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Andre Herrera

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Papers by Andre Herrera

Research paper thumbnail of Relative vaccine protection, disease severity, and symptoms associated with the SARS-CoV-2 omicron subvariant BA.2.86 and descendant JN.1 in Denmark: a nationwide observational study

Lancet. Infectious diseases/˜The œLancet. Infectious diseases, May 1, 2024

Research paper thumbnail of Relative Vaccine Protection, Disease Severity and Symptoms Associated with Infection with SARS-CoV-2 Omicron Subvariant Ba.2.86 and Descendent Jn.1: A Danish Nationwide Register-Based Study

Research paper thumbnail of Virus isolation and neutralisation of SARS-CoV-2 variants BA.2.86 and EG.5.1

The Lancet Infectious Diseases

Research paper thumbnail of O Ministério Público Na Investigação Criminal a Impossibilidade Investigatória Do Ministério Público

Revista Linhas Jurídicas, Nov 30, 2012

Respeitando as eruditas e sábias correntes contrárias, entende-se que o Ministério Público não po... more Respeitando as eruditas e sábias correntes contrárias, entende-se que o Ministério Público não pode investigar criminalmente sozinho, sem qualquer fiscalização. A fiscalização criminal Ministerial não tem regulamentação legal, e, se utilizada, nenhuma autoridade exterior a fiscalizará. O suspeito nem sequer saberá que está sendo investigado e não poderá lançar mão de institutos como o habeas corpus para trancar o procedimento em sua defesa. Nem mesmo seu advogado poderá ter acesso aos autos. E por fim, além de retirar a natural atribuição investigatória da polícia judiciária, fere os princípios do promotor natural e da paridade das armas, pois é claro que quem investiga não tem isenção suficiente para promover uma acusação imparcial.

Research paper thumbnail of Ontology design proposal to formalize knowledge and manage responses in a conversational interface of the Open Campus Initiative

2020 XV Conferencia Latinoamericana de Tecnologias de Aprendizaje (LACLO)

Chatbots are the new technology looking to change the way we interact and get information from sy... more Chatbots are the new technology looking to change the way we interact and get information from systems. Especially in education, chatbots need to be avaliable 24/7 to answer information needs of students. Ontologies are widely used when developing chatbots by structuring information in order to facilitate an answer for the user. In this work an ontology for chatbots is presented as part of an achitercture designed to design and train chatbots with different domains. This ontology is intended to link to an existing Knowledge Base described in RDF. When linking an actual Knowledge Base to this ontology, it is possible to create answer and dialog mechanism. With this new enhaced Knowledge Base, and the architecture developed for this chatbot it is possible to answer demands of information by identifying and structuring information from raw text. The pilot chatbot and the Knowledge Base developed in this work are intented to answer information about an open course iniciative.

Research paper thumbnail of Optic nerve crush alters the light adapted ERG of adult zebrafish

Investigative Ophthalmology & Visual Science, 2018

Research paper thumbnail of Balanço De Produção Científica: Universalização e Democratização Do Ensino Superior: Uma Análise Da Aplicação Das Políticas Afirmartivas Nos Cursos De Direito Da Região Do Vale Do Jauru e De Cáceres – MT No Período De 2009-2019

Research paper thumbnail of Ponencia Central en la Inauguración de la XVI Jornada Universitaria de Desarrollo Científico (JUDC). UNAN-FAREM-Estelí

Revista Científica de FAREM-Estelí, 2016

Research paper thumbnail of Are mitotic index and lymphocyte proliferation kinetics reproducible endpoints in genetic toxicology testing?

Mutation Research Letters, 1992

Research paper thumbnail of SARS-CoV-2 sequencing artifacts associated with targeted PCR enrichment and read mapping

bioRxiv (Cold Spring Harbor Laboratory), May 22, 2024

Protocols and pipelines for SARS-CoV-2 genome sequencing were rapidly established when the COVID-... more Protocols and pipelines for SARS-CoV-2 genome sequencing were rapidly established when the COVID-19 outbreak was declared a pandemic. The most widely used approach for sequencing SARS-CoV-2 includes targeted enrichment by PCR, followed by shotgun sequencing and reference-based genome assembly. As the conHnued surveillance of SARS-CoV-2 worldwide is transiHoning towards a lower level of intensity, it is Hmely to re-visit the sequencing protocols and pipelines established during the acute phase of the pandemic. In the current study, we have invesHgated the impact of primer scheme and reference genome choice by sequencing samples with mulHple primer schemes (ArHc V3, V4.1 and V5.3.2) and reprocessing reads with mulHple reference genomes. We have also analysed the temporal development in ambiguous base calls during the emergence of the BA.2.86.x variant. We found that the primers used for targeted enrichment can result in recurrent ambiguous base calls, which can accumulate rapidly in response to the emergence of a new variant. We also found examples of consistent base calling errors, associated with PCR arHfacts and amplicon drop-out. Similarly, misalignments and parHally mapped reads on the reference genome resulted in ambiguous base calls, as well as defining mutaHons being omiUed from the assembly. These findings highlight some key limitaHons of using targeted enrichment by PCR and reference-based genome assembly for sequencing SARS-CoV-2, and the importance of conHnuously monitoring and updaHng primer schemes and bioinformaHc pipelines.

