bluuebunny/crossref_metadata_2025_split huggingface dataset:
Persistent, Private and Mobile genes: a model for gene dynamics in evolving pangenomes
Authors: Gamblin Jasmine , Lambert Amaury , Blanquart François 
Published: July 2024

AbstractThe pangenome of a species is the set of all genes carried by at least one member of the species. In bacteria, pangenomes can be much larger than the set of genes carried by a single organism. Many questions remain unanswered regarding the evolutionary forces shaping the patterns of presence/absence of genes in pangenomes of a given species. We introduce a new model for bacterial pangenome evolution along a species phylogeny that explicitly describes the timing of appearance of each gene in the species and accounts for three generic types of gene evolutionary dynamics: persistent genes that are present in the ancestral genome, private genes that are specific to a given clade, and mobile genes that are imported once into the gene pool and then undergo frequent horizontal gene transfers. We call this model the Persistent-Private-Mobile (PPM) model. We develop an algorithm fitting the PPM model and apply it to a dataset of 902Salmonella entericagenomes. We show that the best fitting model is able to reproduce the global pattern of some multivariate statistics like the gene frequency spectrum and the parsimony vs. frequency plot. Moreover, the gene classification induced by the PPM model allows us to study the position of accessory genes on the chromosome depending on their category, as well as the gene functions that are most present in each category. This work paves the way for a mechanistic understanding of pangenome evolution, and the PPM model developed here could be used for dynamics-aware gene classification.
Variation in a microbial mutualist has transcriptional and phenotypic consequences for host-parasite interactions
Authors: Buxton-Martin Addison D. , Gluck-Thaler Emile , Yi Eunnuri , Stinchcombe John R. , Wood Corlett W. 
Published: July 2024

AbstractStrains of microbial symbionts often vary in their effect on their host. However, little is known about how the genetic variation in microbial symbiont populations impacts host interactions with other co-colonizing microbes. Here we investigated how different strains of nitrogen-fixing rhizobial bacteria affect their host plant’s response to parasitic root-knot nematodes in the legumeMedicago truncatula. Using dual RNAseq of the root organs harboring rhizobia or nematodes, we identified genes from plant host, rhizobia, and nematode whose expression differed between parasite-infected and -uninfected plants, and between plants inoculated with different rhizobial strains. At the site of host-parasite interactions (in nematode galls), hundreds of host genes and few nematode genes differed in expression between host plants inoculated with different rhizobia strains. At the site of host-mutualist interactions (in rhizobia nodules), hundreds of host genes and few rhizobial genes responded to parasite infection. The vast majority of parasite-induced changes in host gene expression depended on the resident rhizobia strain. We additionally observed phenotypic differences in the gall and nodule counts on host root systems and in some root architecture traits, showing that genetic variation in a mutualist symbiont impacted parasite colonization rates. The transcriptomic and phenotypic differences we observed suggest that microbial indirect genetic effects play an underappreciated role in structuring their host’s interactions with other co-colonizing microorganisms, which may be mediated by changes in host resource budgets, defense response, or developmental trajectories.
Insights into the role of root exudates in bacteriophage infection dynamics
Authors: Novak Vlastimil , van Winden Michelle C. M. , Harwood Thomas V. , Neurath Rachel , Kosina Suzanne M. , Louie Katherine B. , Sullivan Matthew B. , Roux Simon , Zengler Karsten , Mutalik Vivek K. , Northen Trent R. 
Published: July 2024

