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Article ; Online: Identification of plasmids from Brazilian

de Lima, Daniel Chaves / Medeiros, Inácio Gomes / de Cássia Silva-Portela, Rita / da Silva Junior, Francisco Carlos / Fassarela Agnez-Lima, Lucymara / de Souza, Jorge Estefano Santana / Batistuzzo de Medeiros, Silvia R

Canadian journal of microbiology

2021 , Page(s) 1–10

Abstract: Chromobacterium ... ...

Abstract	Chromobacterium violaceum
Language	English
Publishing date	2021-11-15
Publishing country	Canada
Document type	Journal Article
ZDB-ID	280534-0
ISSN	1480-3275 ; 0008-4166
ISSN (online)	1480-3275
ISSN	0008-4166
DOI	10.1139/cjm-2021-0197
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Article ; Online: A small interfering RNA (siRNA) database for SARS-CoV-2

Inácio Gomes Medeiros / André Salim Khayat / Beatriz Stransky / Sidney Santos / Paulo Assumpção / Jorge Estefano Santana de Souza

Scientific Reports, Vol 11, Iss 1, Pp 1-

2021 Volume 10

Abstract: Abstract Coronavirus disease 2019 (COVID-19) rapidly transformed into a global pandemic, for which a demand for developing antivirals capable of targeting the SARS-CoV-2 RNA genome and blocking the activity of its genes has emerged. In this work, we ... ...

Abstract	Abstract Coronavirus disease 2019 (COVID-19) rapidly transformed into a global pandemic, for which a demand for developing antivirals capable of targeting the SARS-CoV-2 RNA genome and blocking the activity of its genes has emerged. In this work, we presented a database of SARS-CoV-2 targets for small interference RNA (siRNA) based approaches, aiming to speed the design process by providing a broad set of possible targets and siRNA sequences. The siRNAs sequences are characterized and evaluated by more than 170 features, including thermodynamic information, base context, target genes and alignment information of sequences against the human genome, and diverse SARS-CoV-2 strains, to assess possible bindings to off-target sequences. This dataset is available as a set of four tables, available in a spreadsheet and CSV (Comma-Separated Values) formats, each one corresponding to sequences of 18, 19, 20, and 21 nucleotides length, aiming to meet the diversity of technology and expertise among laboratories around the world. A metadata table (Supplementary Table S1), which describes each feature, is also provided in the aforementioned formats. We hope that this database helps to speed up the development of new target antivirals for SARS-CoV-2, contributing to a possible strategy for a faster and effective response to the COVID-19 pandemic.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2021-04-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
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Article ; Online: Potential vectors of Leishmania spp. in an Atlantic Forest conservation unit in northeastern Brazil under anthropic pressure.

Pinheiro, Marcos Paulo Gomes / Silva-Inacio, Cássio Lázaro / Silva, Marcel Miranda de Medeiros / Araújo, Paulo Sérgio Fagundes de / Ximenes, Maria de Fátima Freire de Melo

Parasites & vectors

2021 Volume 14, Issue 1, Page(s) 38

Abstract: Background: Phlebotomines are a group of insects which include vectors of the Leishmania parasites that cause visceral leishmaniasis (VL) and cutaneous leishmaniasis (CL), diseases primarily affecting populations of low socioeconomic status. VL in ... ...

