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  1. Article ; Online: ReporType: A Flexible Bioinformatics Tool for Targeted Loci Screening and Typing of Infectious Agents.

    Cruz, Helena / Pinheiro, Miguel / Borges, Vítor

    International journal of molecular sciences

    2024  Volume 25, Issue 6

    Abstract: In response to the pressing need for continuous monitoring of emergence and circulation of pathogens through genomics, it is imperative to keep developing bioinformatics tools that can help in their rapid characterization and classification. Here, we ... ...

    Abstract In response to the pressing need for continuous monitoring of emergence and circulation of pathogens through genomics, it is imperative to keep developing bioinformatics tools that can help in their rapid characterization and classification. Here, we introduce ReporType, a versatile bioinformatics pipeline designed for targeted loci screening and typing of infectious agents. Developed using the snakemake workflow manager, ReporType integrates multiple software for read quality control and de novo assembly, and then applies ABRicate for locus screening, culminating in the production of easily interpretable reports for the identification of pathogen genotypes and/or screening of specific genomic loci. The pipeline accommodates a range of input formats, from Illumina or Oxford Nanopore Technology (ONT) reads (FASTQ) to Sanger sequencing files (AB1), or FASTA files, making it flexible for application in multiple pathogens and with different purposes. ReporType is released with pre-prepared databases for some viruses and bacteria, yet it remains easily configurable to handle custom databases. ReporType performance and functionality were validated through proof-of-concept exercises, encompassing diverse pathogenic species, including viruses such as measles, Newcastle disease virus (NDV), Dengue virus (DENV), influenza, hepatitis C virus (HCV) and Human T-Cell Lymphotropic virus type 1 (HTLV-1), as well as bacteria like
    MeSH term(s) Humans ; Sequence Analysis, DNA ; Computational Biology ; Genomics ; Software ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing
    Language English
    Publishing date 2024-03-09
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms25063172
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Book ; Online: Innovation and Word Usage Patterns in Machine Learning

    Borges, Vítor Bandeira / Cajueiro, Daniel Oliveira

    2023  

    Abstract: In this study, we delve into the dynamic landscape of machine learning research evolution. Initially, through the utilization of Latent Dirichlet Allocation, we discern pivotal themes and fundamental concepts that have emerged within the realm of machine ...

    Abstract In this study, we delve into the dynamic landscape of machine learning research evolution. Initially, through the utilization of Latent Dirichlet Allocation, we discern pivotal themes and fundamental concepts that have emerged within the realm of machine learning. Subsequently, we undertake a comprehensive analysis to track the evolutionary trajectories of these identified themes. To quantify the novelty and divergence of research contributions, we employ the Kullback-Leibler Divergence metric. This statistical measure serves as a proxy for ``surprise'', indicating the extent of differentiation between the content of academic papers and the subsequent developments in research. By amalgamating these insights, we gain the ability to ascertain the pivotal roles played by prominent researchers and the significance of specific academic venues (periodicals and conferences) within the machine learning domain.
    Keywords Computer Science - Machine Learning ; Computer Science - Computation and Language
    Subject code 006
    Publishing date 2023-11-06
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Estratigrafia e zooarqueologia de cerritos de Santa Vitória do Palmar, Rio Grande do Sul. Novos dados sobre o sítio RS-158

    Diego Dias Pavei / Marcos César Pereira Santos / Vitor Hugo Rosa Biffi / Carla Bica / Marlon Borges Pestana / Juliano Bitencourt Campos

    Boletim do Museu Paraense Emílio Goeldi. Ciências Humanas, Vol 17, Iss

    Alberto Talayer

    2022  Volume 2

    Abstract: ... arqueológico RS-158: Alberto Talayer, localizado no município de Santa Vitória do Palmar, Rio Grande do Sul ...

