bluuebunny/crossref_metadata_2025_split huggingface dataset:
NANUQ+: A divide-and-conquer approach to network estimation
Authors: Allman Elizabeth S. , Baños Hector , Rhodes John A. , Wicke Kristina 
Published: November 2024

AbstractInference of a species network from genomic data remains a difficult problem, with recent progress mostly limited to the level-1 case. However, inference of theTree of Blobsof a network, showing only the network’s cut edges, can be performed for any network by TINNiK, suggesting a divide-and-conquer approach to network inference where the tree’s multifurcations are individually resolved to give more detailed structure. Here we develop a method, NANUQ+, to quickly perform such a level-1 resolution. Viewed as part of the NANUQ pipeline for fast level-1 inference, this gives tools for both understanding when the level-1 assumption is likely to be met and for exploring all highly-supported resolutions to cycles.
In a model of parasite-mediated exhaustion, stem-like CD8 T cells differentiate into an unconventional intermediate effector memory subset
Authors: Moretto Magali M. , Chen Keer , Cox Christina , Chen Jie , Khan Imtiaz A 
Published: November 2024

AbstractCD8 T cell exhaustion has been reported in mice susceptible toToxoplasma gondiiinfection. While the differentiation of CD8 exhausted subsets has been extensively reported, most of these studies have been conducted in chronic viral and cancer models. During chronicT. gondiiinfection, phenotypic and transcriptomic analyses of the polyclonal antigen-specific CD8 T cell response characterize four populations based on KLRG1 and CD62L expression. Pop1 (KLRG1+CD62Llo) bears the attributes of a terminal effector subset, and pop2 (KLRG1-CD62Llo) is similar to effector memory CD8 T cells. Akin to chronic viral infection and cancer systems, pop3 (KLRG1-CD62Lhi) exhibits the characteristics of stem-like progenitor CD8 T cells (high Tcf7, Slamf6, and Cxcr5 expression), whereas pop4 (KLRG1+CD62Lhi) closely resembles a transitory subset (elevated Tbx21, low Tcf1, and Tox expression). During chronic viral infection, the stem-like progenitor CD8 T cells transition into a terminally differentiated exhausted subset via an intermediate population. However, in our system, pop3 generates pop4, which does not convert into a conventional terminally differentiated exhausted subset but instead transitions into effector pop1. Notably, during the chronic phase of the infection, pop1 cannot retain its functionality, irrespective of its origin, which may hamper its ability to control reactivation. Our observations emphasize that the differentiation of exhausted CD8 T cells in non-viral infections, like chronic toxoplasmosis, follows a different pattern than established models and highlights the need to develop new immune strategies better tailored for a broad range of pathogens.
In-silico Targeting Phosphodiesterase 5 and In-vivo Evaluation of the Aphrodisiac Effect ofAzanza garckeanaFruit
Authors: InnocentMary Ifedibaluchukwu Ejiofor , Ifeoma Ezeanya Jennifer , Ifeoma Ibe Chioma , Cyril Ogbue Onyeka , Chisom Emodi Rita , Chinwendu Agueze Jennifer , Sylvanus Ani Chibuike 
Published: November 2024