Abstract	Background: Phlebotomines are a group of insects which include vectors of the Leishmania parasites that cause visceral leishmaniasis (VL) and cutaneous leishmaniasis (CL), diseases primarily affecting populations of low socioeconomic status. VL in Brazil is caused by Leishmania infantum, with transmission mainly attributed to Lutzomyia longipalpis, a species complex of sand fly, and is concentrated mainly in the northeastern part of the country. CL is distributed worldwide and occurs in five regions of Brazil, at a higher incidence in the north and northeast regions, with etiological agents, vectors, reservoirs and epidemiological patterns that differ from VL. The aim of this study was to determine the composition, distribution and ecological relationships of phlebotomine species in an Atlantic Forest conservation unit and nearby residential area in northeastern Brazil. Methods: Centers for Disease Control and Shannon traps were used for collections, the former at six points inside the forest and in the peridomestic environment of surrounding residences, three times per month for 36 months, and the latter in a forest area, once a month for 3 months. The phlebotomines identified were compared with climate data using simple linear correlation, Pearson's correlation coefficient and cross-correlation. The estimate of ecological parameters was calculated according to the Shannon-Wiener diversity index, standardized index of species abundance and the dominance index. Results: A total of 75,499 phlebotomines belonging to 11 species were captured in the CDC traps, the most abundant being Evandromyia walkeri, Psychodopygus wellcomei and Lu. longipalpis. Evandromyia walkeri abundance was most influenced by temperature at collection time and during the months preceding collection and rainfall during the months preceding collection. Psychodopygus wellcomei abundance was most affected by rainfall and relative humidity during the collection month and the month immediately preceding collection time. Lutzomyia longipalpis abundance showed a correlation with temperature and the rainfall during the months preceding collection time. The Shannon trap contained a total of 3914 phlebotomines from these different species. Psychodopygus wellcomei, accounting for 91.93% of the total, was anthropophilic and active mainly at night. Conclusions: Most of the species collected in the traps were seasonal and exhibited changes in their composition and population dynamics associated with local adaptions. The presence of vectors Ps. wellcomei and Lu. longipalpis underscore the epidemiological importance of these phlebotomines in the conservation unit and surrounding anthropized areas. Neighboring residential areas should be permanently monitored to prevent VL or CL transmission and outbreaks.
MeSH term(s)	Animals ; Brazil/epidemiology ; Conservation of Natural Resources ; Female ; Forests ; Insect Vectors/classification ; Insect Vectors/parasitology ; Leishmania infantum/physiology ; Leishmaniasis, Cutaneous/epidemiology ; Leishmaniasis, Cutaneous/transmission ; Male ; Population Dynamics ; Psychodidae/classification ; Psychodidae/parasitology ; Psychodidae/physiology ; Seasons ; Temperature
Language	English
Publishing date	2021-01-11
Publishing country	England
Document type	Journal Article
ZDB-ID	2409480-8
ISSN	1756-3305 ; 1756-3305
ISSN (online)	1756-3305
ISSN	1756-3305
DOI	10.1186/s13071-020-04523-2
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: A small interfering RNA (siRNA) database for SARS-CoV-2.

Medeiros, Inácio Gomes / Khayat, André Salim / Stransky, Beatriz / Santos, Sidney / Assumpção, Paulo / de Souza, Jorge Estefano Santana

Scientific reports

2021 Volume 11, Issue 1, Page(s) 8849

Abstract: Coronavirus disease 2019 (COVID-19) rapidly transformed into a global pandemic, for which a demand for developing antivirals capable of targeting the SARS-CoV-2 RNA genome and blocking the activity of its genes has emerged. In this work, we presented a ... ...

Abstract	Coronavirus disease 2019 (COVID-19) rapidly transformed into a global pandemic, for which a demand for developing antivirals capable of targeting the SARS-CoV-2 RNA genome and blocking the activity of its genes has emerged. In this work, we presented a database of SARS-CoV-2 targets for small interference RNA (siRNA) based approaches, aiming to speed the design process by providing a broad set of possible targets and siRNA sequences. The siRNAs sequences are characterized and evaluated by more than 170 features, including thermodynamic information, base context, target genes and alignment information of sequences against the human genome, and diverse SARS-CoV-2 strains, to assess possible bindings to off-target sequences. This dataset is available as a set of four tables, available in a spreadsheet and CSV (Comma-Separated Values) formats, each one corresponding to sequences of 18, 19, 20, and 21 nucleotides length, aiming to meet the diversity of technology and expertise among laboratories around the world. A metadata table (Supplementary Table S1), which describes each feature, is also provided in the aforementioned formats. We hope that this database helps to speed up the development of new target antivirals for SARS-CoV-2, contributing to a possible strategy for a faster and effective response to the COVID-19 pandemic.
MeSH term(s)	COVID-19/virology ; Databases, Genetic ; Humans ; RNA Interference ; RNA, Small Interfering/genetics ; RNA, Viral/genetics ; SARS-CoV-2/genetics
Chemical Substances	RNA, Small Interfering ; RNA, Viral
Language	English
Publishing date	2021-04-23
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-88310-8
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Cyclic alternation of quiet and active sleep states in the octopus.

