bluuebunny/crossref_metadata_2025_split huggingface dataset:
Allometric studies on human- and pig-sized Delphinidae to understand resting metabolic rates with respiratory measurements
Authors: Suzuki Ippei , Niizuma Yasuaki , Inamori Daiki , Watanabe Yurie , Sato Katsufumi , Aoki Kagari 
Published: January 2025

AbstractExponential relationships between basal metabolic rate (BMR) and body mass are known in both terrestrial and marine mammals, with elevated BMR in the latter. However, it remains unclear whether the exponential relationship in marine mammals is different from that in terrestrial mammals. Metabolic rates of animals while resting at the water surface (resting metabolic rates: RMRs) were measured by breath-by-breath respirometry in two species of Delphinidae from temperate regions to elucidate the relationship between RMR and body mass in pantropical spotted dolphins (Stenella attenuate) and Risso’s dolphins (Grampus griseus) with body masses ranging from 71 to 386 kg. The RMRs of rough-toothed dolphins (83–123 kg), common bottlenose dolphins (143–220 kg), and killer whales (3,364–5,318 kg) were obtained from the literature for allometric analyses. Measured RMRs were 344 ± 39 and 1398 ± 160 ml O2min-1, respectively, which were 1.2–2.1 times higher than those predicted for similar-sized terrestrial mammals. A linear mixed-effects model showed the allometric mass exponent of 0.65 (95% CI: 0.54–0.76), which was closer to the 2/3-power of body mass than that of the widely observed 3/4-power commonly reported across a broad range of taxa. The new scaling relationship observed in the Delphinidae indicates that larger dolphins require less energy in aquatic environments, which is consistent with the theory of heat loss associated with a narrower surface area relative to larger volumes. This study suggested a different scaling relationship between aquatic and terrestrial mammals.
Internal/External Bacterial Sources of Subgingival Plaque Reconstitution
Authors: Gibb Andrew , Bhagirath Anjali , Jain Lavanya , Gibson Monica , Williamson Deanna , Altabtbaei Khaled 
Published: January 2025

AbstractObjectivesThe objectives were to quantify the contributions of internal (self) and external (familial) sources to the recolonization of the bacterial content of the subgingival plaque following professional prophylaxis and assess the effect of close-contact activities on modifying this contribution.Materials and MethodsFamilies, each consisting of at least one preschool-aged child and at least one sibling, were recruited for this interventional cohort pilot study. Microbial samples were collected from various oral sites, including saliva, buccal mucosa, tongue, supragingival plaque, and subgingival plaque in all family members. Following the child’s oral prophylaxis, subgingival plaque samples were collected one week later. DNA from these samples was extracted and sequenced using the 16S rRNA gene and estimation of the sources were quantified using Bayesian source tracking models. Additional analyses using generalized linear mixed models, Phylofactorization, and Spearman correlations. Statistical significance was set at p<0.05.ResultsChild’s own subgingival plaque was the primary source of recolonization, contributing 63.7% to the microbial community one-week post-prophylaxis. Siblings contributed approximately 8%, a contribution significantly higher than that from parents, who contributed around 3% each (p<0.05). The analysis revealed a statistically significant positive correlation between the number of siblings and their bacterial contribution to the child’s subgingival plaque. Several close contact activities between parents and children were statistically associated with higher contribution (p<0.05, Spearman correlation). Additionally, 110 bacteria were statistically significantly different in their internal contribution compared to external, after accounting for household association, sample type, and family members (p<0.05, Phylofactor)ConclusionThe findings challenge the traditional focus on parent-child transmission of oral microbes, highlighting the importance of studying families as a whole.
Enterovirus D68 2A protease causes nuclear pore complex dysfunction and motor neuron toxicity
Authors: Zinn Katrina M. , McLaren Mathew W. , Imai Michael T. , Jayaram Malavika M. , Rothstein Jeffrey D. , Elrick Matthew J. 
Published: January 2025