    Abstract Resumo Este estudo visa apresentar os resultados estratigráficos e zooarqueológicos do sítio arqueológico RS-158: Alberto Talayer, localizado no município de Santa Vitória do Palmar, Rio Grande do Sul. O objetivo é revisar as informações estratigráficas das campanhas de escavação dos anos 1970 e apresentar novos resultados zooarqueológicos e estratigráficos da escavação realizada em 2014. Os dados estratigráficos indicam que as ocupações desse sítio possuem uma sequência com mais de 2 metros de profundidade, com cinco camadas e indícios de diferentes níveis de ocupação (níveis arqueológicos IIa e IIIa), marcadas por períodos pré-cerâmico e cerâmico (tradição Vieira). Nos dois montículos que compõem o sítio arqueológico RS-158, a caça de mamíferos teria sido a principal atividade econômica, se destacando com a abundância do veado-campeiro. O problema relativo à sobreposição de diferentes níveis arqueológicos em uma estrutura antrópica encontra nesse estudo um contributo direto com o estabelecimento de variados níveis de ocupação e sua correlação entre os diferentes montículos. Assim, o sítio apresenta características específicas do ambiente no qual se localiza, com interações com os ecossistemas pampeanos, como campos sulinos, rios e lagoas.
    Keywords Cerritos ; Arqueologia pampeana ; Zooarqueologia ; Estratigrafia ; Latin America. Spanish America ; F1201-3799 ; Social Sciences ; H
    Language English
    Publishing date 2022-08-01T00:00:00Z
    Publisher Museu Paraense Emílio Goeldi
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Recurrence, Microevolution, and Spatiotemporal Dynamics of Legionella pneumophila Sequence Type 1905, Portugal, 2014-2022.

    Manageiro, Vera / Borges, Vítor / Rodrigues, Raquel / Bettencourt, Célia / Silva, Cecília / Gomes, João Paulo / Gonçalves, Paulo

    Emerging infectious diseases

    2024  Volume 30, Issue 5, Page(s) 1022–1025

    Abstract: We investigated molecular evolution and spatiotemporal dynamics of atypical Legionella pneumophila serogroup 1 sequence type 1905 and determined its long-term persistence and linkage to human disease in dispersed locations, far beyond the large 2014 ... ...

    Abstract We investigated molecular evolution and spatiotemporal dynamics of atypical Legionella pneumophila serogroup 1 sequence type 1905 and determined its long-term persistence and linkage to human disease in dispersed locations, far beyond the large 2014 outbreak epicenter in Portugal. Our finding highlights the need for public health interventions to prevent further disease spread.
    MeSH term(s) Legionella pneumophila/genetics ; Legionella pneumophila/classification ; Portugal/epidemiology ; Humans ; Legionnaires' Disease/epidemiology ; Legionnaires' Disease/microbiology ; Spatio-Temporal Analysis ; Evolution, Molecular ; Disease Outbreaks ; History, 21st Century ; Recurrence ; Phylogeny ; Serogroup
    Language English
    Publishing date 2024-04-26
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Historical Article
    ZDB-ID 1380686-5
    ISSN 1080-6059 ; 1080-6040
    ISSN (online) 1080-6059
    ISSN 1080-6040
    DOI 10.3201/eid3005.231383
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

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  5. Article ; Online: Raw milk cheeses from Beira Baixa, Portugal-A contributive study for the microbiological hygiene and safety assessment.

    Mendonça, Rita / Furtado, Rosália / Coelho, Anabela / Correia, Cristina Belo / Suyarko, Elena / Borges, Vítor / Gomes, João Paulo / Pista, Angela / Batista, Rita

    Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology

    2024  

    Abstract: Due to specific bacterial microbiota, raw milk cheeses have appreciated sensory properties. However, they may pose a threat to consumer safety due to potential pathogens presence. This study evaluated the microbiological contamination of 98 raw milk ... ...