AbstractSexual dysfunction is a persistent problem affecting men, with erectile dysfunction (ED) and premature ejaculation being the most common. The current treatment involving the use of PhPDE5 inhibitors, such as sildenafil, is faced with some serious side effects. In Nigeria, there are claims thatAzanza garckeanafruit has positive effects in male sexual dysfunction. This study aims to evaluate this claim of the aphrodisiac effects ofAzanza garckeana, using computational and animal models. The 3D structures of the protein target of interest (phosphodiesterase) and 21 phytocompounds already isolated from and identified in the fruit were obtained from the Protein Data Bank and PubChem, respectively. The protein targets and the phytocompounds were prepared for molecular docking simulation using the Autodock tool. The docking was performed using Autodock-vina on the Linux platform. Phytocompounds with high specificity for the protein targets were identified, and their solubility profile was obtained. The fruits were extracted with ethanol using a Soxhlet apparatus at 60°C and concentrated with a rotary evaporator at 40°C. Phytochemical tests were conducted on the extract, and acute toxicity was evaluated using OECD 423 guidelines. The aphrodisiac effect was studied in-vivo using a rat model. Parameters such as mount and intromission frequencies, mount and ejaculation latency and testosterone levels were assessed. Three phytocompounds showed better binding affinity for phosphodiesterase 5 than the reference compounds and were also found to be a good target for the proteins of interest. The extract was found to contain steroids, flavonoids, and terpenoids. The results from the in-vivo study demonstrated significant increases (p<0.05) in mean mounting and intromission frequencies and ejaculatory latency following treatment with the extract at 500 mg/kg body weight. The study also demonstrated a significant decrease (p<0.05) in mount latency. Testosterone levels increased significantly (p<0.05) at 500mg/kg body weight. This study affirms the aphrodisiac effect ofAzanza garckeanafruit in the albino rat model and suggests that the fruit’s ethanol extract holds promise as an important phytomedicine for the development of more effective treatments for male sexual dysfunction.
Ontology-based expansion of virtual gene panels to improve diagnostic efficiency for rare genetic diseases
Authors: Shin Jaemoon , Fujiwara Toyofumi , Saitsu Hirotomo , Yamaguchi Atsuko 
Published: November 2024

AbstractBackgroundVirtual Gene Panels (VGP) comprising disease-associated causal genes are utilized in the diagnosis of rare genetic diseases to evaluate candidate genes identified by whole-genome and whole-exome sequencing. VGPs generated by the PanelApp software were utilized in a UK 100,000 Genome Project pilot study to filter candidate genes, thus enhancing diagnostic efficiency for rare diseases. However, PanelApp also filtered out disease-causing genes in nearly 50% of the cases.MethodsHere, we propose various methods for optimized approach to design VGPs that significantly improve the diagnostic efficiency by leveraging the hierarchical structure of the Mondo disease ontology, without excluding disease-causing genes. We also performed computational experiments on an evaluation dataset comprising 74 patients to determine the optimal VGP design method.ResultsOur results demonstrate that the proposed method can significantly enhance rare disease diagnosis efficiency by automatically identifying candidate genes. The proposed method successfully designed VGPs that improve diagnosis efficiency without excluding disease-causing genes.ConclusionWe have developed novel methods for VGP design that leverage the hierarchical structure of the Mondo disease ontology to improve rare genetic disease diagnosis efficiency. This approach identifies candidate genes without excluding disease-causing genes, and thereby improves diagnostic efficiency.
Development and validation of an all-in-one Bat-Clade genomic sequencing and host identification protocol
Authors: de Souza Godinho Fernanda Marques , Campos Aline , Huff Rosana , Ruivo Amanda Pellenz , Bermann Thales , Bauerman Milena , dos Santos Franciellen Machado , Selayaran Taina Machado , Correa Artur Beineke , dos Santos Raissa Nunes , Roehe Paulo Michel , Wallau Gabriel da Luz , Salvato Richard Steiner 
Published: November 2024

AbstractRabies virus (RABV), a fatal zoonotic pathogen, remains a significant public health concern, with bat-maintained lineages accounting for all currently documented cases in Brazil. Despite the availability of pharmacological prophylaxis for humans and animals, the high genetic diversity of RABV in diverse natural bat hosts and continued circulation in multiple animals pose challenges for effective surveillance. Here, we developed and validated a novel, rapidly deployable amplicon-based sequencing approach for rabies virus (RABV) genomic surveillance. This “all-in-one” protocol integrates whole RABV genome sequencing with host species identification through COI gene amplification and sequencing, addressing the challenges posed by RABV’s high genetic diversity and complex transmission dynamics. We assessed the protocol’s effectiveness by sequencing 25 near-complete RABV genomes from host species across four distinct families (Bovidae, Equidae, Felidae, and Microchiroptera) obtained from the Rabies Control and Surveillance Program in Rio Grande do Sul State, Southern Brazil. The method achieved an average genome coverage of 91.4% at a minimum 5x read depth, with a mean depth coverage of 816x across sequenced genomes. The results demonstrated significant Bat-Clade sublineage diversity, which was classified using the MADDOG RABV lineage system. The protocol successfully identified three bat species (Tadarida brasiliensis, Desmodus rotundus, andMyotis nigricans) among the samples, highlighting its capability for precise host identification. This study presents a powerful tool for high-resolution evaluation of RABV genomic features and host identification, enabling more targeted public health interventions. This new approach has the potential to enhance RABV surveillance capabilities, contributing to more effective rabies control strategies within a One Health framework.
Application of ConvNeXt with Transfer Learning and Data Augmentation for Malaria Parasite Detection in Resource-Limited Settings Using Microscopic Images
Authors: Mmileng Outlwile Pako , Whata Albert , Olusanya Micheal , Mhlongo Siyabonga 
Published: November 2024