ABSTRACTThe picornavirus Enterovirus D68 (EV-D68) is an important pathogen associated with acute flaccid myelitis (AFM). The pathogenesis of AFM involves infection of spinal motor neurons and motor neuron death, however the mechanisms linking EV-D68 infection to selective neurotoxicity are not well understood. Dysfunction of the nuclear pore complex (NPC) has been implicated in motor neuron injury in neurodegenerative diseases such as amyotrophic lateral sclerosis, and the NPC is also modified by picornavirus proteases during the course of infection. We therefore sought to determine the impact of EV-D68 proteases on NPC structure and function and their role in motor neuron toxicity. We demonstrate widespread disruption of NPC composition by EV-D68 2A and 3C proteases via the direct cleavage of a relatively small number of nucleoporins, notably Nup98 and POM121 by 2Apro. Using reporter systems, we demonstrate that 2Aproinhibits nuclear import and export of protein cargoes and also disrupts the permeability barrier of the NPC, while having no apparent effect on RNA export. We further show that 2Aprois toxic to induced pluripotent stem cell derived motor neurons by demonstrating a rescue of toxicity with 2Aproinhibitor telaprevir at concentrations that are insufficient to inhibit viral replication. This study expands our understanding of EV-D68 neuropathogenesis and provides a rationale for targeting the NPC or 2Aprotherapeutically in AFM.
A systematic review and ALE meta-analysis of cognitive control, motivation and effort-based decision-making in schizophrenia and mood disorders: Implications for multidimensional apathy
Authors: Lafond-Brina Giulia , Dormegny-Jeanjean Ludovic C. , Bonnefond Anne 
Published: January 2025

AbstractBackgroundApathy is present in about 50% of patients suffering from schizophrenia (SZ) and mood disorders (MD). Even though these two disorders are different, in psychiatry, apathy refers typically to the same unidimensional clinical entity, sharing the same pathophysiological processes and symptoms regardless of the underlying diagnosis. Neurology proposes another perspective: three forms of apathy —emotional, executive, and initiative— are related to a disturbance in motivational processing, cognitive control, and effort-based decision-making, respectively. We explored whether this latter model can be applied in psychiatry by identifying differences between SZ and MD through a PRISMA meta-analysis of imaging studies on motivational, cognitive control, and effort-based decision-making networks.MethodsWe searched the Sleuth BrainMap database for studies on SZ, MD, and/or healthy controls using tasks that explore motivation, cognitive control, and effort-based decision-making. Twenty-eight functional MRI studies were identified and included for a coordinate-based activation likelihood estimation analysis.ResultsIn SZ, hypoactivity in the motivational structures, a specific hyperactivity in the right cerebellar vermis that has previously been linked to emotional blunting and apathy, and a lack of activation during effort-based decision-making that could imply an impaired reward processing, suggest a dominant form of emotional apathy. In MD, hypoactivity in both cognitive control and motivational structures, which has previously been linked to the co-occurrence of executive difficulty and amotivation, suggests a dominant mix of emotional/executive apathy.ConclusionsDespite a small number of studies, our results could help target new individualized treatment strategies in precision psychiatry based on a multidimensional approach to apathy.Graphical abstractThe results of this meta-analysis highlight different activation profiles in SZ and in MD during motivational, cognitive control, and effort-based decision-making tasks, suggesting a dominant form of emotional apathy in SZ and a dominant coexistence of emotional and executive apathy in MD.
XDH-1 inactivation causes xanthine stone formation inC. eleganswhich is inhibited by SULP-4-mediated anion exchange in the excretory cell
Authors: Snoozy Jennifer , Bhattacharya Sushila , Fettig Robin R. , Asma Ashley Van , Brede Chloe , Warnhoff Kurt 
Published: January 2025

