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View article: Prediction of sporulating Firmicutes from uncultured gut microbiota using SpoMAG, an ensemble learning tool
Prediction of sporulating Firmicutes from uncultured gut microbiota using SpoMAG, an ensemble learning tool Open
Sporulation represents a key adaptive strategy among Firmicutes, facilitating bacterial persistence under environmental stress while mediating host colonization, transmission dynamics, and microbiome stability. Despite the recognized ecolo…
View article: Clustering and visualisation of the GABRIEL network expertise in the field of infectious diseases
Clustering and visualisation of the GABRIEL network expertise in the field of infectious diseases Open
Introduction The Global Approach to Biology Research, Infectious diseases and Epidemics in Low-income countries (GABRIEL) network is an international scientific network of 21 centres coordinated by the Merieux Foundation (Lyon, France). Ma…
View article: Immune and vascular modulation by HERVs: the role of CXCR1 and IL18RAP in dengue severity progression
Immune and vascular modulation by HERVs: the role of CXCR1 and IL18RAP in dengue severity progression Open
Introduction Human Endogenous Retroviruses (HERVs), which can be activated by viral infections, have complex roles in gene regulation and immune modulation. However, their contribution to disease progression is not yet fully understood. De…
View article: Metabolic pathways associated with Firmicutes prevalence in the gut of multiple livestock animals and humans
Metabolic pathways associated with Firmicutes prevalence in the gut of multiple livestock animals and humans Open
Dynamic interspecific interactions and environmental factors deeply impact the composition of microbiotic communities in the gut. These factors intertwined with the host's genetic background and social habits cooperate synergistically as a…
View article: Transcriptomic insights into early mechanisms underlying post-chikungunya chronic inflammatory joint disease
Transcriptomic insights into early mechanisms underlying post-chikungunya chronic inflammatory joint disease Open
Chikungunya virus (CHIKV) infection often results in a chronic joint condition known as Post-Chikungunya Chronic Inflammatory Joint Disease (pCHIKV-CIJD). This condition disrupts individuals' daily lives and contributes to increased health…
View article: Permissive central tolerance plus defective peripheral checkpoints licence pathogenic memory B cells in CASPR2-antibody encephalitis
Permissive central tolerance plus defective peripheral checkpoints licence pathogenic memory B cells in CASPR2-antibody encephalitis Open
Autoimmunity affects 10% of the population. Within this umbrella, autoantibody-mediated diseases targeting one autoantigen provide a unique opportunity to comprehensively understand the developmental pathway of disease-causing B cells and …
View article: “The COVID-19 pandemic in BRICS: Milestones, interventions, and molecular epidemiology”
“The COVID-19 pandemic in BRICS: Milestones, interventions, and molecular epidemiology” Open
Brazil, Russia, India, China, and South Africa (BRICS) are a group of developing countries with shared economic, healthcare, and scientific interests. These countries navigate multiple syndemics, and the COVID-19 pandemic placed severe str…
View article: SARS-CoV-2 strains and clinical profiles of COVID-19 patients in a Southern Brazil hospital
SARS-CoV-2 strains and clinical profiles of COVID-19 patients in a Southern Brazil hospital Open
Introduction The COVID-19 pandemic had a widespread global impact and presented numerous challenges. The emergence of SARS-CoV-2 variants has changed transmission rates and immune evasion, possibly impacting the severity. This study aims t…
View article: Uncovering new <i>Firmicutes</i> species in vertebrate hosts through metagenome-assembled genomes with potential for sporulation
Uncovering new <i>Firmicutes</i> species in vertebrate hosts through metagenome-assembled genomes with potential for sporulation Open
Metagenome-assembled genomes (MAGs) have contributed to identifying non-culturable microorganisms and understanding their ecological functions. MAGs offer an advantage in investigating sporulation-associated genes, especially given the dif…
