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Article ; Online: Tracing Changes in Shape of Historical Artefacts Across Time Using 3D Scans

Giovanni Maria Pala / Lisandra S. Costiner

Journal of Open Humanities Data, Vol

A New Computational Approach

2022 Volume 8

Abstract: This paper pioneers a new computational approach for the study of changes in shape of objects across time. Previously, such a study was undertaken by scholars using a purely visual approach and relied on images of objects or in-person observations. This ... ...

Abstract	This paper pioneers a new computational approach for the study of changes in shape of objects across time. Previously, such a study was undertaken by scholars using a purely visual approach and relied on images of objects or in-person observations. This paper’s approach is based on 3D scans of historical artefacts. Sample points are extracted from these 3D scans and the distance between analogous points across different objects is computed using an approximation of the Wasserstein metric, namely the Sinkhorn distance. In this paper, the approach is demonstrated on a small set of ancient Greek vessels of the Krater, Pelike, and Kylix types, as the variation in their shapes across time is well known to archaeologists. Results offer, for the first time, a way of quantifying differences between objects. Benefits of this approach lie in its ability to quantify change, to study complex 3D material, and to analyse large datasets of objects, opening the possibility of constructing new large-scale studies of object shape across time and geographical regions. These have a range of applications in art history, archaeology, digital humanities, museology and extended reality studies.
Keywords	shape comparison ; 3d models ; digital humanities ; archaeology ; digital art history ; sinkhorn distance ; History of scholarship and learning. The humanities ; AZ20-999 ; Language and Literature ; P
Subject code	930
Language	English
Publishing date	2022-05-01T00:00:00Z
Publisher	Ubiquity Press
Document type	Article ; Online
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Article ; Online: Phylogeography of 27,000 SARS-CoV-2 Genomes

Teresa Rito / Martin B. Richards / Maria Pala / Margarida Correia-Neves / Pedro A. Soares

Microorganisms, Vol 8, Iss 1678, p

Europe as the Major Source of the COVID-19 Pandemic

2020 Volume 1678

Abstract: The novel coronavirus SARS-CoV-2 emerged from a zoonotic transmission in China towards the end of 2019, rapidly leading to a global pandemic on a scale not seen for a century. In order to cast fresh light on the spread of the virus and on the ... ...

Abstract	The novel coronavirus SARS-CoV-2 emerged from a zoonotic transmission in China towards the end of 2019, rapidly leading to a global pandemic on a scale not seen for a century. In order to cast fresh light on the spread of the virus and on the effectiveness of the containment measures adopted globally, we used 26,869 SARS-CoV-2 genomes to build a phylogeny with 20,247 mutation events and adopted a phylogeographic approach. We confirmed that the phylogeny pinpoints China as the origin of the pandemic with major founders worldwide, mainly during January 2020. However, a single specific East Asian founder underwent massive radiation in Europe and became the main actor of the subsequent spread worldwide during March 2020. This lineage accounts for the great majority of cases detected globally and even spread back to the source in East Asia. Despite an East Asian source, therefore, the global pandemic was mainly fueled by its expansion across and out of Europe. It seems likely that travel bans established throughout the world in the second half of March helped to decrease the number of intercontinental exchanges, particularly from mainland China, but were less effective between Europe and North America where exchanges in both directions are visible up to April, long after bans were imposed.
Keywords	phylogeography ; phylogenomics ; molecular epidemiology ; travel bans ; intercontinental founders ; SARS-COV-2 lineages ; Biology (General) ; QH301-705.5
Subject code	950
Language	English
Publishing date	2020-10-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
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Article ; Online: New insights on tuberculosis transmission dynamics and drug susceptibility profiles among the prison population in Southern Brazil based on whole-genome sequencing.