AbstractXanthine dehydrogenase (XDH-1) is a molybdenum cofactor (Moco) requiring enzyme that catabolizes hypoxanthine into xanthine and xanthine into uric acid, the final steps in purine catabolism. Human patients with mutations inxdh-1develop xanthinuria which can lead to xanthine stones in the kidney, recurrent urinary tract infections, and renal failure. Currently there are no therapies for treating human XDH-1 deficiency. Thus, understanding mechanisms that maintain purine homeostasis is an important goal of human health. Here, we used the nematodeC. elegansto model human XDH-1 deficiency using 2 clinically relevant paradigms, Moco deficiency or loss-of-function mutations inxdh-1.Both Moco deficiency andxdh-1mutations caused the formation of autofluorescent xanthine stones inC. elegans. Surprisingly, only 2% ofxdh-1null mutantC. elegansdeveloped a xanthine stone, suggesting additional pathways may regulate this process. To uncover such pathways, we performed a forward genetic screen for mutations that enhance the penetrance of xanthine stone formation inxdh-1null mutantC. elegans. We isolated multiple loss-of-function mutations in the genesulp-4which encodes a transmembrane transport protein homologous to human SLC26 anion exchange proteins. We demonstrated that SULP-4 acts cell- nonautonomously in the excretory cell to limit xanthine stone accumulation. Interestingly,sulp-4mutant phenotypes were suppressed by mutations in genes that encode for cystathionase (cth-2)or cysteine dioxygenase (cdo-1), members of the sulfur amino acid metabolism pathway required for production of the osmolyte taurine. Furthermore,cdo-1mRNA accumulated insulp-4mutant animals, mirroringcdo-1activation observed during hyperosmotic stress inC. elegansand mammals. We propose that loss of SULP-4-mediated anion exchange causes osmotic stress andcdo-1activation, a maladaptive response that promotes xanthine stone accumulation. Supporting the model that the osmotic stress response impacts xanthine stone accumulation, a mutation inosm-8that constitutively activates the osmotic stress response, also promoted xanthine stone accumulation in anxdh-1mutant background. Thus, our work establishes aC. elegansmodel for human XDH-1 deficiency and identifiessulp-4and the osmotic stress response governed bycdo-1as critical players in controlling xanthine stone accumulation.
Genome-wide exploration of the transcriptional regulatory landscape in the early-diverging fungusR. microsporusreveals pervasive DNA methyl adenine regulatory network
Authors: Lax Carlos , Baumgart Leo A. , Tahiri Ghizlane , Nicolás-Muñoz Natalia , Zhang Yu , Blaby Ian K. , O’Malley Ronan C , Ng Vivian , Navarro Eusebio , Grigoriev Igor V , Nicolás Francisco E. , Garre Victoriano 
Published: January 2025

AbstractGenetic regulation mechanisms rely on complex transcriptional networks that are often difficult to decipher. The study of transcription factor (TF) binding sites and their targets has traditionally faced scalability challenges, hindering comprehensive cistrome analyses. However, the development of the DNA affinity purification and sequencing (DAP-seq) technique has allowed unprecedented large-scale studies at genome-wide level of TF binding with high reproducibility. In this study, we apply this technique to the human opportunistic pathogenR. microsporus, a mucoralean fungus belonging to the understudied group of early-diverging fungi (EDF). We characterize genome-wide binding sites of 58 TFs encoded by genes regulated through adenine methylation and representing major TF families, representing the most extensive DAP-seq study in filamentous fungi. This analysis reveals their binding profiles and recognized sequences, expanding and diversifying the catalog of known fungal motifs. By integrating this data with DNA 6-methyladenine profiling, we uncover the extensive direct and indirect impact of this epigenetic modification on the regulation of gene expression. Furthermore, the generated data facilitates the identification and functional characterization of TFs involved in biologically relevant processes, such as zinc metabolism and light response, serving as a proof of concept for the utility of the DAP-seq data. These findings not only enhance our understanding of regulatory mechanisms inR. microsporusbut also provide broader insights into gene regulation across the fungal kingdom.
Blue Light Sonata: Dynamic variation of red:blue ratio during the photoperiod differentially affects leaf photosynthesis, pigments, and growth in lettuce
Authors: Van Brenk Jordan B , Vanderwolk Kimberly R , Seo Sumin , Choi Young Hae , Marcelis Leo FM , Verdonk Julian C 
Published: January 2025

AbstractVertical farming (VF) has unparalleled capacity to highly customize plant growth environments. In VF, red and blue LED lights are predominantly used as the two main wavelengths for photosynthesis. For many plants, red light increases biomass, and blue light can increase nutritional content. Because red light is more cost-and energy-efficient to produce than blue light, refined growth recipes are imperative to mutualistically improve efficiency with crop yield and quality. This study’s aim was to balance lighting energy-use with growth and nutritional quality by using “dynamic lighting” recipes to reduce durations of high-intensity blue light. Lettuce (Lactuca sativaL.) was grown for 21 days at 220 μmol m-2s-1, receiving one of five R:B ratios (R:B100:0, R:B95:5, R:B89:11, R:B50:50, and R:B0:100) for either the whole 18-hour photoperiod (Whole Day), the first six hours of the photoperiod (Morning), or the last six hours of the photoperiod (Evening). Morning and Evening treatments received low blue (R:B89:11) for the remaining 12 hours of the day. The Morning and Evening high blue treatments had greater fresh weight and leaf area than their respective Whole Day treatments, attributed to reduced instantaneous leaf photosynthesis under high blue. High blue reduced photosynthesis during only the six hours of Morning and Evening treatments, compared to the full impact of static high blue for 18-hour Whole Day treatments. Intriguingly, with only six hours of R:B0:100, Morning and Evening treatments had the same high anthocyanin content as lettuce grown for 18 hours under R:B0:100. Therefore, daily blue light fraction can be reduced by using dynamic treatments to more efficiently promote growth and nutritional quality.
Mouse Cortical Cellular Diversification Through Lineage Progression of Radial Glia
Authors: Yang Lin , Gao Yanjing , Wang Ziwu , Li Zhenmeiyu , Liu Guoping , Xu Zhejun , Zhang Zhuangzhi , You Yan , Yang Zhengang , Li Xiaosu 
Published: January 2025

