microGalaxy: A gateway to tools, workflows, and training for reproducible and FAIR analysis of microbial data.

Microbial research generates vast and complex data from diverse omics technologies, necessitating innovative analytical solutions. microGalaxy (Galaxy for Microbiology) addresses these needs with a user-friendly platform that integrates >220 tool suites and >65 curated workflows for microbial analyses, including taxonomic profiling, assembly, annotation, and functional analysis. Hosted on the main EU Galaxy server (microgalaxy.

Investigating proteogenomic divergence in patient-derived xenograft models of ovarian cancer.

Within ovarian cancer research, patient-derived xenograft (PDX) models recapitulate histologic features and genomic aberrations found in original tumors. However, conflicting data from published studies have demonstrated significant transcriptional differences between PDXs and original tumors, challenging the fidelity of these models. We employed a quantitative mass spectrometry-based proteomic approach coupled with generation of patient-specific databases using RNA-seq data to investigate the proteogenomic landscape of serially-passaged PDX models established from two patients with distinct subtypes of ovarian cancer.

Evaluation of methotrexate Pharmacogenomic variation to predict acute neurotoxicity in children with acute lymphoblastic leukemia.

Background: Methotrexate is an important component of curative therapy in childhood acute lymphoblastic leukemia (ALL), but the role of genetic variation influencing methotrexate clearance and transport in toxicity susceptibility in children with ALL is not well established. Therefore, we evaluated the association between suspected methotrexate pharmacogenomic variants and methotrexate-related neurotoxicity.

Methods: This study included children (aged 2-20 years) diagnosed with ALL (2005-2019) at six treatment centers in the southwest United States.

Acute Muscle Weakness in Graves' Disease: A Case Report of Hypokalemic Thyrotoxic Periodic Paralysis.

Thyrotoxic periodic paralysis (TPP) is a rare but significant complication of hyperthyroidism, characterized by episodes of muscle weakness or paralysis and associated hypokalemia. This case report details a 30-year-old Latin American male with a history of Graves' disease, presenting with acute muscle weakness and hypokalemia. The patient reported transient episodes of weakness over recent weeks, culminating in a severe episode prompting emergency evaluation.

Diffuse Glioneuronal Tumor With Oligodendroglioma-Like Features and Nuclear Clusters Relapse in a Seven-Year-Old Boy: An Unusual Case Exhibiting Near-Tetraploidy and Chromosome 14 Diploidy.

Diffuse glioneuronal tumor with oligodendroglioma-like features and nuclear clusters (DGONC) is a rare brain tumor of the central nervous system (CNS). Although only a few cases of DGONC have been reported following the initial description of the tumor, they have a distinct DNA methylation pattern and share a recurrent chromosomal finding of monosomy 14. We encountered a seven-year-old boy who presented with seizures and was found to have a left frontal and suprasellar mass.

Sexually dimorphic metabolic effects of a high fat diet on knee osteoarthritis in mice.

Background: Women have a higher risk of developing osteoarthritis (OA) than men, including with obesity. To better understand this disparity, we investigated sex differences in metabolic and inflammatory factors associated with OA using a diet-induced mouse model of obesity. We hypothesized that 20 weeks of high-fat diet (HFD) would induce sexually dimorphic changes in both systemic and local risk factors of knee OA.

Anhedonia in flux: Understanding the associations of emotion regulation and anxiety with anhedonia dynamics in a sample with major depressive disorder.

Negative rumination and emotion regulation difficulties have been consistently linked with depression. Despite anhedonia-the lack of interest in pleasurable experiences-being a cardinal symptom of depression, emotion regulation of positive emotions, including dampening, are considered far less in the literature. Given that anhedonia may manifest through blunted responses to previously positive or enjoyable experiences, it is vital to understand how different positive emotion regulation strategies impact anhedonia symptom severity and how it can vary or change over time.

Comprehensive protease specificity profiling.

Protease enzymes are of great importance in medicine, industry, and as research tools. Despite the crucial need for detailed knowledge of their proteolytic cleavage specificity, many proteases are poorly characterized. We present a method for fully characterizing the cleavage specificity of proteases through the comprehensive profiling of all possible permutations of octamer peptide substrates in a single experiment.

School food policy in secondary schools in England and its impact on adolescents' diets and dental health: the FUEL multiple-methods study.

Background: School food standards are a legal requirement for state-funded schools in England and are designed to promote healthy eating in pupils. However, state-funded academies/free schools established between 2010 and 2014 are exempt from this legislation. To complement the school food standards, the government launched the School Food Plan in 2013, which outlines voluntary actions that schools can take to support healthy eating and increase school meal uptake.

Treatment of Mild to Severe Acne Vulgaris With a 650-Microsecond 1064-nm Nd:YAG Laser.

Background: Effective treatment of acne remains a challenge to dermatologists.

Objective: To evaluate the efficacy and tolerability of a 650-microsecond, pulsed 1064-nm Nd:YAG laser therapy for mild to severe facial acne vulgaris.

Methods: Human subjects of Fitzpatrick skin types I to VI with mild, moderate, or severe acne enrolled in the prospective, single-center study.

