LIM/01 - Laboratório de Informática Médica

URI Permanente desta comunidade

https://observatorio.fm.usp.br/handle/OPI/3598
O Laboratório de Informática Médica é ligado ao Departamento de Patologia da Faculdade de Medicina da Universidade de São Paulo (FMUSP).

Linhas de pesquisa: aplicações da lógica Fuzzy em biomedicina; aprendizagem e cognição: fisiologia e patologia eletrofisiológica da cognição; engenharia biomédica; epidemiologia das doenças transmissíveis; física matemática; geociências; informática médica; métodos e técnicas de ensino; modelos matemáticos aplicados à epidemiologia; saúde coletiva e telemedicina.

Site oficial: http://limhc.fm.usp.br/portal/lim01-laboratorio-de-informatica-medica/

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Prevalence of Serological and Molecular Markers of Hepatitis B Virus in Patients with Suspected Acute Hepatitis in Brazilian Health Services
(2023) SITNIK, R.; OLIVEIRA, K.; OLIVEIRA, K.; SIQUEIRA, R.; DOMINGUES, T.; ROBINSON, P.; SOUZA, L.; OLIVEIRA, D.; PANICO, C.; INOUE, C.; MALUF, M.; NETO, R.; SOUZA, F.; PINHO, J.
article 0 Citação(ões) na Scopus
Toxoplasma gondii and Neospora caninum antibody seroprevalence and risk factors among dogs treated at Public Veterinary Hospitals in São Paulo, Brazil
(2023) SANTOS, Elidia Zotelli dos; SOARES, Herbert Souza; SANTOS, Stephanie Rodrigues dos; MORAES FILHO, Jonas; PENA, Hilda Fatima de Jesus; AMAKU, Marcos; GENNARI, Solange Maria
Dogs can be infected by Toxoplasma gondii and Neospora caninum, for which they function, respectively, as intermediate, and definitive hosts. In the present study seroprevalence against T. gondii and N. caninum antibodies, were determined by indirect fluorescent antibody test (cut off of 16 and 50, respectively), in dogs that were treated at public veterinary hospitals in the metropolitan region of Sao Paulo and risk factors were identified. Out of the 1,194 samples 125 (10.5%; 95% CI: 8.8-12.3%) were positive for T. gondii and 9 (0.75%, 95% CI: 0.34-1.4%) for N. caninum. For T. gondii, statistical differences were observed between the proportions of positive dogs and different zones of the municipality (p = 0.025), and age (p = 0.02), higher among older dogs. The keepers were invited to answer an epidemiological questionnaire to analyze risk factors, and 471 (39.4%) agreed to be interviewed, and among their dogs 65 (13.8%) were T. gondii seropositive. Age group above 8 years (OR = 3.63; 95% CI: 1.08-12.23) was a risk factor and having a defined breed (OR = 0.49; 95% CI: 0.25-0.96) was a protective factor for T. gondii infection. Because of the low number of dogs positive for N. caninum, risk factors for this coccidium were not determined.
article 0 Citação(ões) na Scopus
Core Promoter and Pre-Core Variants of the Hepatitis B Virus (HBV) Are Frequent in Chronic Hepatitis B HBeAg-Negative Patients Infected by Genotypes A and D
(2023) REUTER, Tania; GOMES-GOUVEA, Michele Soares; CHUFFI, Samira; DUQUE, Ulisses Horst; PERINI, Waltesia; AZEVEDO, Raymundo Soares; PINHO, Joao Renato Rebello; LEWIS-XIMENEZ, Lia L.; VILLAR, Livia Melo; ESPUL, Carlos Alberto; PUJOL, Flor H.; ROMAN, Sonia
In Brazil, hepatitis B virus endemicity is low, moderate, or high in some areas, such as Espirito Santo State in the southeast region. In this study, we intend to characterize the basal core promoter (BCP) and pre-core region (PC) variants and their association with clinical/epidemiological disease patterns in patients infected with genotypes A and D. The study included 116 chronic hepatitis B patients from Espirito Santo State, Southeast Brazil, infected with genotypes A and D. Basal core promoter (BCP) and pre-core mutations were analyzed in these patients. The frequency of BCP and PC mutations was compared with age, HBeAg status, HBV genotype and subgenotype, HBV-DNA level, clinical classification, and transmission route. HBeAg-negative status was found in 101 (87.1%) patients: 87 (75.0%) were infected with genotype A (A1 = 85; A2 = 2) and 29 (25.0%) were infected with genotype D (D3 = 24; D4 = 3; D2 = 2). BCP + PC variants altogether were more frequent (48.1%) in genotype D than in genotype A strains (6.0%) (p < 0.001). When this evaluation was performed considering the cases that presented only the A1762T and/or G1764A (BCP) mutations, it was observed that the frequency was higher in genotype A (67.5%) compared to genotype D (7.4%) (p < 0.001). On the other hand, considering the samples with mutations only in positions G1896A and/or G1899A (PC), the frequency was higher in genotype D (75.8%) than in genotype A (6.9%) (p < 0.001). Interestingly, HBV DNA was lower than 2000 IU/mL especially when both BCP/PC mutations were present (p < 0.001) or when only PC mutations were detected (p = 0.047), reinforcing their role in viral replication.
