bluuebunny/crossref_metadata_2025_split huggingface dataset:
Early development and co-evolution of microstructural and functional brain connectomes: A multi-modal MRI study in preterm and full-term infants
Authors: Andrea Gondová , Sara Neumane , Tomoki Arichi , Jessica Dubois 
Published: September 2024

AbstractIntroductionFunctional networks characterised by coherent neural activity across distributed brain regions have been observed to emerge early in neurodevelopment. Synchronized maturation across regions that relate to functional connectivity (FC) could be partially reflected in the developmental changes in underlying microstructure. Nevertheless, covariation of regional microstructural properties, termed ‘microstructural connectivity’ (MC), and its relationship to the emergence of functional specialization during the early neurodevelopmental period remains poorly understood.MethodsWe investigated the evolution of MC and FC postnatally across a set of cortical and subcortical regions, focusing on 45 preterm infants scanned longitudinally, and compared to 45 matched full-term neonates as part of the developing Human Connectome Project (dHCP) using direct comparisons of grey-matter connectivity strengths as well as network-based analyses.ResultsOur findings revealed a global strengthening of both MC and FC with age, with connection-specific variability influenced by the connection maturational stage. Prematurity at term-equivalent age was associated to significant connectivity disruptions, particularly in FC. During the preterm period, direct comparisons of MC and FC strength showed positive linear relationship, which seemed to weaken with development. On the other hand, overlaps between MC-and FC-derived networks (estimated with Mutual Information) increased with age, suggesting a potential convergence towards a shared underlying network structure that may support the co-evolution of microstructural and functional systems.ConclusionOur study offers novel insights into the dynamic interplay between microstructural and functional brain development and highlights the potential of MC as a complementary descriptor for characterizing the brain network development and alterations due to perinatal insults such as premature birth.KeypointsOur study reveals a significant positive linear relationship between grey-matter functional connectivity and underlying microstructural connectivity during development, that decreases with age and varies across connection types.Despite progressive maturational decoupling of microstructural and functional connectivity, a shared network structure may underlie changes in both properties.Prematurity impacts the maturation of connectivity in both modalities, but with a higher reduction of functional than microstructural connectivity strengths.
The Conformational Space of the SARS-CoV-2 Main Protease Active Site Loops is Determined by Ligand Binding and Interprotomer Allostery
Authors: Lee Ethan , Rauscher Sarah 
Published: September 2024

AbstractThe main protease (Mpro) of SARS-CoV-2 is essential for viral replication and is, therefore, an important drug target. Here, we investigate two flexible loops in Mprothat play a role in catalysis. Using all-atom molecular dynamics simulations, we analyze the structural ensemble of Mproin an apo state and substrate-bound state. We find that the flexible loops can adopt open, intermediate (partly open) and closed conformations in solution, which differs from the partially closed state observed in crystal structures of Mpro. When the loops are in closed or intermediate states, the catalytic residues are more likely to be in close proximity, which is crucial for catalysis. Additionally, we find that substrate binding to one protomer of the homodimer increases the frequency of intermediate states in the bound protomer, while also affecting the structural propensity of the apo protomer’s flexible loops. Using dynamic network analysis, we identify multiple allosteric pathways connecting the two active sites of the homodimer. Common to these pathways is an allosteric hotspot involving the N-terminus, a critical region that comprises part of the binding pocket. Taken together, the results of our simulation study provide detailed insight into the relationships between the flexible loops and substrate binding in a prime drug target for COVID-19.
Antiviral Mechanisms and Preclinical Evaluation of Amantadine Analogs that Continue to Inhibit Influenza A Viruses with M2S31N-Based Drug Resistance
Authors: Tietjen Ian , Kwan Daniel C. , Petrich Annett , Zell Roland , Antoniadou Ivi Theodosia , Gavriilidou Agni , Tzitzoglaki Christina , Rallis Michail , Fedida David , Sureda Francesc X. , Mestdagh Cato , Naesens Lieve , Chiantia Salvatore , Johnson F. Brent , Kolocouris Antonios 
Published: September 2024

