Nextflow4MS-DIAL: A Reproducible Nextflow-Based Workflow for Liquid Chromatography-Mass Spectrometry Metabolomics Data Processing.

Reproducibility in untargeted metabolomics data processing remains a significant challenge due to software limitations and the complex series of steps required. To address these issues, we developed Nextflow4MS-DIAL, a reproducible workflow for liquid chromatography-mass spectrometry (LC-MS) metabolomics data processing, validated with publicly available data from MetaboLights (MTBLS733). Nextflow4MS-DIAL automates LC-MS data processing to minimize human errors from manual data handling.

Metals in Motion: Understanding Labile Metal Pools in Bacteria.

Metal ions are essential for all life. In microbial cells, potassium (K) is the most abundant cation and plays a key role in maintaining osmotic balance. Magnesium (Mg) is the dominant divalent cation and is required for nucleic acid structure and as an enzyme cofactor.

Short-term Patient-Reported Outcomes Following Bilateral Risk-Reducing Mastectomy for Patients at a High Risk for Breast Cancer: A Systematic Review.

Background: Bilateral risk-reducing mastectomies (RRMs) have been proven to decrease the risk of breast cancer in patients at high risk owing to family history or having pathogenic genetic mutations. However, few resources with consolidated data have detailed the patient experience following surgery. This systematic review features patient-reported outcomes for patients with no breast cancer history in the year after their bilateral RRM.

Serial biomarker measurements may be helpful to predict the successful application of high flow nasal cannula in COVID-19 pneumonia patients.

High flow nasal cannula (HFNC) can reduce the need for intubation in patients with coronavirus disease-19 (COVID-19) pneumonia induced acute hypoxemic respiratory failure (AHRF), but predictors of HFNC success could be characterized better. C-reactive protein (CRP) and D-dimer are associated with COVID-19 severity and progression. However, no one has evaluated the use of serial CRP and D-dimer ratios to predict HFNC success.

Data from the All of Us research program reinforces existence of activity inequality.

Large-scale and detailed analyses of activity in the United States (US) remain limited. In this work, we leveraged the comprehensive wearable, demographic, and survey data from the All of Us Research Program, the largest and most diverse population health study in the US to date, to apply and extend the previous global findings on activity inequality within the context of the US. We found that daily steps differed by sex at birth, age, body characteristics, geography, and built environment.

N2GNet tracks gait performance from subthalamic neural signals in Parkinson's disease.

Adaptive deep brain stimulation (DBS) provides individualized therapy for people with Parkinson's disease (PWP) by adjusting the stimulation in real-time using neural signals that reflect their motor state. Current algorithms, however, utilize condensed and manually selected neural features which may result in a less robust and biased therapy. In this study, we propose Neural-to-Gait Neural network (N2GNet), a novel deep learning-based regression model capable of tracking real-time gait performance from subthalamic nucleus local field potentials (STN LFPs).

Treatment patterns for chronic obstructive pulmonary disease under the tiered medical system.

China has implemented the "tiered medical services" policy since 2015, while there is a paucity of data evaluating the the current status of chronic obstructive pulmonary disease (COPD) management under the system. Characteristics and treatments from 11,905 COPD patients in 88 hospitals across different tiers in China were included and analyzed. We assessed the statistical significance of differences by one way analysis of variance (ANOVA) for continuous variables and with the chi-squared test for categorical variables.

Unsupervised self-organising map classification of Raman spectra from prostate cell lines uncovers substratified prostate cancer disease states.

Prostate cancer is a disease which poses an interesting clinical question: Should it be treated? Only a small subset of prostate cancers are aggressive and require removal and treatment to prevent metastatic spread. However, conventional diagnostics remain challenged to risk-stratify such patients; hence, new methods of approach to biomolecularly sub-classify the disease are needed. Here we use an unsupervised self-organising map approach to analyse live-cell Raman spectroscopy data obtained from prostate cell-lines; our aim is to exemplify this method to sub-stratify, at the single-cell-level, the cancer disease state using high-dimensional datasets with minimal preprocessing.

Connecting genomic results for psychiatric disorders to human brain cell types and regions reveals convergence with functional connectivity.

Identifying cell types and brain regions critical for psychiatric disorders and brain traits is essential for targeted neurobiological research. By integrating genomic insights from genome-wide association studies with a comprehensive single-cell transcriptomic atlas of the adult human brain, we prioritized specific neuronal clusters significantly enriched for the SNP-heritabilities for schizophrenia, bipolar disorder, and major depressive disorder along with intelligence, education, and neuroticism. Extrapolation of cell-type results to brain regions reveals the whole-brain impact of schizophrenia genetic risk, with subregions in the hippocampus and amygdala exhibiting the most significant enrichment of SNP-heritability.

Spontaneous base flipping helps drive Nsp15's preferences in double stranded RNA substrates.

Coronaviruses evade detection by the host immune system with the help of the endoribonuclease Nsp15, which regulates levels of viral double stranded RNA by cleaving 3' of uridine (U). While prior structural data shows that to cleave double stranded RNA, Nsp15's target U must be flipped out of the helix, it is not yet understood whether Nsp15 initiates flipping or captures spontaneously flipped bases. We address this gap by designing fluorinated double stranded RNA substrates that allow us to directly relate a U's sequence context to both its tendency to spontaneously flip and its susceptibility to cleavage by Nsp15.