article 0 Citação(ões) na Scopus
Seroprevalence of Zika in Brazil stratified by age and geographic distribution
(2023) BOTOSSO, Viviane Fongaro; PRECIOSO, Alexander Roberto; WILDER-SMITH, Annelies; OLIVEIRA, Danielle Bruna Leal de; OLIVEIRA, Fabyano Bruno Leal de; OLIVEIRA, Cairo Monteiro De; SOARES, Camila Pereira; OLIVEIRA, Lucyana Trindade Leal; SANTO, Ralyria Mello Vieira dos; UTESCHER, Carla Lilian de Agostini; COUTINHO, Francisco Antonio Bezerra; MASSAD, Eduardo
Congenital Zika is a devastating consequence of maternal Zika virus infections. Estimates of age-dependent seroprevalence profiles are central to our understanding of the force of Zika virus infections. We set out to calculate the age-dependent seroprevalence of Zika virus infections in Brazil. We analyzed serum samples stratified by age and geographic location, collected from 2016 to 2019, from about 16,000 volunteers enrolled in a Phase 3 dengue vaccine trial led by the Institute Butantan in Brazil. Our results show that Zika seroprevalence has a remarkable age-dependent and geographical distribution, with an average age of the first infection varying from region to region, ranging from 4.97 (3.03-5.41) to 7.24 (6.98-7.90) years. The calculated basic reproduction number, $ {R}_0 $, varied from region to region, ranging from 1.18 (1.04-1.41) to 2.33 (1.54-3.85). Such data are paramount to determine the optimal age to vaccinate against Zika, if and when such a vaccine becomes available.
article 6 Citação(ões) na Scopus
Better to be in agreement than in bad company A critical analysis of many kappa-like tests
(2023) SILVEIRA, Paulo Sergio Panse; SIQUEIRA, Jose Oliveira
We assessed several agreement coefficients applied in 2x2 contingency tables, which are commonly applied in research due to dichotomization. Here, we not only studied some specific estimators but also developed a general method for the study of any estimator candidate to be an agreement measurement. This method was developed in open-source R codes and it is available to the researchers. We tested this method by verifying the performance of several traditional estimators over all possible configurations with sizes ranging from 1 to 68 (total of 1,028,789 tables). Cohen's kappa showed handicapped behavior similar to Pearson's r, Yule's Q, and Yule's Y. Scott's pi, and Shankar and Bangdiwala's B seem to better assess situations of disagreement than agreement between raters. Krippendorff's alpha emulates, without any advantage, Scott's pi in cases with nominal variables and two raters. Dice's F1 and McNemar's chi-squared incompletely assess the information of the contingency table, showing the poorest performance among all. We concluded that Cohen's kappa is a measurement of association and McNemar's chi-squared assess neither association nor agreement; the only two authentic agreement estimators are Holley and Guilford's G and Gwet's AC1. The latter two estimators also showed the best performance over the range of table sizes and should be considered as the first choices for agreement measurement in contingency 2x2 tables. All procedures and data were implemented in R and are available to download from Harvard Dataverse https://doi.org/10.7910/DVN/HMYTCK.
bookPart 0 Citação(ões) na Scopus
Risk of malaria for travelers with stable malaria transmission
(2011) MASSAD, E.; BEHRENS, R. H.; BURATTINI, M. N.; COUTINHO, F. A. B.
A mathematical model was developed to estimate the risk of non-immune individual acquiring falciparum malaria when traveling to the Amazon region of Brazil. The risk of malaria infection to travelers was calculated as a function of duration of exposure and season of arrival. © 2012 by Apple Academic Press, Inc.
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article 1 Citação(ões) na Scopus
Chronic exposure to cigarette smoke transiently worsens the disease course in a mouse model of pulmonary paracoccidioidomycosis
(2022) BUCCHERI, Renata; DUARTE-NETO, Amaro Nunes; SILVA, Flaviano Luiz Batista; HADDAD, Gabrielle Carvalho; SILVA, Leandro Buffoni Roque da; AZEVEDO NETTO, Raymundo; LEDESMA, Felipe Lourenço; TABORDA, Carlos Pelleschi; BENARD, Gil
