bluuebunny/crossref_metadata_2025_split huggingface dataset:
AEGIS: individual-based modeling of life history evolution
Authors: Bagic Martin , Šajina Arian , Bradshaw William John , Valenzano Dario Riccardo 
Published: November 2024

ABSTRACTNature presents a staggering diversity of life history strategies, ranging from rapid to slow onset of sexual maturity, short or long life, low or high number of offspring, and much more. Each species-specific life history trait reflects on the one hand specific adaptations to unique environments, e.g., nutrient availability, predation, parasite load, seasonality; and on the other hand, depends on past demographic constraints, such as population bottlenecks, migrations, etc. Studying life history diversity in nature and in the laboratory ultimately aims to identify the ecological, demographic, and intrinsic causes contributing to species-specific growth rate distributions, lifetime reproductive outcomes, as well as lifespans. However, for most species, we cannot rewind the evolutionary and demographic past to identify the causal chain of events leading to the present life history traits. We can infer past events only by sampling extant populations.In silicoevolution has the advantage of providing complete time resolution for the events driving life history evolution and enables to directly test the impact of ecological and demographic variables on the evolution of life history traits. We developed AEGIS (Aging of Evolving Genomes In Silico), a software for individual-based modeling of life history trait evolution at the genotype and phenotype level. AEGIS models life history traits evolution in response to a set of factors, including resource availability, extrinsic mortality induced by predators or parasites, different levels of germline mutation rates, population size, sexual vs. asexual reproduction, and more. AEGIS serves as a powerful tool to model life history evolution and allows for parameter inference against ground truths. AEGIS can help generate estimates for the evolution of different life history traits, such as age-dependent mortality and reproduction, in response to different selective pressures and intrinsic genetic constraints.
Impact of Praziquantel Distribution on the Epidemiology of Paragonimiasis Among School-Aged Children: A Cross Sectional Study in the Most Endemic Focus in Cameroon
Authors: Cheuyem Fabrice Zobel Lekeumo , Toubue Jean-Brice Fomeni , Mutarambirwa Henri Donald , Ndibo Guy Roger Pilo 
Published: November 2024

AbstractBackgroundParagonimiasis is a parasitic disease affecting humans and other mammals, caused by infestation with lung flukes of the genusParagonimus. The peri-urban area of Kumba is co-endemic for paragonimiasis and schistosomiasis. The National Schistosomiasis and Soil-Transmitted Helminthiasis Control Program distributes praziquantel annually for schistosomiasis control. The primary objective of this study was to describe the shellfish cooking habits among schoolchildren and to assess the impact of praziquantel mass distribution on the paragonimiasis burden in the most endemic focus in Cameroon.MethodsWe carried out a cross-sectional descriptive study from November 2013 to March 2014. Pupils of five government primary schools in five villages around Kumba underwent both clinical and parasitological investigations in search of signs and symptoms of paragonimiasis. The Chi square and Fisher exact tests were used to compared proportions.p-values<0.05 were considered statistically significant.ResultsWe recruited 175 children, comprising 96 females and 79 males, with a sex ratio (F/M) of 1.2. Their ages ranged from 5 to 15 years, with a mean age of 10 ± 3.74 years. The age group 6-10 years was the most represented. All participants reported consuming crabs. The prevalence of paragonimiasis among the school children was 0.57% (95% CI: 0.0143%-3.143%). This result was statistically significantly lower than that of the last study conducted ten years prior, which used the same diagnostic method in this area (12.3%). Slightly more than half of the students (58.9%) reported preparing their crabs by boiling, and two-thirds (69%) estimated the cooking time to be more than 30 minutes. More than two-thirds (78%) of the children who estimated the cooking time to be more than 30 minutes consumed shrimp with their family. Pulmonary symptoms were the most common, with cough being the most prevalent. Notably, we did not register any cases of hemoptysis. Coinfections were also found in the population studied.ConclusionsThe prevalence of paragonimiasis has decreased in this focus, known to be the most endemic for this disease in Cameroon. This is due to the large distribution of praziquantel in this area and probably to changes from unhealthy cooking habits to healthier ones.
Benchmarking concentration and direct extraction methods for wastewater-based surveillance of eight human respiratory viruses: implications for rapid application to novel pathogens
Authors: Wang Audrey Liwen , Jiang Minxi , Nguyen Allie , Kane Staci R. , Borucki Monica K. , Kantor Rose S. , Nelson Kara L. 
Published: November 2024

