MjCyc: Rediscovering the pathway-genome landscape of the first sequenced archaeon, .

The genome of () DSM 2661 was the first Archaeal genome to be sequenced in 1996. Subsequent sequence-based annotation cycles led to its first metabolic reconstruction in 2005. Leveraging new experimental results and function assignments, we have now re-annotated creating an updated resource with novel information and testable predictions in a pathway-genome database available at BioCyc.

Extracorporeal Membrane Oxygenation in Children with Pulmonary Atresia and Intact Ventricular Septum: Mortality and Associated Outcomes.

Data on outcomes of extracorporeal membrane oxygenation (ECMO) are limited in patients with pulmonary atresia intact ventricular septum (PAIVS). The objective of this study was to describe the use of ECMO and the associated outcomes in patients with PAIVS. We retrospectively reviewed neonates with PAIVS who received ECMO between 2009 and 2019 in 19 US hospitals affiliated with the Collaborative Research for the Pediatric Cardiac Intensive Care Society (CoRe-PCICS).

The mediating role of processing speed on the relationship between executive functions and social cognition in relapsing-remitting multiple sclerosis patients.

This study examined the mediating role of processing speed between executive functions and social cognition in 67 relapsing-remitting multiple sclerosis (RRMS) patients. Executive functions were assessed using the Trail Making Test-Part B (TMT-B) and the Stroop Neuropsychological Screening Test (SNST); social cognition with the Reading the Mind in the Eyes Test (RMET); and processing speed with the Symbol Digit Modalities Test (SDMT). Mediated effects were explored using a series of regression analyses and were further confirmed through bootstrapping procedures.

BioTextQuest v2.0: An evolved tool for biomedical literature mining and concept discovery.

The process of navigating through the landscape of biomedical literature and performing searches or combining them with bioinformatics analyses can be daunting, considering the exponential growth of scientific corpora and the plethora of tools designed to mine PubMed(®) and related repositories. Herein, we present BioTextQuest v2.0, a tool for biomedical literature mining.

scRNA-Explorer: An End-user Online Tool for Single Cell RNA-seq Data Analysis Featuring Gene Correlation and Data Filtering.

In the majority of downstream analysis pipelines for single-cell RNA sequencing (scRNA-seq), techniques like dimensionality reduction and feature selection are employed to address the problem of high-dimensional nature of the data. These approaches involve mapping the data onto a lower-dimensional space, eliminating less informative genes, and pinpointing the most pertinent features. This process ultimately leads to a reduction in the number of dimensions used for downstream analysis, which in turn speeds up the computation of large-scale scRNA-seq data.

Comparison of Ductal Stent Versus Surgical Shunt as Initial Intervention for Neonates with Pulmonary Atresia with Intact Ventricular Septum.

Data comparing surgical systemic-to-pulmonary artery shunt and patent ductus arteriosus (PDA) stent as the initial palliation procedure for patients with pulmonary atresia with intact ventricular septum (PA-IVS) are limited. We sought to compare characteristics and outcomes in a multicenter cohort of patients with PA-IVS undergoing surgical shunts versus PDA stents. We retrospectively reviewed neonates with PA-IVS from 2009 to 2019 in 19 United States centers.

Visualizing metagenomic and metatranscriptomic data: A comprehensive review.

The fields of Metagenomics and Metatranscriptomics involve the examination of complete nucleotide sequences, gene identification, and analysis of potential biological functions within diverse organisms or environmental samples. Despite the vast opportunities for discovery in metagenomics, the sheer volume and complexity of sequence data often present challenges in processing analysis and visualization. This article highlights the critical role of advanced visualization tools in enabling effective exploration, querying, and analysis of these complex datasets.

Remaining Useful Life Estimation of Hollow Worn Railway Vehicle Wheels via On-Board Random Vibration-Based Wheel Tread Depth Estimation.