ABSTRACT Paracoccidioidomycosis (PCM) may present as an acute/subacute clinical form, characterized by a progressive disease arising from the airborne initial infection, or, most often, as an asymptomatic or subclinical infection that may manifest later during an individual’s life, the chronic form. Epidemiological studies show the existence of a strong association between smoking and the development of the chronic form. Current evidence demonstrates that cigarette smoke (CS) has immunosuppressive properties that could be implicated in the increasing susceptibility to the chronic form of PCM. To address this issue, we developed a murine model of a non-progressive pulmonary form of PCM that was exposed to CS at a magnitude that mimicked a moderate smoker. The chronic CS exposure started after 2 weeks and lasted up until 20 weeks post-infection, with the aim of mimicking human natural history, since it is estimated that individuals from endemic areas are infected early in life. The control group consisted of infected but not CS-exposed mice. We assessed the lung fungal burden (colony forming units [CFU]) and the area affected by the granulomatous inflammatory response, fungal dissemination to spleen and liver, and, by immunohistochemistry, the presence of CD4 and CD8 lymphocytes, CD68 and MAC-2 macrophages, and IFN-γ, IL-10 and TNF expressing cells within the granulomatous response. We detected a CS effect as early as 2 weeks after exposure (four weeks post-infection) when the lung CFU of exposed animals was significantly higher than in their non-exposed counterparts. At 12 weeks, the CS-exposed animals presented a more severe disease, as witnessed by the persistent higher lung fungal load (although it did not reach statistical significance [ p = 0.054]), greater dissemination to other organs, greater affected area of the lung, decreased IFN-γ/IL-10 ratio, and higher TNF expression within the granulomas, compared with CS-non-exposed mice. The number of CD4 and CD8 lymphocytes infiltrating the granulomas was similar between both mice groups, but there was a decrease in the number of MAC-2+ macrophages. No difference was noted in the CD68+ macrophage number. However, the follow-up in week 20 showed that the immunological effects of exposure to CS ceased, with both CS and NCS mice showing the same infectious features, i.e., a trend for resolution of the infection. In conclusion, we show that chronic CS-exposure alters the course of the disease in an experimental model of subclinical pulmonary PCM, confirming the epidemiological link between CS-exposure and the chronic form of PCM. However, we also show that this effect is transitory, being detected between 4- and 12-weeks post-infection but not thereafter. The possible immune mechanisms that mediate this effect and the reasons for its transitory effect are discussed.
article 0 Citação(ões) na Scopus
Time-dependent vaccine efficacy estimation quantified by a mathematical model
(2023) LORIA, Jennifer; ALBANI, Vinicius V. L.; COUTINHO, Francisco A. B.; COVAS, Dimas T.; STRUCHINER, Claudio J.; ZUBELLI, Jorge P.; MASSAD, Eduardo
In this paper we calculate the variation of the estimated vaccine efficacy (VE) due to the time-dependent force of infection resulting from the difference between the moment the Clinical Trial (CT) begins and the peak in the outbreak intensity. Using a simple mathematical model we tested the hypothesis that the time difference between the moment the CT begins and the peak in the outbreak intensity determines substantially different values for VE. We exemplify the method with the case of the VE efficacy estimation for one of the vaccines against the new coronavirus SARS-CoV-2.
article 0 Citação(ões) na Scopus
Effects of migration rates and vaccination on the spread of yellow fever in Latin American communities
(2023) SIMON, Sabrina; AMAKU, Marcos; MASSAD, Eduardo
Objective. To assess how relevant the flow of people between communities is, compared to vaccination and type of vector, on the spread and potential outbreaks of yellow fever in a disease-free host community.Methods. Using a SEIRV-SEI model for humans and vectors, we applied numerical simulations to the scenar-ios: (1) migration from an endemic community to a disease-free host community, comparing the performance of Haemagogus janthinomys and Aedes aegypti as vectors; (2) migration through a transit community located on a migratory route, where the disease is endemic, to a disease-free one; and (3) effects of different vaccina-tion rates in the host community, considering the vaccination of migrants upon arrival.Results. Results show no remarkable differences between scenarios 1 and 2. The type of vector and vacci-nation coverage in the host community are more relevant for the occurrence of outbreaks than migration rates, with H. janthinomys being more effective than A. aegypti.Conclusions. With vaccination being more determinant for a potential outbreak than migration rates, vac-cinating migrants on arrival may be one of the most effective measures against yellow fever. Furthermore, H. janthinomys is a more competent vector than A. aegypti at similar densities, but the presence of A. aegypti is a warning to maintain vaccination above recommended levels.