodegradable microplastics to test whether: 1) biodegradable microplastics have a less negative effect on plant community biomass production and diversity than non-biodegradable microplastics, and 2) soil microorganisms differentially mediate the effects of non-biodegradable and biodegradable microplastics on plant community biomass production and diversity. We employed a fully crossed factorial design to grow the six plant communities in the presencevs. absence of the 10 microplastics individually and in live soilvs. sterilized soil.Results show that live soil ameliorated the negative effects of biodegradable microplastics on shoot biomass of the plant communities, but microplastics suppressed plant community diversity more strongly in live soil than in sterilized soil regardless of microplastics types under averaged across all treatments. Furthermore, the specific microplastics polymers were the main drivers of these results.Synthesis and applications:Overall, our findings indicate that even biodegradable microplastics, e.g. PBS, which are considered environmentally friendly, still pose significant ecological risks to the structure and productivity of plant communities with potential implications for functioning of terrestrial ecosystems. Future studies may identify the specific taxa of soil microorganisms that may have degraded the microplastics that we studied, their rates of biodegradation, and the effects thereof on plant community structure and productivity under more natural field conditions in contrasting climatic conditions.
Wellbeing After Stroke (WAterS): feasibility testing of a co-developed Acceptance and Commitment Therapy (ACT) intervention, to support psychological adjustment after stroke
Authors: Patchwood Emma , Foote Hannah , Vail Andy , Cotterill Sarah , Hill Geoff ,   members of the WAterS PCPI Group, Bowen Audrey 
Published: October 2023

AbstractObjectiveFeasibility test a co-developed intervention based on Acceptance and Commitment Therapy (ACT) to support psychological adjustment post-stroke, delivered by a workforce with community in-reach.DesignObservational feasibility study utilising Patient, Carer, Public Involvement (PCPI).SettingOnline. UK.ParticipantsStroke survivors with self-reported psychological distress 4+ months post-strokeInterventionsThe co-developed Wellbeing After Stroke (WAterS) intervention includes: nine weekly, structured, online, group sessions for stroke survivors, delivered via a training programme to upskill staff without previous ACT experience, under Clinical Psychology supervision.Main measuresFeasibility of recruitment and retention; data quality from candidate measures; safety. Clinical and demographic information at baseline; Patient Reported Outcome Measures (PROMs) via online surveys (baseline, pre- and post-intervention, 3 and 6 months after intervention end) including Mood (HADS), Wellbeing (ONS4), Health-Related Quality of Life (EQ5D5L), Psychological Flexibility (AAQ-ABI) and Values-Based Living (VQ).ResultsWe trained eight staff and recruited 17 stroke survivors with mild-to-moderate cognitive and communication difficulties. 12/17 (71%) joined three intervention groups with 98% attendance and no related adverse events. PROMS data were well-completed. The HADS is a possible future primary outcome (self-reported depression lower on average by 1.3 points: 8.5 pre-group to 7.1 at 3 month follow up; 95% CI 0.4 to 3.2).ConclusionThe WAterS intervention warrants further research evaluation. Staff can be trained and upskilled to deliver. It appears safe and feasible to deliver online to groups, and study recruitment and data collection are feasible. Funding has been secured to further develop the intervention, considering implementation and health equality.
Serious mental health diagnoses in children on the Child Protection Register: a record linkage study
Authors: Ball William P , Anderson Caroline , Black Corri , Gordon Sharon , Lackenby Michael , Murchie Martin , Ostrovska Bārbala , O’Sullivan Katherine , Rowlands Helen , Díaz Magdalena Rzewuska , Butler Jessica E 
Published: October 2023

AbstractPurposeChildren with experience of maltreatment, abuse or neglect are known to have a higher prevalence of poor mental health. Child Protection Services identify children most at risk of harm and in need of intervention. Mental healthcare usage in this population is not well understood as registration data is not routinely linked to health records.MethodsWe undertook data linkage to describe the population on the register, their mental healthcare usage and to calculate age- and sex-specific incidence rates of mental health outcomes. We analysed records from the Aberdeen City Council Child Protection Register and for mental health prescribing and referrals to child and adolescent mental health services (CAMHS) for the NHS Grampian region between 1stJanuary 2012 and 31stDecember 2022.ResultsWe identified 1,498 individuals with a Child Protection Register registration, of which 70% were successfully matched to health records. 20% of registrations occurred before birth and the median age of registration was 3 years. 10.1% of children with a registration ever received a mental health prescription, 5.1% for treatment of attention deficit hyperactivity disorder and 1.7% for treatment of depression. 18.9% received a referral to specialist outpatient Child and Adolescent Mental Health Services. Age- and sex- standardised incidence rates for mental health prescribing and referrals are higher for children with a child protection registration compared to the general population.ConclusionChildren identified as being at significant risk of harm and involved with child protection services are at greater risk of seeking or receiving professional mental health support than their peers. Clinical services should investigate additional ways to support this population’s mental well-being as a priority. Efforts to reduce the exposure of children to potentially harmful environments at a societal level should also be pursued.
Investigation of BRCA1 exon 11 genetic variations in breast cancer among Libyan women
Authors: Elshwekh Halla , Alhudiri Inas , Abdul Jalil Hamza Musbah , Mohamed Abdenaser A. , Elkikli Ahmed , Jornaz Naji , Enattah Nabil 
Published: October 2023

AbstractIntroductionThe majority of hereditary breast and ovarian cancers are associated with mutations in two genes, breast cancer type 1 and 2 susceptibility genes (BRCA1 and BRCA2). Here, we describe for the first time analysis of BRCA1 exon 11 in 48 Libyan breast cancer patients with a family history of cancer.MethodsAll patients had a family history of cancer and were included in the study only if they have a family history of breast or ovarian cancer, male breast cancer, or triple negative tumors. PCR was performed using specific primer pairs spanning BRCA1 exon 11 followed by Sanger sequencing. Genetic analysis was done using Sequencher® 5.1.ResultsWe identified 12 genetic variants in BRCA1 exon 11. Three variants were novel (c.1019T>C, c.2363T>G, and c.3192T>C). c.2363T>G was predicted by SIFT as damaging. Six variants were of unknown significance (c.918T>C, c.1853G>C, c.1886G>A, c.2215A>G, c.2612C>T, c.3113A>C and c.3784T>C), and 3 were classified as benign in ClinVar database (c.918T>C, c.2082C>T and c.2311T>C).ConclusionsScanning of the entire BRCA1 is needed to identify any associated deleterious mutations. Although the clinical importance of unclassified variants is unknown, the association of certain variants with deleterious mutations and contralateral breast cancer warrants genetic testing and counseling in the Libyan population.