The problem of remaining useful life estimation (RULE) of hollow worn railway vehicle wheels in terms of remaining mileage via wheel tread depth estimation using on-board vibration signals from a single accelerometer on the bogie frame is presently investigated. This is achieved based on the introduction of a statistical time series method that employs: (i) advanced data-driven stochastic Functionally Pooled models for the modeling of the vehicle dynamics under different wheel tread depths in a range of interest until a critical limit, as well as tread depth estimation through a proper optimization procedure, and (ii) a wheel tread depth evolution function with respect to the vehicle running mileage that interconnects the estimated hollow wear with the remaining useful mileage. The method's RULE performance is investigated via hundreds of Simpack-based Monte Carlo simulations with an Attiko Metro S.

Retinal capillary plexus in Parkinson's disease using optical coherence tomography angiography.

Aim: To evaluate the alterations of the retinal microvasculature and foveal avascular zone in patients with Parkinson's disease (PD) using optical coherence tomography angiography (OCT-A).

Methods: A retrospective study of PD patients examined in the Ophthalmology Department of the General Hospital of Athens, "Georgios Gennimatas" from March 2021 to March 2022 was conducted. Totally 44 patients with PD were included and 18 healthy controls were examined, hence a total of 124 eyes were enrolled in the study.

Bone mineral density, vitamin D and osseous metabolism indices in neurofibromatosis type 1: A systematic review and meta-analysis.

Background: Neurofibromatosis type 1 (NF1) is a genetic autosomal neurocutaneous syndrome correlated with skeletal dysplasia and defects in the osseous microarchitecture. The physiological mechanism for the development of NF1-related bone abnormal turnover is still unclear.

Objectives: A meta-analysis was performed to investigate the effects of NF1 on bone mineral density (BMD) and osseous metabolic indices in order to provide clinical evidence for the pathogenesis of the associated skeletal deformities.

Static Baropodometry for Assessing Short-Term Functional Outcome after Unilateral Total Knee Arthroplasty: Exploring Correlation between Static Plantar Pressure Measurements and Self-Reported Outcomes.

This study aimed to investigate the association between objective baropodometric and radiological measurements and patient self-reported functional outcomes, assessed through the Knee Injury and Osteoarthritis Outcome Score (KOOS). Additionally, it sought to evaluate the effectiveness of static baropodometry in predicting short-term KOOS results following unilateral total knee arthroplasty (TKA). We conducted a prospective single-center study involving 32 patients who underwent unilateral TKA for knee osteoarthritis (KOA).

CGG toolkit: Software components for computational genomics.

Public-domain availability for bioinformatics software resources is a key requirement that ensures long-term permanence and methodological reproducibility for research and development across the life sciences. These issues are particularly critical for widely used, efficient, and well-proven methods, especially those developed in research settings that often face funding discontinuities. We re-launch a range of established software components for computational genomics, as legacy version 1.

Unraveling the Role of Molecular Profiling in Predicting Treatment Response in Stage III Colorectal Cancer Patients: Insights from the IDEA International Study.

Background: This study aimed to investigate the molecular profiles of 237 stage III CRC patients from the international IDEA study. It also sought to correlate these profiles with Toll-like and vitamin D receptor polymorphisms, clinicopathological and epidemiological characteristics, and patient outcomes.

Methods: Whole Exome Sequencing and PCR-RFLP on surgical specimens and blood samples, respectively, were performed to identify molecular profiling and the presence of Toll-like and vitamin D polymorphisms.

Unraveling the functional dark matter through global metagenomics.

Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities. Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyond what is currently possible through the lens of reference genomes, we develop a computational approach to generate reference-free protein families from the sequence space in metagenomes.

The 'Holy Grail' of shoulder dislocations: a systematic review on traumatic bilateral luxatio erecta; is it in reality a once-in-a-lifetime experience for an orthopaedic surgeon?

Introduction: Even though shoulder dislocation is thought to be the most common dislocation treated in the Emergency Department, inferior ones, known as Luxatio Erecta, comprise only 0.5% of them. Taking into consideration the rareness of unilateral Luxatio Erecta, bilateral cases should be even fewer.

From Admission to Discharge: Predicting National Institutes of Health Stroke Scale Progression in Stroke Patients Using Biomarkers and Explainable Machine Learning.

As a result of social progress and improved living conditions, which have contributed to a prolonged life expectancy, the prevalence of strokes has increased and has become a significant phenomenon. Despite the available stroke treatment options, patients frequently suffer from significant disability after a stroke. Initial stroke severity is a significant predictor of functional dependence and mortality following an acute stroke.