AbstractCortical radial glia (RGs) sequentially generate pyramidal neurons (PyNs) and glia. In this study, we investigated the molecular logic underlying cortical cellular diversification using time-series scRNA-seq and snATAC-seq on FlashTag- or hGFAP-GFP-labeled mouse cortical progenitors across embryonic and postnatal stages. Our data revealed that RGs transition from early to late over time, sequentially producing intermediate neuronal progenitors (INPs) and intermediate glial progenitors (IGPs). While INPs expand exclusively to generate PyNs, IGPs progress from young to old, sequentially producing cortical astrocytes, oligodendrocytes, and olfactory bulb interneurons. We constructed comprehensive molecular maps that reflect cell lineage progression. Our study reveals that chromatin accessibility drives cellular diversification by restricting broadly expressed transcription factors to specific stages and cell types. For instance,Lhx2, which is constantly expressed in RGs across all stages, exhibits reduced DNA-binding activity as development progresses.Lhx2maintains neurogenic competence by establishing an active epigenetic state at neurogenic genes. As RGs transition to later stages, the chromatin regions bound by Lhx2 become inaccessible, leading to the loss of neurogenic competence and the acquisition of gliogenic competence.
A comprehensive molecular atlas of the cell types in the mouse liver
Authors: Pietilä Riikka , Genové Guillem , Mocci Giuseppe , Miao Yuyang , Liu Jianping , Leptidis Stefanos , Del Gaudio Francesca , Uhrbom Martin , Vázquez-Liébanas Elisa , Gustafsson Sonja , Buyandelger Byambajav , Raschperger Elisabeth , Björkegren Johan LM. , Hansson Emil M. , Gaengel Konstantin , Mäe Maarja Andaloussi , Jeansson Marie , Vanlandewijck Michael , He Liqun , Strell Carina , Peng Xiao-Rong , Lendahl Urban , Betsholtz Christer , Muhl Lars 
Published: January 2025

AbstractThe liver plays a crucial role in essential physiological processes, and its impaired function due to liver fibrosis from various causes is an increasingly significant health issue. The liver’s functionality relies on the precise arrangement of its cellular structures, yet the molecular architecture of these units remains only partially understood. We created a comprehensive molecular atlas detailing all the major cell types present in the adult mouse liver through deep single-cell RNA sequencing. Our analysis offers new insights into hepatic endothelial and mesenchymal cells, specifically highlighting the differences between the cells of the periportal microvasculature, the sinusoids, and the portal vein, the latter exhibiting a mixed arterio-venous phenotype. We identified distinct subpopulations of hepatic stellate cells, fibroblasts, and vascular mural cells located in different anatomical regions. Comparisons with transcriptomic data from disease models indicate that a previously unrecognized capsular population of hepatic stellate cells expands in response to fibrotic disease. Our findings reveal that various fibroblast subpopulations respond differently to pathological insults. This data resource will be invaluable for advancing therapeutic interventions targeting hepatic diseases.
Comprehensive Mapping of Human dsRNAome Reveals Conservation, Neuronal Enrichment, and Intermolecular Interactions
Authors: Andrews Ryan J. , Bass Brenda L. 
Published: January 2025