AbstractTo better manage seasonal and pandemic influenza infections, new drugs are needed with enhanced activity against contemporary amantadine- and rimantadine-resistant influenza A virus (IAV) strains containing the S31N variant of the viral M2 ion channel (M2S31N). Here we tested 36 amantadine analogs against a panel of viruses containing either M2S31Nor the parental, M2 S31 wild-type variant (M2WT). We found that several analogs, primarily those with sizeable lipophilic adducts, inhibited up to three M2S31N-containing viruses with activities at least 5-fold lower than rimantadine, without inhibiting M2S31Nproton currents or modulating endosomal pH. While M2WTviruses in passaging studies rapidly gained resistance to these analogs through the established M2 mutations V27A and/or A30T, resistance development was markedly slower for M2S31Nviruses and did not associate with additional M2 mutations. Instead, a subset of analogs, exemplified by 2-propyl-2-adamantanamine (38), but not 2-(1-adamantyl)piperidine (26), spiro[adamantane-2,2’-pyrrolidine] (49), or spiro[adamantane-2,2’-piperidine] (60), inhibited cellular entry of infectious IAV following pre-treatment and/or H1N1 pseudovirus entry. Conversely, an overlapping subset of the most lipophilic analogs including compounds26,49,60, and others, disrupted viral M2-M1 protein colocalization required for intracellular viral assembly and budding. Finally, a pilot toxicity study in mice demonstrated that38and49were tolerated at doses approaching those of amantadine. Together, these results indicate that amantadine analogs act on multiple, complementary mechanisms to inhibit replication of M2S31Nviruses.Highlights-Current IAVs have M2 mutations that confer resistance to amantadine and rimantadine-Several amantadine analogs inhibit these viruses without acting on M2 proton currents-Alternative antiviral targets include IAV entry and M2-M1 protein colocalization-Amantadine analogs are also tolerated in mice-Future amantadine antivirals could simultaneously act on multiple IAV mechanisms
Desmoplakin mutations in cardiac fibroblasts cause TGFβ1-mediated pathological fibrogenesis in desmoplakin cardiomyopathy via beclin-1 regulation
Authors: Wei Chuanyu , Chan Shing-Fai , Saguner Ardan M. , Brunckhorst Corinna , Duru Firat , Marine Joseph E. , James Cynthia A. , Calkins Hugh , Judge Daniel P. , Shou Weinian , Chen Huei-Sheng Vincent 
Published: September 2024

AbstractBackgroundPathological fibrosis is a major finding in cardiovascular diseases and can result in arrhythmia and heart failure. Desmosome gene mutations can lead to arrhythmogenic cardiomyopathy (ACM). Among ACM, pathogenic desmoplakin (DSP) variants cause a distinctive cardiomyopathy with excessive cardiac fibrosis that could precede ventricular dysfunction.DSPvariants are also linked to other fibrotic diseases. Whether DSP plays any role in pathological fibrosis remain unknown.MethodsMesenchymal stromal cells (MSCs) are resident fibroblast-like cells that are responsible for fibrogenesis in most organs, including hearts. We first used unbiased genome-wide analyses to generate cardiac fibroblasts-like, induced pluripotent stem cell-derived MSCs from normal donors and ACM patients withDSPmutations. We then studied the fibrogenic responses of cardiac MSCs to transforming growth factor beta-1 (TGF-β1) using Western/Co-IP, autophagy assay, gene knockdowns/over-expressions, genomic analyses, mouse DSP knockdown models, immunostaining, and qPCR.ResultsTGFβ1 induced excessive accumulations of vimentin (VIM)/fibrillar collagens, and over-activated fibrotic genes inDSP-mutant MSCs when compared to normal MSCs. In normal MSCs, VIMs bind to wild-type DSP during normal fibrogenesis after TGFβ1.DSP-mutant MSCs exhibited a haplo-insufficient phenotype with increased DSP-unbound VIMs that sequestered beclin-1 (BECN1) from activating autophagy and caveolin-1 (CAV1)-mediated endocytosis. Decreased autophagy caused collagen accumulations and diminished CAV1 endocytosis resulted in abnormal CAV1 plaque formation that over-activated fibrotic genes [COL1A1, COL3A1,and fibronectin (FN)] via heightened p38 activities after TGFβ1. Genome-wide analysis and DSP knockdown in mouse fibroblasts confirmed this novel role ofDSPmutations in pathological fibrosis. Overexpression of VIM-binding domains of DSP could suppress pathological fibrosis by increasing collagen autophagic degradation and decreasing fibrotic gene expressions.ConclusionsOur data reveal that DSP deficiency in MSCs/fibroblasts leads to exaggerated fibrogenesis in DSP-cardiomyopathy by decreasing BECN1 availability for autophagy and CAV1-endocytosis. Overexpression of VIM binding domains of DSP could be a new strategy to treat pathological fibrosis.
A male seminal fluid protein SFP-1 regulates hermaphrodite post-mating longevity and fat metabolism inCaenorhabditis elegans
Authors: Chen Mingqing , Gong Jianke 
Published: September 2024