Medeiros, Sylvia Lima de Souza / Paiva, Mizziara Marlen Matias de / Lopes, Paulo Henrique / Blanco, Wilfredo / Lima, Françoise Dantas de / Oliveira, Jaime Bruno Cirne de / Medeiros, Inácio Gomes / Sequerra, Eduardo Bouth / de Souza, Sandro / Leite, Tatiana Silva / Ribeiro, Sidarta

iScience

2021 Volume 24, Issue 4, Page(s) 102223

Abstract: Previous observations suggest the existence of 'Active sleep' in cephalopods. To investigate in detail the behavioral structure of cephalopod sleep, we video-recorded four adult specimens ... ...

Abstract	Previous observations suggest the existence of 'Active sleep' in cephalopods. To investigate in detail the behavioral structure of cephalopod sleep, we video-recorded four adult specimens of
Language	English
Publishing date	2021-03-25
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2021.102223
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Article ; Online: Arbovirus expansion: New species of culicids infected by the Chikungunya virus in an urban park of Brazil.

de Melo Ximenes, Maria de Fátima Freire / de Araújo Galvão, Josélio Maria / Inacio, Cássio Lázaro Silva / Macêdo E Silva, Virgínia Penéllope / Pereira, Raíssa Liane do Nascimento / Pinheiro, Marcos Paulo Gomes / de Medeiros Silva, Marcel Miranda / Gomes, Carlos Eduardo Simões

Acta tropica

2020 Volume 209, Page(s) 105538

Abstract: The Dengue, Zika and Chikungunya viruses have been spreading in tropical regions, causing epidemics with high morbidity rates and fatal cases. The aim of this study was to assess the diversity and abundance of culicid species and the presence of ... ...

Abstract	The Dengue, Zika and Chikungunya viruses have been spreading in tropical regions, causing epidemics with high morbidity rates and fatal cases. The aim of this study was to assess the diversity and abundance of culicid species and the presence of arboviruses in mosquitoes, at the epicenter of an epidemic outbreak that occurred in people living near an urban Atlantic Forest park. Mosquitoes were captured with a Shannon trap between 2 and 6 pm in seven months of 2019. The Chikungunya virus was investigated according to the protocol described by Lanciotti (2007). The most abundant species were Wyeomyia bourrouli (66.9%) and Aedes albopictus (23.9%). Also captured were Aedes fluviatilis (3.2%); Haemagogus leucocelaenus (2.2%); Aedes scapularis (2.2%); Aedes aegypti (1.6%); Aedes serratus and (0.3%) and Aedes taeniorhynchus (0.3%). The Chikungunya virus was identified in A. aegypti females; A. albopictus females and males; Aedes fluviatilis and Wy.bourrouli. The presence of the Chikungunya virus in the afore mentioned mosquitoes reinforces the hypothesis that arbovirus expansion is associated with the participation of other mosquito species in the transmission areas, primarily the Chikungunya virus in the study area. The data also demonstrate the need for permanent entomological surveillance and measures to preserve the area, in order to hinder its degradation, the adaptation of culicid species to new habitats and the formation of enzootic cycles of these viruses in the forest.
MeSH term(s)	Aedes/virology ; Animals ; Brazil ; Chikungunya virus/isolation & purification ; Culicidae/classification ; Culicidae/virology ; Female ; Male
Language	English
Publishing date	2020-05-23
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	210415-5
ISSN	1873-6254 ; 0001-706X
ISSN (online)	1873-6254
ISSN	0001-706X
DOI	10.1016/j.actatropica.2020.105538
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Article ; Online: A decision tree to improve identification of pathogenic mutations in clinical practice

Priscilla Machado do Nascimento / Inácio Gomes Medeiros / Raul Maia Falcão / Beatriz Stransky / Jorge Estefano Santana de Souza

BMC Medical Informatics and Decision Making, Vol 20, Iss 1, Pp 1-

2020 Volume 11

Abstract: Abstract Background A variant of unknown significance (VUS) is a variant form of a gene that has been identified through genetic testing, but whose significance to the organism function is not known. An actual challenge in precision medicine is to ... ...