AbstractBacteriophages impact soil bacteria through lysis, altering the availability of organic carbon and plant nutrients. However, the magnitude of nutrient uptake by plants from lysed bacteria remains unknown, partly because this process is challenging to investigate in the field. In this study, we extend ecosystem fabrication (EcoFAB 2.0) approaches to study plant-bacteria-phage interactions by comparing the impact of phage-lysed and uninfected15N-labeled bacterial necromass on plant nitrogen acquisition and rhizosphere exometabolites composition. We show that grassBrachypodium distachyonderives some nitrogen from amino acids in uninfectedPseudomonas putidanecromass but not from virocell necromass. Additionally, the bacterial necromass elicits the formation of rhizosphere exometabolites, some of which (guanosine), alongside tested aromatic acids (p-coumaric and benzoic acid), show distinct effects on bacteriophage-induced lysis when testedin vitro. The study highlights the dynamic feedback between bacterial necromass and plants and suggests that root exudate metabolites can impact bacteriophage infection dynamics.
Psychometric Properties of the Spanish Simultaneous Alcohol and Cannabis Motives Measure (S-SACM) among Young Adults
Authors: Pérez Lucía Vélez , Márquez José Carmona , Ponce Bella M. González , Calderón Fermín Fernández 
Published: July 2024

AbstractBackgroundSimultaneous Alcohol and Cannabis (SAC) use is associated with greater negative consequences than individual use. Motives to use are robust predictors of alcohol and cannabis consumption, both separately and simultaneously. While instruments such as the SAC Motives Scale and its short form have recently been developed, no Spanish adaptation is currently available.AimsTo provide a Spanish adaptation of both versions of the simultaneous alcohol and cannabis motives measure and to examine its psychometric properties in a sample of young adults who simultaneously consume both substances.MethodA targeted sampling procedure was used to recruit 612 young cannabis users, of whom 479 reported SAC use (18-25 years old [M= 21.01,SD =2.14]; 36% female). Following adaptation and translation, participants completed the scale, along with measures of alcohol, cannabis, and simultaneous use, cannabis motives, and alcohol- and cannabis- related negative consequences.ResultsConfirmatory factor analyses showed a four-factor structure (conformity, positive effects, calm/coping, and social). Moreover, the results indicated acceptable internal consistency (.70 - .88), providing evidence of convergent, discriminant, and predictive validity for most dimensions.ConclusionsThe results suggest that both versions of the scale are valuable tools for assessing motives for SAC consumption among young adults. These scales could aid in investigating motives for SAC use and informing interventions to mitigate associated harms.Public Significance StatementThis study provides the first Spanish adapted-version measure to assess motives for Simultaneous Alcohol and Cannabis (SAC) consumption. Our findings support the use of this measure for assessing these motives and guiding interventions aimed at preventing or reducing SAC use and its negative consequences among Spanish-speaking young adults who use alcohol and cannabis simultaneously.
Low muscle strength is associated with cardiovascular autonomic neuropathy in patients with type 2 diabetes
Authors: Jung Chan-Hee , Cho Yoon Young , Choi Dug-Hyun , Kim Bo-Yeon , Jung Sang-Hee , Kim Chul-Hee , Mok Ji-Oh 
Published: July 2024

AbstractBackgroundSeveral studies have investigated whether sarcopenia is associated with diabetic microvascular complications, but very few have examined associations between sarcopenia and cardiovascular autonomic neuropathy (CAN) in patients with type 2 diabetes mellitus (T2DM). Therefore, we investigated associations of muscle strength (handgrip strength [HGS]) and mass (appendicular skeletal muscle mass index [ASMI]) and CAN in patients with T2DM.MethodsWe enrolled 342 T2DM patients (mean age 56.1±11.5 years; 58.2% male) in this retrospective, cross-sectional study. Cardiovascular reflex tests were used to assess CAN according to Ewing’s protocol. Relative HGS was determined after normalizing absolute HGS to body weight (HGS/body weight [kg]). We defined low HGS and low ASMI according to a consensus report of the Asian Group for Sarcopenia. Logistic regression analyses were carried out to assess the associations between relative HGS or ASMI quartiles and the presence of CAN in patients with T2DM.ResultsThe prevalence rates of CAN, low HGS, and low ASMI in the study subjects were 34.8%, 17.3%, and 18.7%, respectively. Low HGS was significantly more prevalent in patients with CAN than those without CAN (23.5% vs. 13.9%, p=0.025). The CAN scores were significantly and negatively correlated with relative HGS but not with ASMI. Relative HGS was negative correlated with age, glycated hemoglobin, fasting plasma glucose, hsCRP, body mass index, and HOMA-IR and positively correlated with ASMI. The prevalence of CAN gradually increased with decreasing quartile of relative HGS (28.4% in Q4, 31.8% in Q3, 34.2% in Q2, and 45.3% in Q1, p=0.02 for trend). Multivariable-adjusted prevalence ratios (PRs) for CAN, determined by comparing the first, second, and third quartiles with the fourth quartile of relative HGS, were 4.4 with a 95% confidence interval (95% CI) of [1.1 to 17.3]), 2.3 (95% CI [0.8 to 6.9]), and 1.2 (95% CI [0.4 to 3.7]), respectively. The prevalence of CAN and the PRs (95% [CI]) for CAN based on ASMI were not statistically significant.ConclusionsOur findings suggest that low muscle strength rather than low muscle mass was significantly associated with the presence of CAN. Therefore, HGS testing could help identify patients who would benefit from screening for earlier diagnosis of CAN.
Bibliometric analysis of emerging trend and top 100 most cited articles in primary central nervous system lymphoma
Authors: Geng Yibo , Liu Yiqi , Wang Yang , Li Xiong 
Published: July 2024