AbstractThere are several causes of mating-induced physiological changes in hermaphrodites exposed to males, such as functional male sperms causing shrinking and the male pheromone mediating shortened lifespan, which utilize different molecular pathways and are shared across species. However, it is unclear whether the male seminal fluid protein contributes to this post-mating regulation. Here, we investigated the transmit way and the impacts of theCaenorhabditismale seminal fluid protein SFP-1 in mated hermaphrodite tissues. We find that SFP-1 is the key component in seminal fluid to induce post-mating physiological changes in mated hermaphrodites. It acts as a cargo packing into exophers which require the phospholipid scramblase ANOH-1 and ANOH-2 to develop in male seminal vesicle. Exophers carrying SFP-1 cross over the somatic gonad uterus and eventually the protein is uptaken by the intestinal cells via endocytosis. Within the intestine, the NTF2-like domain of SFP-1 assists the association and interaction with the transcription factors SKN-1 and DAF-16 to induce post-mating somatic fat depletion and a shortened lifespan. Our study reveals the elaborate strategies of the male seminal fluid protein on triggering mating-induced physiological changes elicited by sexual interactions that could exist in other species.
Development of a Conditional Plasmid for Gene Deletion in Non-ModelFusobacterium nucleatumstrains
Authors: Zhou Peng , Bibek G C , Wu Chenggang 
Published: September 2024

ABSTRACTFusobacterium nucleatumis an opportunistic pathogen with four subspecies:nucleatum(FNN),vincentii(FNV),polymorphum(FNP), andanimalis(FNA), each with distinct disease potentials. Research on fusobacterial pathogenesis has mainly focused on the model strain ATCC 23726 from FNN. However, this narrow focus may overlook significant behaviors of other FNN strains and those from other subspecies, given the genetic and phenotypic diversity withinF. nucleatum. While ATCC 23726 is highly transformable, most otherFusobacteriumstrains exhibit low transformation efficiency, complicating traditional gene deletion methods that rely on non-replicating plasmids. To address this, we developed a conditional plasmid system in which the RepA protein, essential for replication of a pCWU6-based shuttle plasmid, is controlled by an inducible system combining anfdxpromoter with a theophylline-responsive riboswitch. This system allows plasmid replication in host cells upon induction and plasmid loss when the inducer is removed, forcing chromosomal integration via homologous recombination in the presence of the antibiotic thiamphenicol. We validated this approach by targeting thegalKgene, successfully generating mutants in FNN (ATCC 23726, CTI-2), FNP (ATCC 10953), FNA (21_1A), and the closely related speciesFusobacterium periodonticum. Incorporating asacBcounterselection marker in this conditional plasmid enabled the deletion of theradDgene in non-model strains. Interestingly, whileradDdeletion in 23726, 10953, and 21_1A abolished coaggregation withActinomyces oris, the CTI-2 mutant retained this ability, suggesting the involvement of other unknown adhesins. This work significantly advances gene deletion in genetically recalcitrantF. nucleatumstrains, enhancing our understanding of this pathogen.IMPORTANCEFusobacterium nucleatumis implicated in various human diseases, including periodontal disease, preterm birth, and colorectal cancer, often linked to specific strains and reflecting the species’ genetic and phenotypic diversity. Despite this diversity, most genetic research has centered on the model strain ATCC 23726, potentially missing key aspects of other strains’ pathogenic potential. This study addresses a critical gap by developing a novel conditional plasmid system that enables gene deletion in genetically recalcitrant strains ofF. nucleatum. We successfully deleted genes in the clinical strain CTI-2, the FNA strain 21_1A, andF. periodonticumfor the first time. Our findings, particularly the varying behavior of theradDgene production in coaggregation across strains, underscore the complexity ofF. nucleatumand the need for broader genetic studies. This work advances our understanding ofF. nucleatumvirulence at the strain level and provides a valuable tool for future bacterial genetics research.
The food–gut axis: the phyllosphere virome of fresh vegetables is diverse, abundant, and transmitted to the human gut virome
Authors: Park Ji-Woo , Yun Yeo-Eun , Cho Jin Ah , Yoon Su-In , In Su-A , Park Eun-Jin , Kim Min-Soo 
Published: September 2024