View article: The draft genomes of Crassostrea gasar and Crassostrea rhizophorae: key resources for leveraging oyster cultivation in the Southwest Atlantic
The draft genomes of Crassostrea gasar and Crassostrea rhizophorae: key resources for leveraging oyster cultivation in the Southwest Atlantic Open
View article: Transcriptional and Post-Translational Roles of Calcineurin in Cationic Stress and Glycerol Biosynthesis in Cryptococcus neoformans
Transcriptional and Post-Translational Roles of Calcineurin in Cationic Stress and Glycerol Biosynthesis in Cryptococcus neoformans Open
Stress management is an adaptive advantage for survival in adverse environments. Pathogens face this challenge during host colonization, requiring an appropriate stress response to establish infection. The fungal pathogen Cryptococcus neof…
View article: Predicting novel mosquito-associated viruses from metatranscriptomic dark matter
Predicting novel mosquito-associated viruses from metatranscriptomic dark matter Open
The exponential growth of metatranscriptomic studies dedicated to arboviral surveillance in mosquitoes has yielded an unprecedented volume of unclassified sequences referred to as the virome dark matter. Mosquito-associated viruses are cla…
View article: Living in mangroves: a syntrophic scenario unveiling a resourceful microbiome
Living in mangroves: a syntrophic scenario unveiling a resourceful microbiome Open
Background Mangroves are complex and dynamic coastal ecosystems under frequent fluctuations in physicochemical conditions related to the tidal regime. The frequent variation in organic matter concentration, nutrients, and oxygen availabili…
View article: SARS-CoV-2 transmission in a highly vulnerable population of Brazil: a household cohort study
SARS-CoV-2 transmission in a highly vulnerable population of Brazil: a household cohort study Open
Fundação Oswaldo Cruz, CNPq, FAPERJ, Royal Society, Instituto Serrapilheira, FAPESP.
View article: Immune response stability to the SARS-CoV-2 mRNA vaccine booster is influenced by differential splicing of HLA genes
Immune response stability to the SARS-CoV-2 mRNA vaccine booster is influenced by differential splicing of HLA genes Open
Many molecular mechanisms that lead to the host antibody response to COVID-19 vaccines remain largely unknown. In this study, we used serum antibody detection combined with whole blood RNA-based transcriptome analysis to investigate variab…
View article: Whole genomes show contrasting trends of population size changes and genomic diversity for an Amazonian endemic passerine over the late quaternary
Whole genomes show contrasting trends of population size changes and genomic diversity for an Amazonian endemic passerine over the late quaternary Open
The “Amazon tipping point” is a global change scenario resulting in replacement of upland terra‐firme forests by large‐scale “savannization” of mostly southern and eastern Amazon. Reduced rainfall accompanying the Last Glacial Maximum (LGM…
View article: Uncovering the transcriptional molecular dynamics of shelf life extension and system acquired resistance induction to<i>Fusarium pallidoroseum</i>in melon fruits by the use of pulsed-light
Uncovering the transcriptional molecular dynamics of shelf life extension and system acquired resistance induction to<i>Fusarium pallidoroseum</i>in melon fruits by the use of pulsed-light Open
Melon is a globally commercialized fruit, and Fusarium rot disease poses a significant threat to post-harvest losses. The conventional use of fungicides raises concerns about chemical residues, prompting exploration into alternative techno…
View article: Mitochondrial genome structure and composition in 70 fishes: a key resource for fisheries management in the South Atlantic
Mitochondrial genome structure and composition in 70 fishes: a key resource for fisheries management in the South Atlantic Open
View article: Finding microbial composition and biological processes as predictive signature to access the ongoing status of mangrove preservation
Finding microbial composition and biological processes as predictive signature to access the ongoing status of mangrove preservation Open
View article: Cem anos de Johanna Döbereiner