Anselmo, Lívia Maria Pala / Gallo, Juliana Failde / Pinhata, Juliana Maira Watanabe / Peronni, Kamila Chagas / Silva Junior, Wilson Araújo da / Ruy, Patricia de Cássia / Conceição, Emilyn Costa / Dippenaar, Anzaan / Warren, Robin Mark / Monroe, Aline Aparecida / Oliveira, Rosangela Siqueira / Bollela, Valdes Roberto

Revista da Sociedade Brasileira de Medicina Tropical

2023 Volume 56, Page(s) e0181

Abstract: Background: The rate of tuberculosis (TB) infection among the prison population (PP) in Brazil is 28 times higher than that in the general population, and prison environment favors the spread of TB.: Objective: To describe TB transmission dynamics ... ...

Abstract	Background: The rate of tuberculosis (TB) infection among the prison population (PP) in Brazil is 28 times higher than that in the general population, and prison environment favors the spread of TB. Objective: To describe TB transmission dynamics and drug resistance profiles in PP using whole-genome sequencing (WGS). Methods: This was a retrospective study of Mycobacterium tuberculosis cultivated from people incarcerated in 55 prisons between 2016 and 2019; only one isolate per prisoner was included. Information about movement from one prison to another was tracked. Clinical information was collected, and WGS was performed on isolates obtained at the time of TB diagnosis. Results: Among 134 prisoners included in the study, we detected 16 clusters with a total of 58 (43%) cases of M. tuberculosis. Clusters ranged from two to seven isolates with five or fewer single nucleotide polymorphism (SNP) differences, suggesting a recent transmission. Six (4.4%) isolates were resistant to at least one anti-TB drug. Two of these clustered together and showed resistance to rifampicin, isoniazid, and fluoroquinolones, with 100% concordance between WGS and phenotypic drug-susceptibility testing. Prisoners with clustered isolates had a high amount of movement between prisons (two to eight moves) during the study period. Conclusions: WGS demonstrated the recent transmission of TB within prisons in Brazil. The high movement among prisoners seems to be related to the transmission of the same M. tuberculosis strain within the prison system. Screening for TB before and after the movement of prisoners using rapid molecular tests could play a role in reducing transmission.
MeSH term(s)	Humans ; Prisons ; Tuberculosis, Multidrug-Resistant/drug therapy ; Brazil/epidemiology ; Retrospective Studies ; Tuberculosis/diagnosis ; Antitubercular Agents/therapeutic use ; Mycobacterium tuberculosis/genetics ; Latent Tuberculosis ; Microbial Sensitivity Tests
Chemical Substances	Antitubercular Agents
Language	English
Publishing date	2023-02-20
Publishing country	Brazil
Document type	Journal Article
ZDB-ID	1038126-0
ISSN	1678-9849 ; 0037-8682
ISSN (online)	1678-9849
ISSN	0037-8682
DOI	10.1590/0037-8682-0181-2022
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Article ; Online: Mycobacterium tuberculosis spoligotypes and drug-resistant characterization from Beira compared to genotypes circulating in Mozambique

Lívia Maria Pala Anselmo / Emilyn Costa Conceição / Evangelina Namburete / Cinara Feliciano / Silvana Spindola / Christophe Sola / Valdes Roberto Bollela

Revista da Sociedade Brasileira de Medicina Tropical, Vol

2019 Volume 52

Abstract: Abstract INTRODUCTION Mozambique is one of three countries with high prevalence of tuberculosis (TB), TB/human immunodeficiency virus coinfection, and multidrug-resistant TB. We aimed to describe Mycobacterium tuberculosis spoligotypes circulating among ... ...

Abstract	Abstract INTRODUCTION Mozambique is one of three countries with high prevalence of tuberculosis (TB), TB/human immunodeficiency virus coinfection, and multidrug-resistant TB. We aimed to describe Mycobacterium tuberculosis spoligotypes circulating among drug resistant (DR) strains from Beira, Mozambique comparing them with genotypes in the country. METHODS: We performed spoligotyping of 79 M. tuberculosis suspected of DR-TB compared all spoligotype patterns published on the international database and PubMed. RESULTS: Both in Beira and Mozambique (n=578), the main clades were Latin-American-Mediterranean, East-African-Indian, Beijing and T, with no extensively DR TB cases. CONCLUSIONS: Beira and Mozambique share the same population genetic structure of M. tuberculosis.
Keywords	Genotyping ; Spoligotyping ; Tuberculosis ; Arctic medicine. Tropical medicine ; RC955-962
Language	English
Publishing date	2019-11-01T00:00:00Z
Publisher	Sociedade Brasileira de Medicina Tropical (SBMT)
Document type	Article ; Online
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Article ; Online: Helena’s Many Daughters