AbstractFresh vegetables harbor diverse microorganisms on leaf surfaces, yet their viral communities remain unexplored. We investigated the diversity and ecology of phyllosphere viromes of six leafy green vegetables using virus-like particle (VLP) enrichment and shotgun metagenome sequencing. On average, 9.2 × 107viruses were present per gram of leaf tissue. The majority (93.1 ± 6.2%) of these viruses were taxonomically unclassified. Virome compositions were distinct among vegetable types and exhibited temporal variations. Virulent phages with replication-enhancing auxiliary metabolic genes (AMGs) were more dominant than temperate phages with host fitness-benefiting AMGs. Analysis of 1,498 human fecal VLP metagenomes revealed that approximately 10% of vegetable viruses were present in the human gut virome, including viruses commonly observed in multiple studies. These gut-associated vegetable viruses were enriched with short-term vegetable intake, and depleted in individuals with metabolic and immunologic disorders. Overall, this study elucidates the ecological contribution of the fresh vegetable virome to human gut virome diversity.
Lower estimated glomerular filtration rate relates to cognitive impairment and brain alterations
Authors: Rahayel Shady , Goupil Rémi , Genest Dominique Suzanne , Lamarche Florence , Agharazii Mohsen , Ayral Violette , Tremblay Christina , Madore François 
Published: September 2024

ABSTRACTIntroductionChronic kidney disease is associated with cognitive decline and changes in brain structure. However, their associations remain unclear, particularly the selective vulnerability characteristics that make some brain regions more vulnerable.MethodsWe investigated the association between eGFR and cognitive function in 15,897 individuals from the CARTaGENE cohort. We performed vertex-based MRI analyses between eGFR and cortical thickness in the 1,397 participants who underwent brain MRI after six years. Imaging transcriptomics was used to characterize the gene expression and neurodegenerative features associated with this association.ResultsLower eGFR correlated with reduced cognitive performance and brain structure. Brain regions associated with eGFR were enriched for mitochondrial and inflammatory-related genes. These associations occurred independently from age, sex, education, body mass index, Framingham risk score, and white matter lesion volume.DiscussionThis study highlights the link between reduced eGFR, cognitive impairment, and brain structure, revealing some of the kidney-brain axis mechanisms.
Decoding the Deadly Dance: NETosis Genes Predict Neonatal Sepsis Fate
Authors: Shaw Deepshikha , Santhanam Sridhar , Som Tapas Kumar , Bhattacharjee Samsiddhi , Mohapatra Saroj Kant 
Published: September 2024

AbstractBackgroundNeonatal sepsis, a systemic inflammatory response to infection, is a major cause of morbidity and mortality in newborns. Neutrophil extracellular trap formation (NETosis), while crucial for pathogen clearance, can contribute to organ dysfunction in sepsis. This study aimed to identify key NETosis-related genes for prognostication in neonatal sepsis.MethodsWe analysed whole blood transcriptome datasets (GSE26440, GSE26378, GSE25504) from neonates with sepsis and controls. Differentially expressed NETosis genes (DE-NET genes) were identified, and a machine learning approach was used to select the most influential genes. A NET score model was constructed and validated using single-sample gene set enrichment analysis (ssGSEA). The model’s performance was evaluated using ROC analysis. The interplay between key-NET genes and the complement-coagulation (CC) system was investigated. Clinical samples were also collected for validation.ResultsSixteen DE-NET genes were identified, and LASSO further refined these to 8 key-NET genes. The key-NET gene signature and NET score model showed excellent predictive performance (AUCs > 89%) in distinguishing survivors from non-survivors. Mediation analysis revealed that key-NET gene expression precedes and potentially drives complement-coagulation activation.ConclusionsWe present an 8-gene prognostic model for risk stratification in neonatal sepsis, based on early blood transcript signatures in neonates. Our findings underscore the central role of NETosis in sepsis- induced coagulopathy, revealing potential therapeutic targets for intervention.Abstract Figure
ROBIN: A unified nanopore-based sequencing assay integrating real-time, intraoperative methylome classification and next-day comprehensive molecular brain tumour profiling for ultra-rapid tumour diagnostics
Authors: Deacon S , Cahyani I , Holmes N , Fox G , Munro R , Wibowo S , Murray T , Mason H , Housley M , Martin D , Sharif A , Patel A , Goldspring R , Brandner S , Sahm F , Smith S , Paine SML , Loose M 
Published: September 2024