AbstractWastewater monitoring is rapidly expanding to provide surveillance for a growing number of epidemic and endemic pathogens. To provide early warning and support rapid response to a novel virus through wastewater surveillance, it would be ideal to understand in advance which concentration and extraction methods are likely to be effective for dPCR-based methods, depending on virus characteristics. In this study, we spiked wastewater samples with eight human respiratory viruses and processed them with four commercial methods that concentrate and/or extract nucleic acids from both liquid and solid fractions (Promega, Nanotrap, InnovaPrep), or only the solid fraction of wastewater (Solids). Our findings provide encouraging evidence that all four concentration/extraction methods combined with dPCR could detect an emerging virus in wastewater, although they differed in sensitivity. The pattern of recovery efficiency for adenoviruses, coronaviruses, and influenza A viruses was consistent across methods, while distinct patterns were observed for coxsackieviruses. Promega produced higher median recovery efficiencies based on dPCR for all viruses except for coxsackieviruses, even though it had the highest dPCR inhibition. We suggest caution in applying Nanotrap to new targets, based on the low recovery of coxsackievirus B5 compared to the other viruses. We also quantified the endogenous indicators PMMoV and Carjivirus (formerly crAssphage), illustrating how normalization could either improve or worsen the comparison of virus concentrations measured by different methods. These findings can guide the selection of concentration and extraction methods for wastewater monitoring based on the properties of target viruses, thus enhancing pandemic preparedness.Synopsis StatementBenchmarking scalable concentration and extraction methods on respiratory viruses with diverse properties facilitates the rapid application of wastewater-based surveillance to emerging viruses.
Decontaminating genomic data for accurate species delineation and hybrid detection in theLasiusant genus
Authors: Jecha Kristine , Lavanchy Guillaume , Schwander Tanja 
Published: November 2024

AbstractSpecies identification and delineation by molecular methods has become a widely used technique and has revealed hybrids between species previously believed to be completely reproductively isolated. However, the application of molecular methods is associated with a risk of DNA contamination, which can result in the identification of false hybrids and generate inaccurate conclusions about the species’ identities and characteristics. Here, we generate and analyze a dataset of nuclear SNP data and mitochondrial DNA sequences from over 1,000Lasiusants to accurately investigate the species delineation and hybridization proclivity within the genus. We describe an approach, based on a combination of competitive mapping and allelic depth ratio analysis, that allows us to identify DNA contaminations and filter them from large-scale datasets. By applying this approach to theLasiusants, we are able to remove interspecific contamination, and to clearly delineate each species genetically as well as identify a hybrid individual betweenL. emarginatusandL. platythorax.SignificanceNext-generation sequencing enables large-scale studies of population structure, species delineation, and introgression for a wide range of taxa. However, the potential for cross- contamination during sample preparation is rarely considered, despite potential major impacts on the conclusions. Here, we develop a new decontamination pipeline and apply it to a large- scale genotyping dataset to study species delineation and hybridization in the ant genusLasius. We find only one hybrid in a thousand individuals, a very different picture from the contaminated dataset. Testing for and removing contamination should be part of every population genomics study.
A Portable and Scalable Genomic Analysis Pipeline forStreptococcus pneumoniaeSurveillance: GPS Pipeline
Authors: Hung Harry C. H. , Kumar Narender , Dyster Victoria , Yeats Corin , Metcalf Benjamin , Li Yuan , Hawkins Paulina A. , McGee Lesley , Bentley Stephen D. , Lo Stephanie W. 
Published: November 2024