Managing xylazine-involved overdoses in a community harm reduction setting: lessons from Tijuana, Mexico.

Background: Xylazine is a α2-adrenergic receptor agonist, used for sedation in veterinary contexts. Although it is increasingly found in overdose deaths across North America, the clinical management of xylazine-involved overdoses has not been extensively studied, especially in community-based harm reduction settings. Here we present a clinical series of xylazine-involved overdose and share the clinical approach and lessons learned by a community overdose response team in Tijuana, Mexico amidst the arrival of xylazine.

Measuring the uptake of clinic-based HIV treatment and prevention services following HIV testing and referral at private pharmacies in Kenya.

Background: Despite their ubiquity across sub-Saharan Africa, private pharmacies are underutilized for HIV service delivery beyond the sale of HIV self-test kits. To understand what uptake of HIV prevention and treatment services might look like if private pharmacies offered clients free HIV self-testing and referral to clinic-based HIV services, we conducted a pilot study in Kenya.

Methods: At 20 private pharmacies in Kisumu County, Kenya, pharmacy clients (≥ 18 years) purchasing sexual health-related products (e.

Exploring the potential of machine learning models to predict nasal measurements through facial landmarks.

Statement Of Problem: Information on predicting the measurements of the nose from selected facial landmarks to assist in maxillofacial prosthodontics is lacking.

Purpose: The objective of this study was to identify the efficiency of machine learning models in predicting the length and width of the nose from selected facial landmarks.

Material And Methods: Two-dimensional frontal and lateral photographs were made of 100 men and 100 women.

Continent catheterizable channels: Does "hitching" the bladder reduce complications?

Background: Continent catheterizable channels (CCC) are a mainstay for reconstruction in patients with neurogenic bladders. Common complications include false passage, channel stenosis/difficult catheterization, channel incontinence, and stomal stenosis. This may result in the need for surgical revision or replacement.

Hand therapy utilization following digital flexor tendon repair: Trends, timing, predictive factors, and association with reoperation.

Background: Physical rehabilitation is considered an important component of recovery following digital flexor tendon repair (FTR), but no studies have thoroughly characterized nationwide therapy utilization in the United States.

Purpose: The current study characterized national trends in the timing and amount of hand therapy utilization following FTR and assessed factors associated with the lack of postoperative hand therapy.

Study Design: Retrospective cohort study.

Evaluation and Treatment of Nasal Valve Compromise in non-Caucasian Rhinoplasty.

The number of non-Caucasian patients with nasal valve compromise seeking functional rhinoplasty is projected to increase in tandem with an increasingly diverse population in the United States. Gaining a deeper appreciation for the variances in nasal morphology amongst different ethnicities will help rhinoplasty surgeons perform accurate preoperative evaluations, optimize functional and esthetic outcomes, and maintain ethnic congruence with surgery.

Imprecision nutrition? Intraindividual variability of glucose responses to duplicate presented meals in adults without diabetes.

Background: Continuous glucose monitors (CGMs) are used to characterize postprandial glucose responses and provide personalized dietary advice to minimize glucose excursions. The efficacy of such advice depends on reliable glucose responses.

Objectives: To explore within-subject variability of CGM responses to duplicate presented meals in an inpatient setting.

Reliability and reproducibility of systematic reviews informing the 2020-2025 Dietary Guidelines for Americans: a pilot study.

Background: Although high-quality nutrition systematic reviews (SRs) are important for clinical decision making, there remains debate on their methodological quality and reporting transparency.

Objectives: The objective of this study was to assess the reliability and reproducibility of a sample of SRs produced by the Nutrition Evidence Systematic Review (NESR) team to inform the 2020-2025 Dietary Guidelines for Americans (DGAs).

Methods: We evaluated a sample of 8 SRs from the DGA dietary patterns subcommittee for methodological quality using the Assessment of Multiple Systematic Reviews 2 (AMSTAR 2) tool and for reporting transparency using the PRISMA 2020 and PRISMA literature search extension (PRISMA-S) checklists.

Genetic Insights Into Coronary Microvascular Disease.

Coronary microvascular disease (CMVD) affects the coronary pre-arterioles, arterioles, and capillaries and can lead to blood supply-demand mismatch and cardiac ischemia. CMVD can present clinically as ischemia or myocardial infarction with no obstructive coronary arteries (INOCA or MINOCA, respectively). Currently, therapeutic options for CMVD are limited, and there are no targeted therapies.

MRI Free Targeting of Deep Brain Structures in the Anterior Cingulate Cortex Using Facial Landmarks.

Emerging neurostimulation methods aim to selectively modulate deep brain structures. Guiding these therapies has presented a substantial chal- lenge, since imaging modalities such as MRI limit the spectrum of benefi- ciaries. In this study, we assess the guidance accuracy of a neuronavigation method that does not require taking MRI scans.

Altered thalamotemporal structural connectivity is associated with autistic traits in children with ASD.

Background: Thalamocortical functional and structural connectivity alterations may contribute to clinical phenotype of Autism Spectrum Disorder. As previous studies focused mainly on thalamofrontal connections, we comprehensively investigated between-group differences of thalamic functional networks and white matter pathways projecting also to temporal, parietal, occipital lobes and their associations with core and co-occurring conditions of this population.

Methods: A total of 38 children (19 with Autism Spectrum Disorder) underwent magnetic resonance imaging and behavioral assessment.