International Journal of Molecular Sciences, Vol 23, Iss 6725, p

More Mitogenome Diversity behind the Most Common West Eurasian mtDNA Control Region Haplotype in an Extended Italian Population Sample

2022 Volume 6725

Abstract: The high number of matching haplotypes of the most common mitochondrial (mt)DNA lineages are considered to be the greatest limitation for forensic applications. This study investigates the potential to solve this constraint by massively parallel ... ...

Abstract	The high number of matching haplotypes of the most common mitochondrial (mt)DNA lineages are considered to be the greatest limitation for forensic applications. This study investigates the potential to solve this constraint by massively parallel sequencing a large number of mitogenomes that share the most common West Eurasian mtDNA control region (CR) haplotype motif (263G 315.1C 16519C). We augmented a pilot study on 29 to a total of 216 Italian mitogenomes that represents the largest set of the most common CR haplotype compiled from a single country. The extended population sample confirmed and extended the huge coding region diversity behind the most common CR motif. Complete mitogenome sequencing allowed for the detection of 163 distinct haplotypes, raising the power of discrimination from 0 (CR) to 99.6% (mitogenome). The mtDNAs were clustered into 61 named clades of haplogroup H and did not reveal phylogeographic trends within Italy. Rapid individualization approaches for investigative purposes are limited to the most frequent H clades of the dataset, viz. H1, H3, and H7.
Keywords	massively parallel sequencing ; next-generation sequencing ; forensics ; most common haplotype ; power of discrimination ; mtDNA haplogroup H ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Language	English
Publishing date	2022-06-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
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Article: Xpert MTB/RIF performance to diagnose tuberculosis and rifampicin resistance in a reference centre in southern Brazil.

Feliciano, Cinara Silva / Menon, Lucas José Bazzo / Anselmo, Livia Maria Pala / Dippenaar, Anzaan / Warren, Robin Mark / Silva, Wilson Araújo / Bollela, Valdes Roberto

ERJ open research

2019 Volume 5, Issue 3

Abstract: Effective treatment of tuberculosis (TB) remains a serious public health problem in many countries, including Brazil, especially when considering drug-resistant disease. Xpert MTB/RIF has been implemented in many countries to reduce the time to TB ... ...

Abstract	Effective treatment of tuberculosis (TB) remains a serious public health problem in many countries, including Brazil, especially when considering drug-resistant disease. Xpert MTB/RIF has been implemented in many countries to reduce the time to TB diagnosis and to rapidly detect rifampicin resistance. The study aimed to describe and evaluate Xpert MTB/RIF performance in diagnosing pulmonary TB and rifampicin resistance in a tertiary healthcare facility in Brazil. A cross-sectional study was performed, which included all isolates of confirmed pulmonary TB patients from 2015 to 2018. Both Xpert MTB/RIF and GenoType MTBDR
Language	English
Publishing date	2019-08-05
Publishing country	England
Document type	Journal Article
ZDB-ID	2827830-6
ISSN	2312-0541
ISSN	2312-0541
DOI	10.1183/23120541.00043-2019
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Article ; Online: Mycobacterium tuberculosis spoligotypes and drug-resistant characterization from Beira compared to genotypes circulating in Mozambique.

Anselmo, Lívia Maria Pala / Conceição, Emilyn Costa / Namburete, Evangelina / Feliciano, Cinara / Spindola, Silvana / Sola, Christophe / Bollela, Valdes Roberto

Revista da Sociedade Brasileira de Medicina Tropical

2019 Volume 52, Page(s) e20190257

Abstract: Introduction: Mozambique is one of three countries with high prevalence of tuberculosis (TB), TB/human immunodeficiency virus coinfection, and multidrug-resistant TB. We aimed to describe Mycobacterium tuberculosis spoligotypes circulating among drug ... ...