AbstractBackgroundOver the past thirty years, numerous studies on primary central nervous system lymphoma (PCNSL) have been conducted, encompassing epidemiology, diagnosis, treatment, and mechanisms. However, no bibliometric analysis has been performed in this field. Therefore, we conducted a bibliometric analysis to elucidate the evolution and current status of PCNSL research and identify the most-cited articles across various disciplines.Material and MethodsLiterature published between January 1992 and June 2024 in the Web of Science Core Collection (WoSCC) was extracted and classified. Three platforms (R-bibliometrix, VOSviewer, and Citespace) were used for the bibliometric analysis. Negative binomial regression was employed to establish a model for the risk ratio of citation.ResultsA total of 1,798 publications were included in the analysis. The annual number of publications has shown a steady increase over time. The United States emerged as the leading country in terms of both the number of publications and total citations. Among individual researchers, Hoang-Xuan Khe from Sorbonne University was the most prolific in terms of publication count, while Lisa M. DeAngelis from Memorial Sloan Kettering Cancer Center received the highest number of citations. The study titled “Report of an International Workshop to Standardize Baseline Evaluation and Response Criteria for Primary CNS Lymphoma” was identified as the most cited work in this field. Keyword analysis indicated that immune therapy and non-invasive diagnosis are the primary focal points of current research. Among the top 100 most-cited articles, interventional studies demonstrated a higher citation ratio (RR = 1.357, 95% CI 1.044-1.764, P=0.023), whereas chemoradiotherapy studies exhibited a lower citation ratio (RR = 0.763, 95% CI 0.603-0.965, P=0.024).ConclusionResearch hotspots and trends in PCNSL were identified and explored using bibliometric and visual methods. The highly cited articles across multiple disciplines related to PCNSL may help generate high-quality research ideas, particularly in the fields of immunotherapy and non-invasive diagnosis.
Seed banking alters native seed microbiome composition and function relative to natural populations
Authors: Russell Dylan , Rajabal Vaheesan , Alfonzetti Matthew , Van der Merwe Marlien M. , Gallagher Rachael V. , Tetu Sasha G. 
Published: July 2024