AbstractEver increasing global sequencing capacity provides an unprecedented opportunity in utilising genomic information captured from whole-genome sequencing to enhance pathogen surveillance. However, there is a growing need for developing user-friendly tools to effectively analyse the increasing volume of data. To meet this need, we have developed a genomic analysis pipeline, GPS Pipeline, which is portable and scalable to analyse genomes ofStreptococcus pneumoniae, a major bacterial pathogen that is estimated to cause 317,000 child deaths worldwide every year. The GPS Pipeline is based on Nextflow and containerisation technology, and designed to enable researchers generating public health relevant output, includingin silicoserotypes, pneumococcal lineages (i.e. GPSCs), multilocus sequence types, and antimicrobial susceptibilities against 20 commonly used antibiotics,with minimal software setup requirements and bioinformatic expertise, in order to analyse genomic data at scale with ease. The GPS Pipeline provides a streamlined workflow that improves responsiveness in genomic surveillance on pneumococci.Data SummaryThe GPS Pipeline is available on GitHub atgithub.com/GlobalPneumoSeq/gps-pipeline. Published data from the GPS Database is available on Monocle Data Viewer atdata.monocle.sanger.ac.ukand associated sequence read files are searchable and downloadable in the European Nucleotide Archive atebi.ac.uk/enavia their ERR accession numbers.Impact StatementThe GPS Pipeline advances global genomic surveillance ofStreptococcus pneumoniaeby providing a scalable, portable, and user-friendly tool for analysing whole-genome sequencing data. Leveraging Nextflow and containerisation technology, it minimises bioinformatics expertise requirements and infrastructure needs, making it particularly valuable in low- and middle-income countries where pneumococcal disease burden is high. This pipeline ensures reproducibility and stability across platforms, facilitating rapid and accurate pneumococci genomic analysis. By streamlining data processing, the GPS Pipeline enhances pathogen surveillance, generates evidence to support vaccine strategy development, and empowers researchers worldwide, ultimately contributing to improved public health outcomes.
Postoperative Chemoradiotherapy causes Less Fibrosis and Better Anorectal Function compared with preoperative: A retrospective study in Rectal Cancer
Authors: Zhang Ming , Li Shuai , Yu Guan Yu , Zhou Le Qi , Lu Hai Di , Gong Hai Feng , Liu Lian Jie , Lou Zheng , Hao Li Qiang , Shen Fu , Gao Xian Hua , Zhang Wei , Yu Yue 
Published: November 2024

ABSTRACTBACKGROUNDRadiotherapy with or without chemotherapy has been widely used to improve patient outcomes due to locally advanced rectal cancer. The differential degree of pelvic fibrosis and anorectal function after preoperative or postoperative chemoradiotherapy has not been studied previously.METHODSData of patients who received chemoradiotherapy and radical resection of rectal cancer in our hospital from January 2000 to Aug 2021 were retrospectively analyzed. Anastomotic fibrosis scores and perirectal fibrosis scores based on magnetic resonance imaging findings were used to evaluate the extent of fibrosis one year postoperatively. The overall level of anorectal function and percentage of patients eligible for ileostomy reversal were assessed two years postoperatively.RESULTS1331 patients were finally included, with 522 and 809 patients in in the preoperative and postoperative chemoradiotherapy groups, respectively. The postoperative chemoradiotherapy group had a higher percentage of patients undergoing ileostomy reversal and had lower anastomotic fibrosis scores, perirectal fibrosis scores, Wexner scores, and percentage of patients with temporary ileostomy than the preoperative group; this difference persisted after propensity score matching. Univariate and multivariate analyses demonstrated that the timing of chemoradiotherapy was an independent predictor of the anastomotic fibrosis score, perirectal fibrosis score, percentage of patients with temporary ileostomy, and percentage of patients eligible for ileostomy reversal.CONCLUSIONSPostoperative chemoradiotherapy is associated with less pelvic fibrosis and better anorectal function than preoperative chemoradiotherapy in the treatment of patients with locally advanced rectal cancer.
A Large-Scale Foundation Model for RNA Function and Structure Prediction
Authors: Zou Shuxian , Tao Tianhua , Mahbub Sazan , Ellington Caleb N. , Algayres Robin , Li Dian , Zhuang Yonghao , Wang Hongyi , Song Le , Xing Eric P. 
Published: November 2024

