Complete genomes of the hydrogenotrophic methanogen species Pt1 and Ki8-1.

species grow within sheaths containing 1-50 or more cells and often in association with syntrophic bacteria that together metabolize a variety of aliphatic and aromatic compounds. Here, we report the complete genomes of Pt1 Ki8-1.

Whole genome sequence of the syntrophic benzoate-degrading bacterium, DSM 102354.

The syntrophic obligate proton-reducing bacterium DSM 102354, isolated from anaerobic digester sludge, degrades benzoate and possibly hydrocinnamate (phenyl-3-propionate) when grown with a suitable hydrogenotrophic partner. The complete genome sequence data provide insight regarding aromatic compound degradation under thermodynamically limiting conditions when exogenous electron acceptors are absent.

Clustering and classification of early knee osteoarthritis using machine-learning analysis of step-up and down test kinematics in recreational table tennis players.

Objective: Early detection of knee osteoarthritis is crucial for improving patient outcomes. While conventional imaging methods often fail to detect early changes and require specialized expertise for interpretation, this study aimed to investigate the use of frontal plane kinematic data during step-up (SU) and step-down (SD) tests to classify and predict early osteoarthritis (EOA) using machine-learning techniques.

Methods: Forty-three recreational table tennis players (eighty-six legs: 42 with EOA and 44 without EOA) underwent SU and SD tests.

Olfactory ensheathing cells from adult female rats are hybrid glia that promote neural repair.

Olfactory ensheathing cells (OECs) are unique glial cells found in both central and peripheral nervous systems where they support continuous axonal outgrowth of olfactory sensory neurons to their targets. Previously, we reported that following severe spinal cord injury, OECs transplanted near the injury site modify the inhibitory glial scar and facilitate axon regeneration past the scar border and into the lesion. To better understand the mechanisms underlying the reparative properties of OECs, we used single-cell RNA-sequencing of OECs from adult rats to study their gene expression programs.

Machine learning for clustering and classification of early knee osteoarthritis using single-leg standing kinematics.

Objective: Detection of early osteoarthritis (EOA) of the knee is crucial for effective management and improved outcomes. This study investigated the application of machine learning techniques to single-leg standing (SLS) kinematics to classify and predict EOA. (1) To identify distinct groups based on SLS kinematic patterns using unsupervised learning algorithms, (2) to develop supervised learning models to predict EOA status, and (3) to identify the most influential kinematic variables associated with EOA.

Evaluating pelvic rotator strength: Investigating asymmetry and its correlation with pelvic rotation angle during active straight leg raise.

Background: Although lumbopelvic rotation control muscle is important to maintain pelvic neutral alignment during active straight leg raise (ASLR), pelvic rotator strength has not been evaluated. Thus, a novel method is needed to measure pelvic rotator strength and to determine whether pelvic rotator muscle asymmetry is related to side difference in transverse plane pelvic rotation angle (TrPRA) during ASLR.

Objective: To find average pelvic rotator strength, verify the reliability of pelvic rotator strength measurement method, and identify the correlation between pelvic rotator strength asymmetry and side difference in TrPRA during ASLR.

Gut-microbiota-based ensemble model predicts prognosis of pediatric inflammatory bowel disease.

Developing microbiome-based markers for pediatric inflammatory bowel disease (PIBD) is challenging. Here, we evaluated the diagnostic and prognostic potential of the gut microbiome in PIBD through a case-control study and cross-cohort analyses. In a Korean PIBD cohort (24 patients with PIBD, 43 controls), we observed that microbial diversity and composition shifted in patients with active PIBD versus controls and recovered at remission.

Complete genomes of SNA2 and sp. cycad4: microbes with the potential for plant growth promotion.

species have been isolated from various environments, often in association with plants. Here, we report the complete genomes of SNA2 and sp. cycad4.

A genomic analysis reveals the diversity of cellulosome displaying bacteria.

Introduction: Several species of cellulolytic bacteria display cellulosomes, massive multi-cellulase containing complexes that degrade lignocellulosic plant biomass (LCB). A greater understanding of cellulosome structure and enzyme content could facilitate the development of new microbial-based methods to produce renewable chemicals and materials.

Methods: To identify novel cellulosome-displaying microbes we searched 305,693 sequenced bacterial genomes for genes encoding cellulosome proteins; dockerin-fused glycohydrolases (DocGHs) and cohesin domain containing scaffoldins.

Complete genome of sp. EBFNA2, isolated from a surface-sterilized fava bean nodule.

We report the complete genome sequence of sp. EBFNA2, a fava bean nodule endophyte. The strain appears to be a new species, and its genome provides insight into its interactions with host plants and potential to promote plant growth and crop yield.

DNA contamination within recombinant adeno-associated virus preparations correlates with decreased CD34 cell clonogenic potential.

Recombinant adeno-associated viruses (rAAV) are promising for applications in many genome editing techniques through their effectiveness as carriers of DNA homologous donors into primary hematopoietic stem and progenitor cells (HSPCs), but they have many outstanding concerns. Specifically, their biomanufacturing and the variety of factors that influence the quality and consistency of rAAV preps are in question. During the process of rAAV packaging, a cell line is transfected with several DNA plasmids that collectively encode all the necessary information to allow for viral packaging.

Genome of 55, a desert-isolated microbe with plant growth-promoting properties for grain crops.