Abstract	Introduction: Mozambique is one of three countries with high prevalence of tuberculosis (TB), TB/human immunodeficiency virus coinfection, and multidrug-resistant TB. We aimed to describe Mycobacterium tuberculosis spoligotypes circulating among drug resistant (DR) strains from Beira, Mozambique comparing them with genotypes in the country. Methods: We performed spoligotyping of 79 M. tuberculosis suspected of DR-TB compared all spoligotype patterns published on the international database and PubMed. Results: Both in Beira and Mozambique (n=578), the main clades were Latin-American-Mediterranean, East-African-Indian, Beijing and T, with no extensively DR TB cases. Conclusions: Beira and Mozambique share the same population genetic structure of M. tuberculosis.
MeSH term(s)	Bacterial Typing Techniques ; Genetic Variation/genetics ; Genotype ; Humans ; Mozambique ; Mutation/genetics ; Mycobacterium tuberculosis/genetics ; Phylogeny ; Tuberculosis, Multidrug-Resistant/microbiology
Language	English
Publishing date	2019-11-25
Publishing country	Brazil
Document type	Comparative Study ; Journal Article
ZDB-ID	1038126-0
ISSN	1678-9849 ; 0037-8682
ISSN (online)	1678-9849
ISSN	0037-8682
DOI	10.1590/0037-8682-0257-2019
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Article ; Online: Xpert MTB/RIF performance to diagnose tuberculosis and rifampicin resistance in a reference centre in southern Brazil

Cinara Silva Feliciano / Lucas José Bazzo Menon / Livia Maria Pala Anselmo / Anzaan Dippenaar / Robin Mark Warren / Wilson Araújo Silva / Valdes Roberto Bollela

ERJ Open Research, Vol 5, Iss

2019 Volume 3

Abstract	Effective treatment of tuberculosis (TB) remains a serious public health problem in many countries, including Brazil, especially when considering drug-resistant disease. Xpert MTB/RIF has been implemented in many countries to reduce the time to TB diagnosis and to rapidly detect rifampicin resistance. The study aimed to describe and evaluate Xpert MTB/RIF performance in diagnosing pulmonary TB and rifampicin resistance in a tertiary healthcare facility in Brazil. A cross-sectional study was performed, which included all isolates of confirmed pulmonary TB patients from 2015 to 2018. Both Xpert MTB/RIF and GenoType MTBDRplus assays were performed to detect rifampicin and isoniazid resistance. In addition, isolates with detected resistance to rifampicin and/or isoniazid were analysed by phenotypic testing using MGIT-960 SIRE kit and whole-genome sequencing (WGS) using Illumina MiSeq Sequencing System. 2148 respiratory specimens tested with Xpert MTB/RIF were included: n=1556 sputum, n=348 bronchoalveolar lavage and n=244 gastric washing. The overall Xpert MTB/RIF sensitivity in sputum was 94% and the overall specificity was 98%. The negative predictive value in sputum of all the patients was 99% with a positive predictive value of 89%. The concordance between Xpert MTB/RIF and phenotypic susceptibility test was 94.1%, while its concordance with WGS was 78.9%. Xpert MTB/RIF is a rapid and accurate diagnostic strategy for pulmonary TB, which can contribute to improvement in TB control. However, detection of rifampicin resistance might be associated with false-positive results.
Keywords	Medicine ; R
Subject code	610
Language	English
Publishing date	2019-08-01T00:00:00Z
Publisher	European Respiratory Society
Document type	Article ; Online
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Article ; Online: A predictive score followed by nucleic acid amplification for adult tuberculous meningitis diagnosis in Southern Brazil.

Anselmo, Lívia Maria Pala / Feliciano, Cinara / Mauad, Fernando / do Nascimento, Margarida Passeri / Pocente, Renata Candido / Silva, Jorgete Maria / Bollela, Valdes Roberto

Journal of the neurological sciences

2017 Volume 379, Page(s) 253–258

Abstract: From 2012 to 2013, 300 adults under investigation of tuberculous meningitis (TBM) were tested with polymerase chain reaction (PCR) in central spinal fluid (CSF), followed by TBM score calculation. There were 33(11%) confirmed TBM cases based on clinical ... ...