Abstract	Abstract Background A variant of unknown significance (VUS) is a variant form of a gene that has been identified through genetic testing, but whose significance to the organism function is not known. An actual challenge in precision medicine is to precisely identify which detected mutations from a sequencing process have a suitable role in the treatment or diagnosis of a disease. The average accuracy of pathogenicity predictors is 85%. However, there is a significant discordance about the identification of mutational impact and pathogenicity among them. Therefore, manual verification is necessary for confirming the real effect of a mutation in its casuistic. Methods In this work, we use variables categorization and selection for building a decision tree model, and later we measure and compare its accuracy with four known mutation predictors and seventeen supervised machine-learning (ML) algorithms. Results The results showed that the proposed tree reached the highest precision among all tested variables: 91% for True Neutrals, 8% for False Neutrals, 9% for False Pathogenic, and 92% for True Pathogenic. Conclusions The decision tree exceptionally demonstrated high classification precision with cancer data, producing consistently relevant forecasts for the sample tests with an accuracy close to the best ones achieved from supervised ML algorithms. Besides, the decision tree algorithm is easier to apply in clinical practice by non-IT experts. From the cancer research community perspective, this approach can be successfully applied as an alternative for the determination of potential pathogenicity of VOUS.
Keywords	Decision tree ; VOUS ; Pathogenicity ; Mutation ; Predictor ; Precision medicine ; Computer applications to medicine. Medical informatics ; R858-859.7
Subject code	006
Language	English
Publishing date	2020-03-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
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Article: Identification of plasmids from Brazilian Chromobacterium violaceum strains

Canadian journal of microbiology. 2022, v. 68, no. 1

2022

Abstract: Chromobacterium violaceum is an opportunistic pathogen found in tropical and subtropical regions worldwide. Chromobacterium violaceum infections are difficult to treat, and many strains are resistant to antibiotics. Recently, a novel plasmid (pChV1) was ... ...

Abstract	Chromobacterium violaceum is an opportunistic pathogen found in tropical and subtropical regions worldwide. Chromobacterium violaceum infections are difficult to treat, and many strains are resistant to antibiotics. Recently, a novel plasmid (pChV1) was discovered in the type strain ATCC 12472, suggesting that other C. violaceum strains may harbor extra-chromosomal DNA. The aim of the present study was to detect and compare new plasmids in Brazilian strains of C. violaceum using next-generation sequencing techniques. We obtained draft genomes of six plasmids from strains isolated from the Amazon region and aligned them with pChV1. At least three plasmids, CVAC05, CVACO2, and CVT8, were similar to pChV1. Phylogenetic analysis suggested that these new extra-chromosomal DNA sequences have a common origin with pChV1 but have diverged. Many of the ORFs detected were related to plasmid segregation/maintenance, viral structural proteins, and proteins with unknown functions. These findings may enable better genetic manipulation of C. violaceum, which will enhance our ability to exploit this valuable microorganism in industrial and clinical applications.
Keywords	Chromobacterium violaceum ; genetic engineering ; genome ; microbiology ; opportunistic pathogens ; phylogeny ; plasmids ; Amazonia
Language	English
Size	p. 45-54.
Publishing place	Canadian Science Publishing
Document type	Article
ZDB-ID	280534-0
ISSN	1480-3275 ; 0008-4166
ISSN (online)	1480-3275
ISSN	0008-4166
DOI	10.1139/cjm-2021-0197
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Article ; Online: A decision tree to improve identification of pathogenic mutations in clinical practice.

do Nascimento, Priscilla Machado / Medeiros, Inácio Gomes / Falcão, Raul Maia / Stransky, Beatriz / de Souza, Jorge Estefano Santana

BMC medical informatics and decision making

2020 Volume 20, Issue 1, Page(s) 52

Abstract: Background: A variant of unknown significance (VUS) is a variant form of a gene that has been identified through genetic testing, but whose significance to the organism function is not known. An actual challenge in precision medicine is to precisely ... ...