    Abstract Due to specific bacterial microbiota, raw milk cheeses have appreciated sensory properties. However, they may pose a threat to consumer safety due to potential pathogens presence. This study evaluated the microbiological contamination of 98 raw milk cheeses from Beira Baixa, Portugal. Presence and enumeration of Coagulase Positive Staphylococci (CPS), Listeria monocytogenes, Salmonella spp., pathogenic Escherichia coli, and indicator microorganisms (non-pathogenic E. coli and Listeria spp.) was attained. E. coli antimicrobial resistance (AMR) was also evaluated. PCR and/or Whole genome sequencing (WGS) was used to characterize E. coli, Salmonella spp. and L. monocytogenes isolates. Sixteen cheeses (16.3%) were classified as Satisfactory, 59 (60.2%) as Borderline and 23 (23.5%) as Unsatisfactory/Potential Injurious to Health. L. monocytogenes, CPS > 10
    Language English
    Publishing date 2024-04-15
    Publishing country Brazil
    Document type Journal Article
    ZDB-ID 2017175-4
    ISSN 1678-4405 ; 1517-8382
    ISSN (online) 1678-4405
    ISSN 1517-8382
    DOI 10.1007/s42770-024-01332-y
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  6. Article ; Online: ReporTree: a surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data.

    Mixão, Verónica / Pinto, Miguel / Sobral, Daniel / Di Pasquale, Adriano / Gomes, João Paulo / Borges, Vítor

    Genome medicine

    2023  Volume 15, Issue 1, Page(s) 43

    Abstract: Background: Genomics-informed pathogen surveillance strengthens public health decision-making, playing an important role in infectious diseases' prevention and control. A pivotal outcome of genomics surveillance is the identification of pathogen genetic ...

    Abstract Background: Genomics-informed pathogen surveillance strengthens public health decision-making, playing an important role in infectious diseases' prevention and control. A pivotal outcome of genomics surveillance is the identification of pathogen genetic clusters and their characterization in terms of geotemporal spread or linkage to clinical and demographic data. This task often consists of the visual exploration of (large) phylogenetic trees and associated metadata, being time-consuming and difficult to reproduce.
    Results: We developed ReporTree, a flexible bioinformatics pipeline that allows diving into the complexity of pathogen diversity to rapidly identify genetic clusters at any (or all) distance threshold(s) or cluster stability regions and to generate surveillance-oriented reports based on the available metadata, such as timespan, geography, or vaccination/clinical status. ReporTree is able to maintain cluster nomenclature in subsequent analyses and to generate a nomenclature code combining cluster information at different hierarchical levels, thus facilitating the active surveillance of clusters of interest. By handling several input formats and clustering methods, ReporTree is applicable to multiple pathogens, constituting a flexible resource that can be smoothly deployed in routine surveillance bioinformatics workflows with negligible computational and time costs. This is demonstrated through a comprehensive benchmarking of (i) the cg/wgMLST workflow with large datasets of four foodborne bacterial pathogens and (ii) the alignment-based SNP workflow with a large dataset of Mycobacterium tuberculosis. To further validate this tool, we reproduced a previous large-scale study on Neisseria gonorrhoeae, demonstrating how ReporTree is able to rapidly identify the main species genogroups and characterize them with key surveillance metadata, such as antibiotic resistance data. By providing examples for SARS-CoV-2 and the foodborne bacterial pathogen Listeria monocytogenes, we show how this tool is currently a useful asset in genomics-informed routine surveillance and outbreak detection of a wide variety of species.
    Conclusions: In summary, ReporTree is a pan-pathogen tool for automated and reproducible identification and characterization of genetic clusters that contributes to a sustainable and efficient public health genomics-informed pathogen surveillance. ReporTree is implemented in python 3.8 and is freely available at https://github.com/insapathogenomics/ReporTree .
    MeSH term(s) Humans ; Phylogeny ; COVID-19 ; SARS-CoV-2 ; Genomics/methods ; Computational Biology ; Bacteria/genetics
    Language English
    Publishing date 2023-06-15
    Publishing country England
    Document type Journal Article
    ZDB-ID 2484394-5
    ISSN 1756-994X ; 1756-994X
    ISSN (online) 1756-994X
    ISSN 1756-994X
    DOI 10.1186/s13073-023-01196-1
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  7. Article ; Online: Mastoidite aguda

