380 documents found, page 1 of 38

Comparative assessment of protein large language models for enzyme commission n...

Background: Protein large language models (LLM) have been used to extract representations of enzyme sequences to predict their function, which is encoded by enzyme commission (EC) numbers. However, a comprehensive comparison of different LLMs for this task is still lacking, leaving questions about their relative performance. Moreover, protein sequence alignments (e.g. BLASTp or DIAMOND) are often combined with ...

Cellular and biochemical alterations induced by diesel oil in the brown alga Sa...

The effect of the in vitro acute exposure to diesel oil (0.001%, 0.01%, 0.1%, and 1%, v/v) has been evaluated in the brown seaweed Sargassum cymosum var. stenoplhyllum by determining the contents of photosynthetic pigments, phenolic compounds, and morphological and cellular changes. In vitro cultures of S. cymosum were exposed to diesel oil for 30min, 1h, 12h, and 24h under laboratory-controlled conditions. Chl...

TROPPO: tissue-specific reconstruction and phenotype prediction using omics data

The increasing availability of high-throughput technologies in systems biology has advanced predictive tools like genome-scale metabolic models. Despite this progress, integrating omics data to create accurate, context-specific metabolic models for different tissues or cells remains challenging. A significant issue is that many existing tools rely on proprietary software, which limits accessibility. We introduc...

Implementing metabolic transformation algorithms and their application in agein...

This work presents the Python-based implementation and validation of the Metabolic Transformation Algorithm (MTA) and its robust counterpart (rMTA), originally developed in MATLAB. MTA/rMTA facilitates the identification of therapeutic metabolic interventions by simulating gene knockouts and evaluating their potential to redirect metabolic fluxes toward healthier phenotypes. The transition to Python capitalizes...

Combination HIV Prevention Strategies in the Lisbon Cohort of Men who Have Sex ...

Predicting precursors of plant specialized metabolites using DeepMol automated ...

Plants produce specialized metabolites, which play critical roles in defending against biotic and abiotic stresses. Due to their chemical diversity and bioactivity, these compounds have significant economic implications, particularly in the pharmaceutical and agrotechnology sectors. Despite their importance, the biosynthetic pathways of these metabolites remain largely unresolved. Automating the prediction of t...

Co-creating a Mpox Elimination Campaign in the WHO European Region: The Central...

Viral genetics and transmission dynamics in the second wave of mpox outbreak in...

Orogenital and anal infection by Chlamydia trachomatis, Neisseria gonorrhoeae, ...

Background: Men who have sex with men (MSM) are at risk for sexually transmitted infections (STIs), but more data on extragenital carriage are needed. Aim: We assessed the genital and extragenital prevalence of bacterial and other STIs in MSM in a Lisbon sexual health clinic. Methods: We screened oral, anal, and urine samples of MSM visiting the GAT-CheckpointLX clinic June 2017-December 2021 for Chlamydia trac...

Bias-Motivated Physical or Verbal Violence Among Men Who Have Sex with Men: Fin...