AbstractMalaria is one of the most widespread and deadly diseases across the globe, especially in sub-Saharan Africa and other parts of the developing world. This is primarily because of incorrect or late diagnosis. Existing diagnostic techniques mainly depend on the microscopic identification of parasites in the blood smear stained with special dyes, which have drawbacks such as being time-consuming, depending on skilled personnel and being vulnerable to errors.This work seeks to overcome these challenges by proposing a deep learning-based solution in the ConvNeXt architecture incorporating transfer learning and data augmentation to automate malaria parasite identification in thin blood smear images. This study’s dataset was a set of blood smear images of equal numbers of parasitised and uninfected samples drawn from a public database of malaria patients in Bangladesh. To detect malaria in the given dataset of parasitised and uninfected blood smears, the ConvNeXt models were fine-tuned. To improve the effectiveness of these models, a vast number of data augmentation strategies was used so that the models could work well in various image capture conditions and perform well even in environments with limited resources. The ConvNeXt Tiny model performed better, particularly the re-tuned version, than other models, such as Swin Tiny, ResNet18, and ResNet50, with an accuracy of 95%. On the other hand, the re-modified version of the ConvNeXt V2 Tiny model reached 98% accuracy. These findings show the potential to implement ConvNeXt-based systems in regions with scarce healthcare facilities for effective and affordable malaria diagnosis.
Single-cell multiomics of pediatric BM reveals age-dependent differences in lineage differentiation linked to stromal cell heterogeneity
Authors: Hanemaaijer Evelyn S. , Müskens Konradin F. , Kal Ireen J. , te Pas Brigit M. , Fryzik Patrycja , Epskamp Nina , Balwierz Aleksandra , Candelli Tito , de Jonge Wim J. , Margaritis Thanasis , Belderbos Mirjam E. 
Published: November 2024

AbstractChildhood is critical for hematopoietic development and the onset of hematologic diseases. To explore hematopoietic changes from infancy through adolescence, we generated a multi-modal single-cell atlas capturing mRNA and surface protein expression of 90.710 bone marrow (BM) cells. This includes hematopoietic stem/progenitor cells and mesenchymal stromal cells, from seven pediatric individuals and two young adults. We demonstrate that young pediatric BM is distinct from adolescents/young adults (AYA), shifting from B-lineage dominance in early childhood to myeloid and T-lineage bias in adolescence. We uncover two distinct lymphoid progenitors (LyPs) subsets regulating this shift: CD127-positive LyPs with B-lineage output, most abundant in early childhood, and CD127-negative LyPs with lymphoid and myeloid features, more common in AYAs. Age-related changes in stromal composition and signaling, mediated by IL-7 and TGF-β1, correspond with this lineage shift. This study provides an in-depth resource for understanding healthy hematologic development and potential early-life perturbations underlying pediatric hematologic diseases.
The combined use of scRNA-seq and network propagation highlights key features of pan-cancer Tumor-Infiltrating T cells
Authors: Mangelinck Adèle , Molitor Elodie , Marchiq Ibtissam , Alaoui Lamine , Bouaziz Matthieu , Andrade-Pereira Renan , Darville Hélène , Becht Etienne , Lefebvre Céline 
Published: November 2024