Social Cognition Impairments in Association to Clinical, Cognitive, Mood, and Fatigue Features in Multiple Sclerosis: A Study Protocol.

Multiple sclerosis (MS) is a chronic immune-mediated disease of the central nervous system (CNS), characterized by the diffuse grey and white matter damage. Cognitive impairment (CI) is a frequent clinical feature in patients with MS (PwMS) that can be prevalent even in early disease stages, affecting the physical activity and active social participation of PwMS. Limited information is available regarding the influence of MS in social cognition (SC), which may occur independently from the overall neurocognitive dysfunction.

LIRcentral: a manually curated online database of experimentally validated functional LIR motifs.

Several selective macroautophagy receptor and adaptor proteins bind members of the Atg8 (autophagy related 8) family using short linear motifs (SLiMs), most often referred to as Atg8-family interacting motifs (AIMs) or LC3-interacting regions (LIRs). AIM/LIR motifs have been extensively studied during the last fifteen years, since they can uncover the underlying biological mechanisms and possible substrates for this key catabolic process of eukaryotic cells. Prompted by the fact that experimental information regarding LIR motifs can be found scattered across heterogeneous literature resources, we have developed LIRcentral (https://lircentral.

Impact of COVID-19 Pandemic on Fragility Fractures of the Hip: An Interrupted Time-Series Analysis of the Lockdown Periods in Western Greece and Review of the Literature.

Since December 2019, the COVID-19 pandemic has had a significant impact on healthcare systems worldwide, prompting policymakers to implement measures of isolation and eventually adopt strict national lockdowns, which affected mobility, healthcare-seeking behavior, and services, in an unprecedented manner. This study aimed to analyze the effects of these lockdowns on hip-fracture epidemiology and care services, compared to nonpandemic periods in previous years. We retrospectively collected data from electronic patient records of two major hospitals in Western Greece and included patients who suffered a fragility hip fracture and were admitted during the two 5-week lockdown periods in 2020, compared to time-matched patients from 2017-2019.

Atrial arrhythmias following lung transplant: a single pediatric center experience.

Background: Outcomes after lung transplant (LTx) in children have slowly improved. Although atrial arrhythmia (AA) is a common and adverse complication following LTx among adults, there is limited data on pediatric recipients. We detail our pediatric single-center experience while providing further insights on occurrence and management of AA following LTx.

A Prospective, Observational Study Assessing Effectiveness, Safety, and QoL of Greek Patients with Multiple Sclerosis Under Treatment with Fingolimod.

Introduction: Fingolimod is the first approved oral therapy for relapsing-remitting multiple sclerosis (RRMS). The present study aimed to further characterize fingolimod's safety profile, and to assess the patient-reported treatment satisfaction and impact of fingolimod on the quality of life (QoL) of patients with multiple sclerosis (MS) treated in routine care in Greece.

Methods: This was a multicenter, prospective, observational, 24-month study conducted in Greece by hospital-based and private practice neurologists who specialize in MS.

Genome-Wide Analysis of lncRNA-mRNA Co-Expression Networks in CD133+/CD44+ Stem-like PDAC Cells.

Pancreatic ductal adenocarcinoma (PDAC), the second most prevalent gastrointestinal malignancy and the most common type of pancreatic cancer is linked with poor prognosis and, eventually, with high mortality rates. Early detection is seldom, while tumor heterogeneity and microarchitectural alterations benefit PDAC resistance to conventional therapeutics. Although emerging evidence suggest the core role of cancer stem cells (CSCs) in PDAC aggressiveness, unique stem signatures are poorly available, thus limiting the efforts of anti-CSC-targeted therapy.

Subchondral Bone Cyst Development in Osteoarthritis: From Pathophysiology to Bone Microarchitecture Changes and Clinical Implementations.

Osteoarthritis is a degenerative joint disease affecting middle-aged and elderly patients. It mainly involves weight-bearing joints such as the hip, knee and spine as well as the basilar joint of the thumb, causing dysfunction and painful symptoms. Often, joint arthritis is accompanied by cartilage defects, joint space narrowing, osteophytes, bone sclerosis and subchondral bone cysts (SBC).