SUMMARYSeed banks are a vital resource for preserving plant species diversity globally. However, seedling establishment and survival rates from banked seeds can be poor. Despite a growing appreciation for the role of seed microbiota in supporting seed quality and plant health, our understanding of the effects of conventional seed banking processes on seed microbiomes remains limited.We investigated the composition and functional potential of the epiphytic seed microbiome of a native plant species using both 16S rRNA gene sequencing and culture-based approaches.Comparing the bacterial community composition of freshly collected seeds and those sourced from seed banking organisations, we found stored seeds hosted significantly less diverse bacterial populations, with substantial reductions in both low-abundance taxa and some core community members identified in unstored seeds. Bacteria with key plant growth promoting traits including IAA production, ACC deaminase activity, phosphate solubilisation, siderophore activity, and nitrogen fixation were identified in seed epiphytic communities, but these beneficial traits were less prevalent in stored seed compared to fresh seeds.Overall, these results suggest that epiphytic seed microbiomes may undergo significant changes during the storage process, selecting for bacteria tolerant to storage conditions, and potentially reducing the population of plant-growth promoting bacteria on seeds.
Prefrontal metabolite alterations in individuals with posttraumatic stress disorder: a 7T magnetic resonance spectroscopy study
Authors: Reid Meredith A. , Whiteman Sarah E. , Camden Abigail A. , Jeffirs Stephanie M. , Weathers Frank W. 
Published: July 2024

ABSTRACTBackgroundEvidence from animal and human studies suggests glutamatergic dysfunction in posttraumatic stress disorder (PTSD). The purpose of this study was to investigate glutamate abnormalities in the dorsolateral prefrontal cortex (DLFPC) of individuals with PTSD using 7T MRS, which has better spectral resolution and signal-to- noise ratio than lower field strengths, thus allowing for better spectral quality and higher sensitivity. We hypothesized that individuals with PTSD would have lower glutamate levels compared to trauma-exposed individuals without PTSD and individuals without trauma exposure. Additionally, we explored potential alterations in other neurometabolites and the relationship between glutamate and psychiatric symptoms.MethodsIndividuals with PTSD (n=27), trauma-exposed individuals without PTSD (n=27), and individuals without trauma exposure (n=26) underwent 7T MRS to measure glutamate and other neurometabolites in the left DLPFC. The severities of PTSD, depression, anxiety, and dissociation symptoms were assessed.ResultsWe found that glutamate was lower in the PTSD and trauma-exposed groups compared to the group without trauma exposure. Furthermore,N-acetylaspartate (NAA) was lower and lactate was higher in the PTSD group compared to the group without trauma exposure. Glutamate was negatively correlated with depression symptom severity in the PTSD group. Glutamate was not correlated with PTSD symptom severity.ConclusionIn this first 7T MRS study of PTSD, we observed altered concentrations of glutamate, NAA, and lactate. Our findings provide evidence for multiple possible pathological processes in individuals with PTSD. High-field MRS offers insight into the neurometabolic alterations associated with PTSD and is a powerful tool to probe trauma- and stress-related neurotransmission and metabolismin vivo.
Acid cleavable biotin-alkyne improves sensitivity for direct detection of biotin labeled peptides in BONCAT analysis
Authors: McClatchy Daniel B. , Yates John R. 
Published: July 2024

AbstractBONCAT (Biorthogonal noncanonical amino acid tagging) is a labeling strategy that covalently adds a biotin-alkyne (BA) to methionine analogs via a click reaction. When methionine analogs are incorporated into a proteome, enrichment of the BA-labeled proteins allows the detection of newly synthesized proteins (NSP) by mass spectrometry. We previously reported that using our Direct Detection of Biotin-containing Tags (DidBIT) strategy, protein identifications and confidence are increased by enriching for BA-peptides instead of BA-proteins. We compared cleavable BA (DADPS) and uncleavable BA in the identification and TMT quantification of NSP. More than fifty percent more proteins were identified and quantified using DADPS than with uncleavable BA. Interrogation of the data revealed that multiple factors are responsible for the superior performance of DADPS.
A novel c.515delCHSPB8-multisystem proteinopathy associated with inclusion body myopathy with cardiomyopathy
Authors: Tan Jiayan , Duong Han , Milone Margherita , Gibbs Liliane , Tedesco Barbara , Poletti Angelo , Kimonis Virginia 
Published: July 2024