AbstractImproving the selectivity and effectiveness of drugs represents a crucial issue for future therapeutic developments in immuno-oncology. Traditional bulk transcriptomics faces limitations in this context for the early phase of target discovery as resulting gene expression levels represent the average measure from multiple cell populations. Alternatively, single cell RNA sequencing can dive into unique cell populations transcriptome, facilitating the identification of specific targets. Here, we generated Tumor-Infiltrating regulatory T cells (TI-Tregs) and exhausted T cells (Tex) gene signatures from a single cell RNA-seq pan-cancer T cell atlas. To overcome noise and sparsity inherent to single cell transcriptomics, we then propagated the gene signatures by diffusion in a protein-protein interaction network using the Patrimony high-throughput computing platform. This methodology enabled the refining of signatures by rescoring genes based on their biological connectivity and shed light not only on processes characteristics of TI-Treg and Tex development and functions but also on their immunometabolic specificities. The combined use of single cell transcriptomics and network propagation may thus represent an innovative and effective methodology for the characterization of cell populations of interest and eventually the development of new therapeutic strategies in immuno-oncology.
Dual fragmentation via collision-induced and oxygen attachment dissociations using water and its radicals for C=C position-resolved lipidomics
Authors: Takeda Hiroaki , Okamoto Mami , Takahashi Hidenori , Buyantogtokh Bujinlkham , Kishi Noriyuki , Okano Hideyuki , Kamiguchi Hiroyuki , Tsugawa Hiroshi 
Published: November 2024

AbstractOxygen attachment dissociation (OAD) is a tandem mass spectrometry (MS/MS) technique used to annotate the positions of double bonds (C=C) in complex lipids. Although OAD has been used for untargeted lipidomics, its availability has been limited to the positive-ion mode, requiring the independent use of a collision-induced dissociation (CID) method. In this study, we demonstrated the OAD-MS/MS technique in the negative-ion mode for profiling phosphatidylserines, phosphatidylglycerols, phosphatidylinositols, and sulfatides, where the fragmentation mechanism remained consistent with that in the positive-ion mode. Furthermore, we proposed optimal conditions for the simultaneous acquisition of CID– and OAD-specific fragment ions, termed OAciD. In the collision cell for OAD, oxygen atoms and hydroxy radicals facilitate C=C position-specific fragmentation, while residual water vapor induces cleavage of low-energy covalent bonds, such as ester and peptide bonds, at higher collision energy values, preserving OAD-specific ions under high collision energy conditions. Finally, theoretical fragment ions were implemented in MS-DIAL 5 to accelerate C=C position-resolved untargeted lipidomics. The OAciD methodology was applied to lipid profiling of five marmoset brain regions: the frontal lobe, hippocampus, midbrain, cerebellum, and medulla. Region-specific marmoset lipidomes were characterized with C=C positional information, where the ratios of C=C positional isomers such as delta 9– and delta 11 of fatty acid 18:1 in phosphatidylcholine were also estimated using OAciD-MS/MS. In addition, we characterized the profiles of polyunsaturated fatty acid-containing complex lipids with C=C positional information, where lipids containing omega-3 fatty acids were enriched in the cerebellum, while those containing omega-6 fatty acids were more abundant in the hippocampus and frontal lobe.
Antigen mobility regulates the dynamics and precision of antigen capture in the B cell immune synapse
Authors: McArthur Hannah C. W. , Iliopoulou Maro , Bajur Anna T. , Spillane Katelyn M. 
Published: November 2024

AbstractB cells discriminate antigens in immune synapses by capturing them from antigen-presenting cells. This discrimination relies on the application of mechanical force to B cell receptor (BCR)-antigen bonds, allowing B cells to selectively disrupt low-affinity interactions while internalizing high-affinity antigens. Using DNA-based tension sensors combined with high-resolution imaging, we demonstrate that the magnitude, location, and timing of forces within the immune synapse are influenced by the fluidity of the antigen-presenting membrane. Transitioning antigens from a high-mobility to a low-mobility substrate significantly increases the probability and speed of antigen extraction while also improving affinity discrimination. This shift in antigen mobility also reshapes the synapse architecture, altering spatial patterns of antigen uptake. Despite these adaptations, B cells maintain consistent levels of proximal and downstream signaling pathway activation regardless of antigen mobility. They also efficiently transport internalized antigens to major histocompatibility complex class II (MHCII)-positive compartments for processing. These results demonstrate that B cells mount effective responses to antigens across diverse physical environments, though the characteristics of that environment may influence the speed and accuracy of B cell adaptation during an immune response.
Fertility Preservation of Vacuum-Dried Ram Spermatozoa Stored for Four Years at Room Temperature
Authors: Moncada Margherita , Lo Sterzo Martina , Palazzese Luca , Boffa Francesca , Anzalone Debora Agata , Iuso Domenico , Czernik Marta , Gioia Luisa , Turri Federica , Mislei Beatrice , Bucci Diego , Bonnet Jacques , Colotte Marthe , Tuffet Sophie , Bochenek Michał , Loi Pasqualino 
Published: November 2024