National school food standards in England: a cross-sectional study to explore compliance in secondary schools and impact on pupil nutritional intake.

Background: Many countries have introduced school food standards to improve the dietary intakes of school-aged children. England has school food standards (SFS) legislation in place but little is known about how well secondary schools comply with this. We aimed to assess compliance with the SFS legislation in English secondary schools and explore the impact of the SFS on pupils' nutritional intake.

Discovering Novel Proteoforms Using Proteogenomic Workflows Within the Galaxy Bioinformatics Platform.

Proteogenomics is a growing "multi-omics" research area that combines mass spectrometry-based proteomics and high-throughput nucleotide sequencing technologies. Proteogenomics has helped in genomic annotation for organisms whose complete genome sequences became available by using high-throughput DNA sequencing technologies. Apart from genome annotation, this multi-omics approach has also helped researchers confirm expression of variant proteins belonging to unique proteoforms that could have resulted from single-nucleotide polymorphism (SNP), insertion and deletions (Indels), splice isoforms, or other genome or transcriptome variations.

A constitutional isomer selective chemical proteomic strategy for system-wide profiling of protein lysine 5-hydroxylation.

Lysine 5-hydroxylation (5-Hyl) has been well recognized as an essential protein post-translational modification regulating cellular structural stability, RNA alternative splicing and epigenetic gene expression. System-wide enrichment and quantification of 5-Hyl targets have been challenging due to their chemical inert nature and difficulties in differentiating structural isomers in a complex biological sample. Here, we report the development of an efficient chemical proteomic workflow for affinity enrichment and constitutional isomer specific profiling of endogenous 5-Hyl substrates based on highly selective periodate chemistry.

Data-Independent Acquisition Mass Spectrometry as a Tool for Metaproteomics: Interlaboratory Comparison Using a Model Microbiome.

Mass spectrometry (MS)-based metaproteomics is used to identify and quantify proteins in microbiome samples, with the frequently used methodology being Data-Dependent Acquisition mass spectrometry (DDA-MS). However, DDA-MS is limited in its ability to reproducibly identify and quantify lower abundant peptides and proteins. To address DDA-MS deficiencies, proteomics researchers have started using Data-Independent Acquisition Mass Spectrometry (DIA-MS) for reproducible detection and quantification of peptides and proteins.

The impact of social deprivation on development and progression of diabetic kidney disease.

Introduction: Diabetes is one of the leading causes of chronic kidney disease. Social deprivation is recognised as a risk factor for complications of diabetes, including diabetic kidney disease. The effect of deprivation on rate of decline in renal function has not been explored in the Irish Health System to date.

Comparing the Diagnostic Yield of Germline Exome Versus Panel Sequencing in the Diverse Population of the Texas KidsCanSeq Pediatric Cancer Study.

Purpose: To evaluate the relative diagnostic yield of clinical germline genomic tests in a diverse pediatric cancer population.

Patients And Methods: The KidsCanSeq study enrolled pediatric cancer patients across six sites in Texas. Germline analysis included both exome sequencing and a therapy-focused pediatric cancer gene panel.

Novel approach to exploring protease activity and targets in HIV-associated obstructive lung disease using combined proteomic-peptidomic analysis.

Background: Obstructive lung disease (OLD) is increasingly prevalent among persons living with HIV (PLWH). However, the role of proteases in HIV-associated OLD remains unclear.

Methods: We combined proteomics and peptidomics to comprehensively characterize protease activities.

Teaming up to overcome challenges toward translation of new therapeutics for osteoarthritis.

As a leading global cause of musculoskeletal-related disability, osteoarthritis (OA) represents a public health urgency. Understanding of disease pathogenesis has advanced substantially in the past decade, yet no disease-modifying therapeutics have advanced to the clinic. To address this challenge, the CARE-AP (Cartilage Repair strategies to alleviate Arthritis Pain) collaborative research team was convened to bring together relevant multidisciplinary expertise and perspectives from across the VA research community nationwide.

MoodCapture: Depression Detection Using In-the-Wild Smartphone Images.

MoodCapture presents a novel approach that assesses depression based on images automatically captured from the front-facing camera of smartphones as people go about their daily lives. We collect over 125,000 photos in the wild from N=177 participants diagnosed with major depressive disorder for 90 days. Images are captured naturalistically while participants respond to the PHQ-8 depression survey question: .

Intravenous Golimumab in Children With Polyarticular-Course Juvenile Idiopathic Arthritis: Long-Term Extension of an Open-Label Phase III Study.

Objective: To report pharmacokinetics (PK), immunogenicity, clinical effect, and safety of intravenous (IV) golimumab in children with active polyarticular-course juvenile idiopathic arthritis (pcJIA) who participated in A Study to Evaluate the Pharmacokinetics, Efficacy and Safety of Intravenous Golimumab in Pediatric Participants With Active Polyarticular Course Juvenile Idiopathic Arthritis Despite Methotrexate Therapy (GO-VIVA)'s open-label, long-term extension (LTE) through week 252.

Methods: GO-VIVA participants who continued IV golimumab (80 mg/m every 8 weeks) after week 52 were included. PK and safety were assessed through week 244 (last dose) and week 252, respectively, and clinical response through week 116.