AbstractOriginally marginalized as an intermediate in the information flow from DNA to protein, RNA has become the star of modern biology, holding the key to precision therapeutics, genetic engineering, evolutionary origins, and our understanding of fundamental cellular processes. Yet RNA is as mysterious as it is prolific, serving as an information store, a messenger, and a catalyst, spanning many underchar-acterized functional and structural classes. Deciphering the language of RNA is important not only for a mechanistic understanding of its biological functions but also for accelerating drug design. Toward this goal, we introduce AIDO.RNA, a pre-trained module for RNA in an AI-driven Digital Organism [1]. AIDO.RNA contains a scale of 1.6 billion parameters, trained on 42 million non-coding RNA (ncRNA) sequences at single-nucleotide resolution, and it achieves state-of-the-art performance on a comprehensive set of tasks, including structure prediction, genetic regulation, molecular function across species, and RNA sequence design. AIDO.RNA after domain adaptation learns to model essential parts of protein translation that protein language models, which have received widespread attention in recent years, do not. More broadly, AIDO.RNA hints at the generality of biological sequence modeling and the ability to leverage the central dogma to improve many biomolecular representations. Models and code are available through ModelGenerator inhttps://github.com/genbio-ai/AIDOand onHugging Face.
A wide diversity of viruses detected in African mammals involved in the wild meat supply chain
Authors: Geraerts Mare , Gombeer Sophie , Nebesse Casimir , Akaibe Douglas , Akaibe Dudu , Baelo Pascal , Chaber Anne-Lise , Gembu Guy-Crispin , Gaubert Philippe , Joffrin Léa , Laudisoit Anne , Laurent Nicolas , Leirs Herwig , Mande Claude , Mariën Joachim , Ngoy Steve , Těšíková Jana , Vanderheyden Ann , van Vredendaal Rianne , Verheyen Erik , Gryseels Sophie 
Published: November 2024

ABSTRACTThe processes involved in acquiring, trading, preparing, and consuming wild meat pose significant risks for the emergence of zoonotic infectious diseases. Several major viral outbreaks have been directly linked to the wild meat supply chain, yet our knowledge of the virome in many mammals involved in this chain remains limited and disproportionately focused on certain mammalian taxa and pathogens.This report presents the findings of a metagenomic viral screening of 99 specimens belonging to 27 wild African mammal species and one domesticated species, all traded for their meat. The study focuses on tissue and swab samples collected from various regions in the Democratic Republic of the Congo and in Brussels, Belgium.A total of fifteen virus strains were detected, belonging to the familiesArteriviridae,RetroviridaeandSedoreoviridae(primates),Picobirnaviridae(primates and rodents),Picornaviridae(rodents),Hepadnaviridae(hyrax),Orthoherpesviridae(artiodactylid and carnivore) andSpinareoviridae(carnivore). Several strains were detected in mammalian hosts for the first time, expanding their host range and genetic diversity. Of note is the presence of viruses genetically related to recognised zoonotic pathogens, i.e., human picobirnavirus (Orthopicobirnavirus hominis) (primates and rodents), simian foamy viruses (Simiispumavirus) (primates), and rotavirus A (Rotavirus alphagastroenteritidis) (primates). The presence of these viruses in primates is concerning as non-human primates are phylogenetically closely related to humans, which can facilitate interspecies viral transmission. These findings underscore the high diversity of mammalian viruses and the potential risk of human infection through cross-species transmission during the close interactions with wildlife in the wild meat supply chain.
Advanced human cerebral organoids as a model for investigating glioma stem cell interactions with microglia and vascular cells and response to radiotherapy
Authors: Raguin Jérémy , Kortulewski Thierry , Bergiers Oriane , Granotier-Beckers Christine , Chatrousse Laure , Benchoua Alexandra , Gauthier Laurent R. , Boussin François D. , Mouthon Marc-André 
Published: November 2024

ABSTRACTThe recent development of human brain organoids from induced pluripotent stem cells (IPSCs) enables the modeling of brain biology and pathophysiology, such as gliomas. However, most models lack vascular and/or immune systems, both of which play essential roles in maintaining brain health and in pathophysiological mechanisms. We have established a new method for generating vascularized complex cerebral organoids (CCOs) containing microglial cells (brain-resident macrophages) by incorporating bipotent hematopoietic/endothelial progenitors derived from the same IPSC lines during the early stages of development. This approach led to the formation of extensive vascular-like structures with blood-brain barrier characteristics, which were perfused upon transplantation into immunodeficient mice. Additionally, microglial cells exhibiting typical phenotypes and functionalities also developed within the CCOs. By coculturing CCOs with glioma stem cells, we demonstrated that this model effectively recapitulates the tumor niche of glioblastoma, showing vascular co-option, reprogramming of microglia into tumor-associated macrophages, and recurrence after radiotherapy. In conclusion, our vascularized and immunocompetent CCO model will be invaluable for understanding human brain development, exploring how this process is disrupted in diseases like gliomas, and discovering new therapeutic strategies.
Branched DNA Processing by a Thermostable CAS-Cas4 fromThermococcus onnurineus: Expanding Biochemical Landscape of Nuclease Activity
Authors: Jain Muskan , Pattnayak Asish Kumar , Aggarwal Sakshi , Rai Praveen , Kavya J , Chandrayan Sanjeev , Goel Manisha , Gaur Vineet 
Published: November 2024