Cem anos de Johanna Döbereiner Open
View article: KBase Narrative - Metabolic_reconstruction_ETDI_mangrove
KBase Narrative - Metabolic_reconstruction_ETDI_mangrove Open
Mangroves are complex and dynamic coastal ecosystems under frequent fluctuations in physicochemical conditions related to the tidal regime. The frequent variation in organic matter concentration, nutrients, and oxygen availability, among o…
View article: SARS-CoV-2 transmission in a highly vulnerable population of Brazil: results from a household longitudinal study
SARS-CoV-2 transmission in a highly vulnerable population of Brazil: results from a household longitudinal study Open
We estimated within/extra-household SARS-CoV-2 infection risk and associated factors in a household cohort study in one of the most vulnerable neighborhoods in Rio de Janeiro city. Individuals ≥1 years-old with suspected or confirmed COVID…
View article: ALTERAÇÕES TRANSCRICIONAIS PRECOCEMENTE ENVOLVIDAS NA PROGRESSÃO DE PACIENTES PARA DOENÇA ARTICULAR CRÔNICA PÓS-CHIKUNGUNYA
ALTERAÇÕES TRANSCRICIONAIS PRECOCEMENTE ENVOLVIDAS NA PROGRESSÃO DE PACIENTES PARA DOENÇA ARTICULAR CRÔNICA PÓS-CHIKUNGUNYA Open
Introdução/Objetivo: Infecções pelo vírus Chikungunya (CHIKV) podem frequentemente resultar no desenvolvimento de Doença Articular Inflamatória Crônica pós-Chikungunya (pCHIKV-CIJD). Essa condição gera impactos na qualidade de vida dos pac…
View article: Differential Type-I Interferon Response in Buffy Coat Transcriptome of Individuals Infected with SARS-CoV-2 Gamma and Delta Variants
Differential Type-I Interferon Response in Buffy Coat Transcriptome of Individuals Infected with SARS-CoV-2 Gamma and Delta Variants Open
The innate immune system is the first line of defense against pathogens such as the acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The type I-interferon (IFN) response activation during the initial steps of infection is essential t…
View article: Genetic screening in a Brazilian cohort with inborn errors of immunity
Genetic screening in a Brazilian cohort with inborn errors of immunity Open
View article: Assessing whole-exome sequencing data from undiagnosed Brazilian patients to improve the diagnostic yield of inborn errors of immunity
Assessing whole-exome sequencing data from undiagnosed Brazilian patients to improve the diagnostic yield of inborn errors of immunity Open
View article: Inference of differentially expressed genes using generalized linear mixed models in a pairwise fashion
Inference of differentially expressed genes using generalized linear mixed models in a pairwise fashion Open
Background Technological advances involving RNA-Seq and Bioinformatics allow quantifying the transcriptional levels of genes in cells, tissues, and cell lines, permitting the identification of Differentially Expressed Genes (DEGs). DESeq2 …
View article: The Omicron Lineages BA.1 and BA.2 (Betacoronavirus SARS-CoV-2) Have Repeatedly Entered Brazil through a Single Dispersal Hub
The Omicron Lineages BA.1 and BA.2 (Betacoronavirus SARS-CoV-2) Have Repeatedly Entered Brazil through a Single Dispersal Hub Open
Brazil currently ranks second in absolute deaths by COVID-19, even though most of its population has completed the vaccination protocol. With the introduction of Omicron in late 2021, the number of COVID-19 cases soared once again in the c…
View article: Differential haplotype expression in class I MHC genes during SARS-CoV-2 infection of human lung cell lines
Differential haplotype expression in class I MHC genes during SARS-CoV-2 infection of human lung cell lines Open
Introduction Cell entry of SARS-CoV-2 causes genome-wide disruption of the transcriptional profiles of genes and biological pathways involved in the pathogenesis of COVID-19. Expression allelic imbalance is characterized by a deviation fro…
View article: Clinical markers of post-Chikungunya chronic inflammatory joint disease: A Brazilian cohort
Clinical markers of post-Chikungunya chronic inflammatory joint disease: A Brazilian cohort Open
Background Chikungunya-fever (CHIKF) remains a public health major issue. It is clinically divided into three phases: acute, post-acute and chronic. Chronic cases correspond to 25–40% individuals and, though most of them are characterized …