ABSTRACTDry storage at room temperature (RT) could simplify spermatozoa banking. Here, we explored DNA stability andin vitroandin vivodevelopment of embryos derived from vacuum-dried encapsulated (VDE) ram spermatozoa stored for four years or after accelerated aging. While some genomic damage was detected at time 0, DNA fragmentation increased from 3.32±3% (time 0) to 37.64±4% (4 years). A decrease in blastocyst rate was observed after four years of storage and 6.7 years of simulated storage (10.2% and 9%versus13.16% at time 0). Embryo quality, assessed based onCdx2and Inf-τ gene expression, declined over time. Only two of the 23 embryos transferred into synchronized ewes were implanted but were lost by day 40.In conclusion, dry spermatozoa generated blastocysts after four years of RT storage, but their post-implantation development was impaired. Optimization of the water extraction and storage conditions could better preserve the spermatozoa’s DNA integrity, resulting in improved embryo quality, compatible with development to term.
ATGL-mediated lipolysis is essential for myocellular mitochondrial function and augments PPARδ-induced improvements in mitochondrial respiration
Authors: Gemmink Anne , van de Weijer Tineke , Schaart Gert , Grabner Gernot F. , Kornips Esther , Knoops Kèvin , Zechner Rudolf , Schweiger Martina , Hesselink Matthijs K.C. 
Published: November 2024

ABSTRACTDefects in ATGL-mediated myocellular LD lipolysis results in mitochondrial dysfunction of unknown origin, which can be rescued by PPAR agonists. Here we examine whether ATGL-mediated lipolysis is required to maintain mitochondrial network connectivity and function. Moreover, we explored if the functional implications of ATGL deficiency for mitochondrial network dynamics and function can be alleviated by promoting PPARα and/or PPARδ transcriptional activity. To this end, we cultured human primary myotubes from patients with neutral lipid storage disease with myopathy (NLSDM), a rare metabolic disorder caused by a mutation in the PNPLA2 gene. These myotubes possess dysfunctional ATGL and compromised LD lipolysis. In addition, mitochondria-LD contacts, mitochondrial network dynamics, and TMRM intensity were abrogated. Using a humanized ATGL inhibitor in myotubes cultured form healthy donors, revealed similar results. Upon stimulating PPARδ transcriptional activity, mitochondrial respiration improved by more than 50% in human primary myotubes from healthy lean individuals. This increase in respiration was dampened in myotubes with dysfunctional ATGL. Stimulation of PPARδ transcriptional activity had no effect on mitochondria-LD contacts, mitochondrial network dynamics, and TMRM intensity. Our results demonstrate that dysfunctional ATGL results in compromised mitochondrial-LD contacts and mitochondrial dynamics, and that functional ATGL is required to improve mitochondrial respiratory capacity upon stimulation of PPARδ transcriptional activity.
Model-free photon analysis of diffusion-based single-molecule FRET experiments
Authors: Terterov Ivan , Nettels Daniel , Lastiza-Male Tanya , Bartels Kim , Loew Christian , Vancraenenbroeck Rene , Carmel Itay , Rosenblum Gabriel , Hofmann Hagen 
Published: November 2024

AbstractPhoton-by-photon analysis tools for diffusion-based single-molecule Förster resonance energy transfer (smFRET) experiments often describe protein dynamics with Markov models. However, FRET efficiencies are only projections of the conformational space such that the measured dynamics can appear non-Markovian. Model-free methods to quantify FRET efficiency fluctuations would be desirable in this case. Here, we present such an approach. We determine FRET efficiency correlation functions free of artifacts from the finite length of photon trajectories or the diffusion of molecules through the confocal volume. We show that these functions capture the dynamics of proteins from micro-to milliseconds both in simulation and experiment, which provides a rigorous validation of current model-based analysis approaches.