AbstractThe adaptive immune function of CRISPR-Cas systems in bacteria and archaea is mediated throughCRISPR-Associated Proteins (Cas). The adaptation module, typically involving Cas1, Cas2, and Cas4, helps integrate viral “spacer” sequences into the host genome. Cas4 proteins are classified into two types based on neighboring genes: CAS-Cas4, flanked by othercasgenes, and Solo-Cas4, which exist independently. While CAS-Cas4 proteins are implicated in adaptation, they remain biochemically uncharacterized in archaea, unlike archaeal Solo-Cas4 proteins. This study biochemically characterizes TON_0321, a CAS-Cas4 protein from the Type IV-C CRISPR cassette ofThermococcus onnurineus. TON_0321 exhibits 5′ to 3′ exonuclease activity and unique structure-dependent endonuclease activity, shedding light on CAS-Cas4 functional diversity. A distinct spatial organization of the catalytic site, angled with the positively charged patch on the protein surface, enables TON_0321 to recognize branching points in DNA substrates. Furthermore, this spatial arrangement facilitates cleavage 2 to 3 nucleotides away from the branch point in the 5′ direction, demonstrating structure-specific endonuclease activity.
Anatomical and functional examination of superior colliculus projections to the inferior olivary neurons in mice
Authors: David Deviana , Nusselder Hugo , Uusisaari Marylka Yoe 
Published: November 2024

AbstractThe Inferior olive (IO) is an important region for motor learning and movement coordination. Its climbing fibers projection to the Purkinje neurons in the cerebellar cortex is a sole source of the complex spikes, characterized by a strong depolarization in the Purkinje neuron’s dendrites. To generate spikes, the IO relies on inputs from various regions of the brain, including the superior colliculus (SC), a midbrain structure known for its role in orienting behaviors.This study investigates SC projections to the IO using viral tracers, calcium imaging, and optogenetic stimulation. We reveal that, in addition to the known projections to the medial accessory olive (MAO), SC axons also project to the ventral principal olive (PO). Despite projecting to different parts of the IO, SC-MAO and SC-PO neurons are intermingled within the lateral part of the SC with similar gross morphology. We show that SC axons terminate on both dendritic shafts and spines of IO neurons, potentially influencing not only spiking probability, but also the network synchronization mediated by gap junctions coupling on the dendritic spines.As a proof of principle, we recorded the in-vivo activity of neurons in ventral PO using calcium indicators and show that optogenetic activation of SC inputs can evoke spiking and enhance synchronization in IO neurons.
Pleasant smells: a privileged gateway to soothing autonomic responses and improving brain-body rhythm coupling
Authors: Ghibaudo Valentin , Turrel Matthias , Granget Jules , Garcia Samuel , Plailly Jane , Buonviso Nathalie 
Published: November 2024

AbstractAromatherapy commonly uses odors to improve well-being through their evocation of positive emotions. Although knowledge in this area is often very empirical, the olfactory stimulus has different properties which, taken together, could explain why it can relax. First, olfactory sense have a direct access to the limbic system, without thalamic relay processing, which confers it a strong emotional valence. Second, when appreciated, odors can slow down breathing and cardiac rates. Third, when slow and deep, breathing can entrain brain activity, due to the mechano-sensitivity of olfactory receptors to airflows. We hypothesized that, thanks to these properties, pleasant odors could enhance the subjective feeling of relaxation, slow down body rhythms, and facilitate entrainment of brain activity by respiration. Comparing the effects of a personally pleasant odor to a personally pleasant music on psychological, physiological and neuronal responses, we showed a tendency for both odors and music to enhance subjective relaxation. However, only pleasant odors were able to 1) decrease heart rate while increasing its variability, and 2) decrease respiratory rate while enhancing the respiratory drive of brain activities, regardless of the music tempo. Overall, we demonstrated that the positive emotion evoked by a personally pleasant smell is sufficient to evoke an olfactomotor response, which, by slowing breathing, synchronizes respiration, fluctuations of heart rate and brain activity.