Research paper thumbnail of Relative vaccine protection, disease severity, and symptoms associated with the SARS-CoV-2 omicron subvariant BA.2.86 and descendant JN.1 in Denmark: a nationwide observational study

Lancet. Infectious diseases/˜The œLancet. Infectious diseases, May 1, 2024

Research paper thumbnail of Relative Vaccine Protection, Disease Severity and Symptoms Associated with Infection with SARS-CoV-2 Omicron Subvariant Ba.2.86 and Descendent Jn.1: A Danish Nationwide Register-Based Study

Research paper thumbnail of Virus isolation and neutralisation of SARS-CoV-2 variants BA.2.86 and EG.5.1

The Lancet Infectious Diseases

Research paper thumbnail of O Ministério Público Na Investigação Criminal a Impossibilidade Investigatória Do Ministério Público

Revista Linhas Jurídicas, Nov 30, 2012

Respeitando as eruditas e sábias correntes contrárias, entende-se que o Ministério Público não po... more Respeitando as eruditas e sábias correntes contrárias, entende-se que o Ministério Público não pode investigar criminalmente sozinho, sem qualquer fiscalização. A fiscalização criminal Ministerial não tem regulamentação legal, e, se utilizada, nenhuma autoridade exterior a fiscalizará. O suspeito nem sequer saberá que está sendo investigado e não poderá lançar mão de institutos como o habeas corpus para trancar o procedimento em sua defesa. Nem mesmo seu advogado poderá ter acesso aos autos. E por fim, além de retirar a natural atribuição investigatória da polícia judiciária, fere os princípios do promotor natural e da paridade das armas, pois é claro que quem investiga não tem isenção suficiente para promover uma acusação imparcial.

Research paper thumbnail of Ontology design proposal to formalize knowledge and manage responses in a conversational interface of the Open Campus Initiative

2020 XV Conferencia Latinoamericana de Tecnologias de Aprendizaje (LACLO)

Chatbots are the new technology looking to change the way we interact and get information from sy... more Chatbots are the new technology looking to change the way we interact and get information from systems. Especially in education, chatbots need to be avaliable 24/7 to answer information needs of students. Ontologies are widely used when developing chatbots by structuring information in order to facilitate an answer for the user. In this work an ontology for chatbots is presented as part of an achitercture designed to design and train chatbots with different domains. This ontology is intended to link to an existing Knowledge Base described in RDF. When linking an actual Knowledge Base to this ontology, it is possible to create answer and dialog mechanism. With this new enhaced Knowledge Base, and the architecture developed for this chatbot it is possible to answer demands of information by identifying and structuring information from raw text. The pilot chatbot and the Knowledge Base developed in this work are intented to answer information about an open course iniciative.

Research paper thumbnail of Optic nerve crush alters the light adapted ERG of adult zebrafish

Investigative Ophthalmology & Visual Science, 2018

Research paper thumbnail of Balanço De Produção Científica: Universalização e Democratização Do Ensino Superior: Uma Análise Da Aplicação Das Políticas Afirmartivas Nos Cursos De Direito Da Região Do Vale Do Jauru e De Cáceres – MT No Período De 2009-2019

Research paper thumbnail of Ponencia Central en la Inauguración de la XVI Jornada Universitaria de Desarrollo Científico (JUDC). UNAN-FAREM-Estelí

Revista Científica de FAREM-Estelí, 2016

Research paper thumbnail of Are mitotic index and lymphocyte proliferation kinetics reproducible endpoints in genetic toxicology testing?

Mutation Research Letters, 1992

Research paper thumbnail of SARS-CoV-2 sequencing artifacts associated with targeted PCR enrichment and read mapping

bioRxiv (Cold Spring Harbor Laboratory), May 22, 2024

Protocols and pipelines for SARS-CoV-2 genome sequencing were rapidly established when the COVID-... more Protocols and pipelines for SARS-CoV-2 genome sequencing were rapidly established when the COVID-19 outbreak was declared a pandemic. The most widely used approach for sequencing SARS-CoV-2 includes targeted enrichment by PCR, followed by shotgun sequencing and reference-based genome assembly. As the conHnued surveillance of SARS-CoV-2 worldwide is transiHoning towards a lower level of intensity, it is Hmely to re-visit the sequencing protocols and pipelines established during the acute phase of the pandemic. In the current study, we have invesHgated the impact of primer scheme and reference genome choice by sequencing samples with mulHple primer schemes (ArHc V3, V4.1 and V5.3.2) and reprocessing reads with mulHple reference genomes. We have also analysed the temporal development in ambiguous base calls during the emergence of the BA.2.86.x variant. We found that the primers used for targeted enrichment can result in recurrent ambiguous base calls, which can accumulate rapidly in response to the emergence of a new variant. We also found examples of consistent base calling errors, associated with PCR arHfacts and amplicon drop-out. Similarly, misalignments and parHally mapped reads on the reference genome resulted in ambiguous base calls, as well as defining mutaHons being omiUed from the assembly. These findings highlight some key limitaHons of using targeted enrichment by PCR and reference-based genome assembly for sequencing SARS-CoV-2, and the importance of conHnuously monitoring and updaHng primer schemes and bioinformaHc pipelines.

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