    Godofredo Campos Borges / Vitor Salles Minussi / Emanuela Yumi

    Revista da Faculdade de Ciências Médicas de Sorocaba (2022)

    2022  

    Abstract: A mastoidite aguda é uma complicação da otite média. Descrevemos a seguir um caso de mastoidite aguda. Nesse trabalho apresentamos o caso de JIB, 1 ano, que se iniciou com queixa de dor e coceira em orelha direita que evoluiu para o caso apresentado de ... ...

    Abstract A mastoidite aguda é uma complicação da otite média. Descrevemos a seguir um caso de mastoidite aguda. Nesse trabalho apresentamos o caso de JIB, 1 ano, que se iniciou com queixa de dor e coceira em orelha direita que evoluiu para o caso apresentado de mastoidite aguda. A mastoidite aguda possui a manifestações clínicas polimórficas, variando entre formas assintomáticas de resolução espontânea e doença progressiva com complicações graves. Alguns casos podem levar a complicações intracranianas ou extracranianas.
    Keywords mastoidite ; doença aguda ; otite média ; Medicine ; R
    Language Portuguese
    Publishing date 2022-10-01T00:00:00Z
    Publisher Pontifícia Universidade Católica de São Paulo
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article: Unveiling a

    Rodrigues, Inês C / Ribeiro-Almeida, Marisa / Silveira, Leonor / Prata, Joana C / de Carvalho, André Pinto / Roque, Carla / Gomes, João Paulo / Borges, Vítor / Pista, Ângela / Martins da Costa, Paulo

    Microorganisms

    2024  Volume 12, Issue 4

    Abstract: ... Listeria ... ...

    Abstract Listeria monocytogenes
    Language English
    Publishing date 2024-04-12
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2720891-6
    ISSN 2076-2607
    ISSN 2076-2607
    DOI 10.3390/microorganisms12040785
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Molecular Capture of

    Macedo, Rita / Isidro, Joana / Ferreira, Rita / Pinto, Miguel / Borges, Vítor / Duarte, Sílvia / Vieira, Luís / Gomes, João Paulo

    International journal of molecular sciences

    2023  Volume 24, Issue 3

    Abstract: The application of whole genome sequencing ... ...

    Abstract The application of whole genome sequencing of
    MeSH term(s) Humans ; Mycobacterium tuberculosis/genetics ; Antitubercular Agents/pharmacology ; Antitubercular Agents/therapeutic use ; Phylogeny ; Whole Genome Sequencing ; Sputum/microbiology ; Tuberculosis/drug therapy ; Tuberculosis/epidemiology ; Tuberculosis/microbiology ; Microbial Sensitivity Tests
    Chemical Substances Antitubercular Agents
    Language English
    Publishing date 2023-02-02
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms24032912
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  10. Article: Listeria monocytogenes

    Praça, Joana / Furtado, Rosália / Coelho, Anabela / Correia, Cristina Belo / Borges, Vítor / Gomes, João Paulo / Pista, Angela / Batista, Rita

    Microorganisms

    2023  Volume 11, Issue 2

    Abstract: Traditional cheeses are part of the Portuguese gastronomic identity, and raw milk of autochthonous species is a common primary ingredient. Here, we investigated the presence ... ...

    Abstract Traditional cheeses are part of the Portuguese gastronomic identity, and raw milk of autochthonous species is a common primary ingredient. Here, we investigated the presence of
    Language English
    Publishing date 2023-01-27
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2720891-6
    ISSN 2076-2607
    ISSN 2076-2607
    DOI 10.3390/microorganisms11020322
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