AbstractMutations in theHSPB8, or heat shock protein family B (small) member 8, is a member of the chaperone-assisted selective autophagy complex and has recently been associated with rimmed vacuolar myopathy. We report a family with aHSPB8rimmed vacuolar myopathy caused by a novel c.515delC variant with progressive muscle weakness, pathological findings of rimmed vacuoles of muscle biopsy, and one individual who died of cardiomyopathy. Whole exome sequencing analyses revealed a c.515delC, resulting in a translational frameshift expected to elongate the protein by an additional 49 amino acid tail. We reviewed the clinical characteristics of all reported patients (N= 26, 15 males and 11 females) in the literature, and performed a genotype/phenotype analysis. Males in the families appeared to present with an earlier age of onset, more severe muscle weakness compared to females, and a higher prevalence of other organ system complications including cardiomyopathy in two males. In conclusion, this family expands the phenotype/genotype correlations inHSPB8-associated myopathy with rimmed vacuoles and c.515 delC. We note that c.515 appears to be a hot spot, and the phenotype appears to be more severe in males in this disease, with an earlier onset of the myopathy.
A Development Framework for Trustworthy Artificial Intelligence in Health with Example Code Pipelines
Authors: de-Manuel-Vicente Carlos , Fernández-Narro David , Blanes-Selva Vicent , García-Gómez Juan M , Sáez Carlos 
Published: July 2024

AbstractTechnological trends point to Artificial Intelligence (AI) as a crucial tool in healthcare, but its development must respect human rights and ethical standards to ensure robustness and safety. Despite general good practices are available, health AI developers lack a practical guide to address the construction of trustworthy AI. We introduce a development framework to serve as a reference guideline for the creation of trustworthy AI systems in health. The framework provides an extensible Trustworthy AI matrix that classifies technical methods addressing the EU guideline for Trustworthy AI requirements (privacy and data governance; diversity, non-discrimination and fairness; transparency; and technical robustness and safety) across the different AI lifecycle stages (data preparation; model development, deployment and use, and model management). The matrix is complemented with generic but customizable example code pipelines for the different requirements with state-of-the-art AI techniques using Python. A related checklist is provided to help validate the application of different methods on new problems. The framework is validated using two representative open datasets, and it is provided as Open Source to the scientific and development community. The presented framework provides health AI developers with a theoretical development guideline with practical examples, aiming to ensure the development of robust and safe health AI and Clinical Decision Support Systems. GitHub repository:https://github.com/bdslab-upv/trustworthy-ai
Democratizing Infectious Disease Modeling: An AI Assistant for Generating, Simulating, and Analyzing Dynamic Models
Authors: Proctor Joshua L. , Chabot-Couture Guillaume 
Published: July 2024

AbstractUnderstanding and forecasting infectious disease spread is pivotal for effective public health management. Traditional dynamic disease modeling is an essential tool for characterization and prediction, but often requires extensive expertise and specialized software, which may not be readily available in low-resource environments. To address these challenges, we introduce an AI-powered modeling assistant that utilizes advanced capabilities from OpenAI’s latest models and functionality. This tool enhances the accessibility and usability of infectious disease models and simulation frameworks by allowing users to generate or modify model configurations through intuitive natural language inputs or by importing explicit model descriptions. Our prototype integrates with an established open-source disease simulation framework called the Compartmental Modeling Software (CMS) to provide a seamless modeling experience from setup to analysis. The AI assistant efficiently interprets disease model parameters, constructs accurate model files, executes simulations in a controlled environment, and assists in result interpretation using advanced analytics tools. It encapsulates expert knowledge and adheres to best practices to support users ranging from novices to expert modelers. Furthermore, we discuss the limitations of this AI assistant, particularly its performance in complex scenarios where it might generate inaccurate specifications. By enhancing the ease of disease modeling and supporting ongoing capacity-building initiatives, we believe that AI assistants like this one could significantly contribute to global health efforts by empowering researchers, especially in regions with limited resources, to develop and refine their disease models independently. This innovative approach has the potential to democratize disease modeling in global health, offering a scalable solution that adapts to diverse needs across a wide-range of geographies, languages, and populations.