Here, we report the genome sequence of 55, isolated from the Negev Desert, Israel. 55 was found to promote the growth of several cereal crops (corn, wheat, and pearl millet) in greenhouse and field studies.

Complete genomes of two endophytes isolated from surface-sterilized alfalfa nodules.

species catabolize a wide range of natural and industrial products and have been shown to be integral rhizosphere inhabitants. Here, we report the complete genomes of 2u118 and . sp.

Data-driven decomposition and staging of flortaucipir uptake in Alzheimer's disease.

Introduction: Previous approaches pursuing in vivo staging of tau pathology in Alzheimer's disease (AD) have typically relied on neuropathologically defined criteria. In using predefined systems, these studies may miss spatial deposition patterns which are informative of disease progression.

Methods: We selected discovery (n = 418) and replication (n = 132) cohorts with flortaucipir imaging.

Relationships and Mendelian Randomization of Gut Microbe-Derived Metabolites with Metabolic Syndrome Traits in the METSIM Cohort.

The role of gut microbe-derived metabolites in the development of metabolic syndrome (MetS) remains unclear. This study aimed to evaluate the associations of gut microbe-derived metabolites and MetS traits in the cross-sectional Metabolic Syndrome In Men (METSIM) study. The sample included 10,194 randomly related men (age 57.

Olfactory ensheathing cells from adult female rats are hybrid glia that promote neural repair.

Olfactory ensheathing cells (OECs) are unique glial cells found in both central and peripheral nervous systems where they support continuous axonal outgrowth of olfactory sensory neurons to their targets. Previously we reported that following severe spinal cord injury, OECs transplanted near the injury site modify the inhibitory glial scar and facilitate axon regeneration past the scar border and into the lesion. To better understand the mechanisms underlying the reparative properties of OECs, we used single-cell RNA-sequencing of OECs from adult rats to study their gene expression programs.

Patterns of Glucose Metabolism in [ F]FDG PET Indicate Regional Variability and Neurodegeneration in the Progression of Alzheimer's Dementia.

Unlabelled: In disorders of cognitive impairment, such as Alzheimer's disease, neurodegeneration is the final common pathway of disease progression. Modulating, reversing, or preventing disease progression is a clinical imperative most likely to succeed following accurate and explanatory understanding of neurodegeneration, requiring enhanced consistency with quantitative measurements and expanded interpretability of complex data. The on-going study of neurodegeneration has robustly demonstrated the advantages of accumulating large amounts of clinical data that include neuroimaging, motiving multi-center studies such as the Alzheimer's Disease Neuroimaging Initiative (ADNI).

Ketogenic diet therapy for pediatric epilepsy is associated with alterations in the human gut microbiome that confer seizure resistance in mice.

The gut microbiome modulates seizure susceptibility and the anti-seizure effects of the ketogenic diet (KD) in animal models, but whether these relationships translate to KD therapies for human epilepsy is unclear. We find that the clinical KD alters gut microbial function in children with refractory epilepsy. Colonizing mice with KD-associated microbes promotes seizure resistance relative to matched pre-treatment controls.

Prostate lineage-specific metabolism governs luminal differentiation and response to antiandrogen treatment.

Lineage transitions are a central feature of prostate development, tumourigenesis and treatment resistance. While epigenetic changes are well known to drive prostate lineage transitions, it remains unclear how upstream metabolic signalling contributes to the regulation of prostate epithelial identity. To fill this gap, we developed an approach to perform metabolomics on primary prostate epithelial cells.

Scalable NMF via linearly optimized data compression.

Orthonormal projective non-negative matrix factorization (opNMF) has been widely used in neuroimaging and clinical neuroscience applications to derive representations of the brain in health and disease. The non-negativity and orthonormality constraints of opNMF result in intuitive and well-localized factors. However, the advantages of opNMF come at a steep computational cost that prohibits its use in large-scale data.

Scalable Orthonormal Projective NMF via Diversified Stochastic Optimization.

The increasing availability of large-scale neuroimaging initiatives opens exciting opportunities for discovery science of human brain structure and function. Data-driven techniques, such as Orthonormal Projective Non-negative Matrix Factorization (opNMF), are well positioned to explore multivariate relationships in big data towards uncovering brain organization. opNMF enjoys advantageous interpretability and reproducibility compared to commonly used matrix factorization methods like Principal Component Analysis (PCA) and Independent Component Analysis (ICA), which led to its wide adoption in clinical computational neuroscience.

Machine learning to predict ceftriaxone resistance using single nucleotide polymorphisms within a global database of genomes.

Antimicrobial resistance in is an urgent global health issue. The objectives of the study were to use a global collection of 12,936 . genomes from the PathogenWatch database to evaluate different machine learning models to predict ceftriaxone susceptibility/decreased susceptibility using 97 mutations known to be associated with ceftriaxone resistance.

Neurotoxicity of diesel exhaust extracts in zebrafish and its implications for neurodegenerative disease.

Long-term air pollution (AP) exposure, including diesel exhaust exposure, is increasingly being recognized as a major contributor to the development of neurodegenerative diseases such as Parkinson's and Alzheimer's disease. How AP increases the risk of neurodegeneration is not well understood but might include direct neurotoxicity and CNS inflammation. We investigated the impact of diesel exhaust particulate extract (DEPe) exposure on the brain and the mechanisms by which microglia and astroglia might mediate neuronal changes.