Abstract	From 2012 to 2013, 300 adults under investigation of tuberculous meningitis (TBM) were tested with polymerase chain reaction (PCR) in central spinal fluid (CSF), followed by TBM score calculation. There were 33(11%) confirmed TBM cases based on clinical findings, CSF-culture; biopsy/necropsy exams and clinical improvement after tuberculosis specific treatment. Other 267 adults were classified as non-TBM. Based on the original score there were 143 possible cases (6≤score≤11) and 20(60.6%) out of 33 TBM; among 27 probable TBM (score≥12) there were 13/33 (39.4%) confirmed cases. The CSF-PCR detected 48% (16/33) of TBM. Based on these findings, a new cut-off point was proposed to differentiate probable (score≥10) from possible (6≤score≤9) TBM. After score adjustment, there were 61 probable TBM with 26/33 (78.8%) TBM, and among the 109 possible TBM there were 7/33(21.2%) confirmed cases. In both systems, there were 130 non-TBM (score≤5) and no confirmed TBM. The association of adjusted score (≥10) and CSF-PCR showed high sensitivity (90.9%) and specificity (86.9%), positive and negative predictive value of 46.2% and 98.9%, respectively. The combination of CSF-PCR and TBM score is a useful tool for the management of adults under investigation of TBM, but the best cut-off point may need local/regional adjustments.
Language	English
Publishing date	2017-08-15
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	80160-4
ISSN	1878-5883 ; 0022-510X ; 0374-8642
ISSN (online)	1878-5883
ISSN	0022-510X ; 0374-8642
DOI	10.1016/j.jns.2017.06.016
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Article ; Online: Molecular epidemiology of Mycobacterium tuberculosis in Brazil before the whole genome sequencing era

Emilyn Costa Conceição / Richard Steiner Salvato / Karen Machado Gomes / Arthur Emil dos Santos Guimarães / Marília Lima da Conceição / Ricardo José de Paula Souza e Guimarães / Abhinav Sharma / Ismari Perini Furlaneto / Regina Bones Barcellos / Valdes Roberto Bollela / Lívia Maria Pala Anselmo / Maria Carolina Sisco / Cristina Viana Niero / Lucilaine Ferrazoli / Guislaine Refrégier / Maria Cristina da Silva Lourenço / Harrison Magdinier Gomes / Artemir Coelho de Brito / Marcos Catanho /

Rafael Silva Duarte / Philip Noel Suffys / Karla Valéria Batista Lima

Memórias do Instituto Oswaldo Cruz., Vol

a literature review

2021 Volume 116

Abstract: Molecular-typing can help in unraveling epidemiological scenarios and improvement for disease control strategies. A literature review of Mycobacterium tuberculosis transmission in Brazil through genotyping on 56 studies published from 1996-2019 was ... ...

Abstract	Molecular-typing can help in unraveling epidemiological scenarios and improvement for disease control strategies. A literature review of Mycobacterium tuberculosis transmission in Brazil through genotyping on 56 studies published from 1996-2019 was performed. The clustering rate for mycobacterial interspersed repetitive units - variable tandem repeats (MIRU-VNTR) of 1,613 isolates were: 73%, 33% and 28% based on 12, 15 and 24-loci, respectively; while for RFLP-IS6110 were: 84% among prison population in Rio de Janeiro, 69% among multidrug-resistant isolates in Rio Grande do Sul, and 56.2% in general population in São Paulo. These findings could improve tuberculosis (TB) surveillance and set up a solid basis to build a database of Mycobacterium genomes.
Keywords	tuberculosis ; Mycobacterium tuberculosis ; genotyping ; MIRU-VNTR typing ; RFLP-IS6110 ; Brazil ; Arctic medicine. Tropical medicine ; RC955-962 ; Microbiology ; QR1-502
Language	English
Publishing date	2021-03-01T00:00:00Z
Publisher	Instituto Oswaldo Cruz, Ministério da Saúde
Document type	Article ; Online
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