Abstract	Background: A variant of unknown significance (VUS) is a variant form of a gene that has been identified through genetic testing, but whose significance to the organism function is not known. An actual challenge in precision medicine is to precisely identify which detected mutations from a sequencing process have a suitable role in the treatment or diagnosis of a disease. The average accuracy of pathogenicity predictors is 85%. However, there is a significant discordance about the identification of mutational impact and pathogenicity among them. Therefore, manual verification is necessary for confirming the real effect of a mutation in its casuistic. Methods: In this work, we use variables categorization and selection for building a decision tree model, and later we measure and compare its accuracy with four known mutation predictors and seventeen supervised machine-learning (ML) algorithms. Results: The results showed that the proposed tree reached the highest precision among all tested variables: 91% for True Neutrals, 8% for False Neutrals, 9% for False Pathogenic, and 92% for True Pathogenic. Conclusions: The decision tree exceptionally demonstrated high classification precision with cancer data, producing consistently relevant forecasts for the sample tests with an accuracy close to the best ones achieved from supervised ML algorithms. Besides, the decision tree algorithm is easier to apply in clinical practice by non-IT experts. From the cancer research community perspective, this approach can be successfully applied as an alternative for the determination of potential pathogenicity of VOUS.
MeSH term(s)	Algorithms ; Decision Trees ; Humans ; Mutation ; Precision Medicine/methods ; Supervised Machine Learning ; Virulence/genetics
Language	English
Publishing date	2020-03-10
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2046490-3
ISSN	1472-6947 ; 1472-6947
ISSN (online)	1472-6947
ISSN	1472-6947
DOI	10.1186/s12911-020-1060-0
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Article ; Online: Vaginal cancer: Why should we care? Anatomy, staging and in-depth imaging-based review of vaginal malignancies focusing on MRI and PET/CT.

Albuquerque, Kamila Seidel / Zoghbi, Karina Kuhl / Gomes, Natália Borges Nunes / Libânio, Bruna Brandão / Souza E Silva, Tábata Xavit / de Araújo, Eduardo Medeiros / Lewin, Fabio / Pedroso, Maria Helena Naves Inácio / Torres, Ulysses S / D'Ippolito, Giuseppe / Racy, Douglas Jorge / Bernardo, Graziela Campos Oliveira

Clinical imaging

2022 Volume 84, Page(s) 65–78

Abstract: Vaginal cancer often poses a challenge for clinical and radiological diagnosis, and its risk factors, progression, and treatment are still poorly established. Although vaginal malignancies are rare, even globally, their rates have increased due to the ... ...

Abstract	Vaginal cancer often poses a challenge for clinical and radiological diagnosis, and its risk factors, progression, and treatment are still poorly established. Although vaginal malignancies are rare, even globally, their rates have increased due to the increased access to healthcare and the evolution of screening measures and diagnostic methods. Because the vaginal cavity is a virtual space, it can harbor lesions that often go unnoticed and, not infrequently, diagnosed belatedly. MRI and, more recently, PET/CT are part of the imaging armamentarium that have already been incorporated into the clinical staging and management of gynecological tumors, allowing excellent morphological characterization of the lesion, its topography and relationship with adjacent structures for the investigation of disease dissemination, overcoming limitations of clinical methods, such as speculum examination, usually restricted to observation only of the superficial characteristics of these lesions. Some vaginal neoplasms have characteristic MRI patterns, which, combined with expert knowledge of anatomy, allow identification of local macroscopic details (such as the mucosal, submucosal, and muscle layers). Furthermore, the application of PET/CT, already well established for identifying systemic disease, has a large impact on patient prognosis. The objective of this work is to review the epidemiological aspects of primary vaginal cancers and the imaging patterns of their main histological subtypes based on MRI and PET/CT, with a brief discussion of the local anatomy, oncological staging, and treatment.
MeSH term(s)	Female ; Fluorodeoxyglucose F18 ; Humans ; Magnetic Resonance Imaging/methods ; Neoplasm Staging ; Positron Emission Tomography Computed Tomography/methods ; Positron-Emission Tomography/methods ; Prognosis ; Vaginal Neoplasms/diagnostic imaging
Chemical Substances	Fluorodeoxyglucose F18 (0Z5B2CJX4D)
Language	English
Publishing date	2022-02-03
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	1028123-x
ISSN	1873-4499 ; 0899-7071
ISSN (online)	1873-4499
ISSN	0899-7071
DOI	10.1016/j.clinimag.2022.01.009
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