SUMMARYThe human transcriptome contains millions of A-to-I editing sites arising from an unclear number of poorly characterized dsRNAs. Editing sites are often used to infer presence of dsRNA, but this method is limited by transcription levels, read depth, ADAR expression and cannot identify unedited dsRNA. To address these limitations, we developed dsRNAscan. Applying dsRNAscan to the human genome predicted 5 million dsRNAs. Genomic distribution of dsRNAs encompassing repetitive elements was widespread, but non-repetitive dsRNAs were sparse and enriched at chromosomal tips. dsRNAscan predicted hundreds of long, highly paired dsRNAs suspected to be immunogenic, but only one was in a 3′UTR, and thus likely to challenge cytoplasmic immune sensors. We observed several thousand editing enriched regions suspected to arise from intermolecular structures, and dozens of neuronally enriched dsRNAs conserved across vertebrates. This study offers the first comprehensive set of dsRNA annotations for the human genome, available as a resource athttps://dsrna.chpc.utah.edu/.
Genome assembly ofBougainvilliacf.muscus(Cnidaria: Hydrozoa)
Authors: Macias-Muñoz Aide , Varney Rebecca , Katcher Eva , Everhart Maia , Oakley Todd H. 
Published: January 2025

AbstractBackgroundAs one of just a handful of non-Bilaterian animal phyla, Cnidaria are key to understanding genome evolution across Metazoa. Despite their importance and diversity, the genomes of most species in the phylum are unsequenced, due in large part to difficulties cultivating them in a laboratory. Here, we present a genome sequence ofBougainvilliacf.mucus, a hydrozoan with four marginal bulbs each containing seven simple eyes (ocelli). This species appeared in our tanks from contamination. While we lacked sufficient samples for transcriptomic or functional studies, we were able to expand our knowledge of how the genome of this species compares to the few, better studied members of hydrozoans by investigating synteny to other cnidarians, repetitive element content, and phylogenetics and synteny of vision-related genes in this eyed species compared to eyeless relatives.ResultsThe genome sequence consists of 350 contigs with an N50 of 10 Mb, a total genome length of 375.328 Mb, a BUSCO score of 90.1%, and predicted protein coding genes totaling 46,431. We found a high degree of macrosynteny conservation withHydra vulgarisandHydractinia symbiolongicarpus. Repetitive elements make up 62% of thisBougainvilliagenome. For vision-related genes, we identified 20 cnidarian opsins (cnidops) inBougainvilliaand found instances of gene duplication and loss in families associated with bilaterian eye development, phototransduction, and visual cycling.ConclusionsThis high-quality, contiguous genome in an eyed Hydrozoan will be a valuable resource for additional comparative genomic studies.
Decoding Demosponge Diversity: Bayesian Analysis of Biodiversity, Extinction Events and Environmental Influences throughout the Phanerozoic
Authors: Schuster Astrid , Canfield Donald E. 
Published: January 2025

AbstractSponges (phylum Porifera) have been essential to marine ecosystems for over 600 million years, contributing to nutrient cycling, reef building, and ecological stability. Despite their evolutionary importance, the drivers of their diversity dynamics remain poorly understood. This study investigates the diversification patterns of Demospongiae, the largest class of sponges with a well-documented fossil record throughout the Phanerozoic Eon (541–0 Ma). Using fossil occurrence data and a Bayesian framework, we modeled origination and extinction rates to understand their evolutionary history.Our findings reveal key extinction events, including three previously unrecognized events in the Cambrian, Late Silurian, and Late Jurassic, alongside known events such as the Permian-Triassic and Triassic-Jurassic extinctions. Notably, there was no statistical evidence for mass extinction during the Late Ordovician or Late Devonian. Additionally, Demosponges underwent a significant decline prior to the Cretaceous-Paleogene extinction.To explore abiotic influences, we applied the Multivariate Birth-Death (MBD) model across all extinction events. This analysis identified correlations between major speciation and extinction events and key variables, including temperature, continental fragmentation, oxygen levels, and sea level, as well as geochemical proxies such as sulfur and strontium, which may reflect underlying drivers like anoxia, weathering, or tectonic activity. Temperature and oxygen levels, in particular, correlated with speciation and extinction during the Permian-Triassic extinction.These findings underscore the role of environmental fluctuations in shaping demosponge diversity and highlight the complex interplay between changes in abiotic factors and sponge evolution. Our work provides critical insights into the factors driving sponge biodiversity and offers perspectives on how modern sponges might respond to ongoing climate change.Significance StatementSponges are ancient and ecologically pivotal marine organisms that have persisted through Earth’s major environmental upheavals. Despite their resilience, the mechanisms driving their evolutionary responses to past climate shifts remain unclear. By leveraging the fossil record of Demospongiae, this study identifies previously unrecognized extinction events and elucidates how abiotic factors, including temperature and oxygen levels, shaped their diversity during these crises. These findings enhance our understanding of sponge evolutionary dynamics and resilience, offering critical insights into the vulnerability of marine ecosystems under current and future climate change scenarios.