AbstractBackgroundAdvances in our technological capacity to interrogate brain tumour biology has led to the ever-increasing use of genomic sequencing in routine diagnostic decision making. Presently, brain tumours are routinely classified based on their epigenetic signatures, leading to a paradigm shift in diagnostic pathways. Such testing can be performed so rapidly using nanopore sequencing that results can be provided intraoperatively. This information greatly improves upon the fidelity of smear diagnosis and can help surgeons tailor their approach, balancing the risks of surgery with the likely benefit. Nevertheless, full integrated diagnosis may require subsequent additional assays to detect pathognomonic somatic mutations and structural variants, thereby delaying the time to final diagnosis.MethodsHere, we present ROBIN, a tool based upon PromethION nanopore sequencing technology that can provide both real-time, intraoperative methylome classification and next-day comprehensive molecular profiling within a single assay. ROBIN uniquely integrates three methylation classifiers1–3to improve diagnostic performance in the intraoperative setting.FindingsWe demonstrate classifier performance on 50 prospective intraoperative cases, achieving a diagnostic turnaround time under 2 hours and generating robust tumour classifications within minutes of sequencing. Furthermore, ROBIN can detect single nucleotide variants (SNVs), copy number variants (CNVs) and structural variants (SVs) in real-time, and is able to inform a complete integrated diagnosis within 24 hours. Classifier performance demonstrated concordance with final integrated diagnosis in 90% of prospective cases.InterpretationNanopore sequencing can greatly improve upon the turnaround times for standard of care diagnostic testing, including sequencing, and is furthermore able to reliably provide clinically actionable intraoperative tumour classification.FundingThe Jean-Shanks Foundation, the Pathological Society of Great Britain and Ireland, the British Neuropathological Society, and the Wellcome Trust.
Cardiovascular Risk Factors in Nurses at a Teaching Hospital
Authors: Kleebank Fernandes Lucas , Brasil Nobre Chaves Rangel Gisele , Luís Martins Renan , Fernando Martin Danilo , Fernandes de Godoy Moacir 
Published: September 2024

ABSTRACTObjectiveTo identify the prevalence of modifiable and non-modifiable risk factors related to cardiovascular diseases [CVDs] in the nursing team of a tertiary hospital in the interior of the state of São Paulo and suggest preventive practices.MethodsThis is a prospective-analytical epidemiological study, of a quantitative nature, carried out on 226 employees, in two stages: collection of self-declared data and measurement of anthropometric data.ResultsRisk factors such as family history of CVD (82.7%), alcoholism (57.1%), sedentary lifestyle (49.1%), insufficient sleep time (27.9%), high consumption of processed meals (98.2%) and sugary beverages (81.7%) were observed, among others. From anthropometric data, it was identified that 69.4% of participants are overweight (38.7%) or obese (30.6%) - evidenced by high waist circumference (48.6%) and a high waist-to-hip ratio (64.0%) - in addition to 17.1% who had blood pressure levels indicative of arterial hypertension. The majority reported not having a diagnosis of CVDs (76.1%), however, among those who do, more than half (53.7%) do not treat them properly.ConclusionIt is observed that the prevalence of CVDs is not irrelevant in the group evaluated and that there is the presence of risk factors indicating a tendency for participants to develop new CVDs or worsen existing ones, due to the presence of harmful habits associated with an unhealthy lifestyle and lack of adherence to treatments. This study suggests the implementation of multidisciplinary action programs with employees, so that the main areas identified as deficient are addressed.