Predicting the outcome for COVID-19 patients by applying time series classification to electronic health records

Background

COVID-19 caused more than 622 thousand deaths in Brazil. The infection can be asymptomatic and cause mild symptoms, but it also can evolve into a severe disease and lead to death. It is difficult to predict which patients will develop severe disease. There are, in the literature, machine learning models capable of assisting diagnose and predicting outcomes for several diseases, but usually these models require laboratory tests and/or imaging.

Methods

We conducted a observational cohort study that evaluated vital signs and measurements from patients who were admitted to Hospital das Clínicas (São Paulo, Brazil) between March 2020 and October 2021 due to COVID-19. The data was then represented as univariate and multivariate time series, that were used to train and test machine learning models capable of predicting a patient’s outcome.

Results

Time series-based machine learning models are capable of predicting a COVID-19 patient’s outcome with up to 96% general accuracy and 81% accuracy considering only the first hospitalization day. The models can reach up to 99% sensitivity (discharge prediction) and up to 91% specificity (death prediction).

Conclusions

Results indicate that time series-based machine learning models combined with easily obtainable data can predict COVID-19 outcomes and support clinical decisions. With further research, these models can potentially help doctors diagnose other diseases.

Correlating drug prescriptions with prognosis in severe COVID-19: first step towards resource management

BACKGROUND

Optimal COVID-19 management is still undefined. In this complicated scenario, the construction of a computational model capable of extracting information from electronic medical records, correlating signs, symptoms and medical prescriptions, could improve patient management/prognosis.

METHODS

The aim of this study is to investigate the correlation between drug prescriptions and outcome in patients with COVID-19. We extracted data from 3674 medical records of hospitalized patients: drug prescriptions, outcome, and demographics. The outcome evaluated was hospital outcome. We applied correlation analysis using a Logistic Regression algorithm for machine learning with Lasso and Matthews correlation coefficient.

RESULTS

We found correlations between drugs and patient outcomes (death/discharged alive). Anticoagulants, used very frequently during all phases of the disease, were associated with good prognosis only after the first week of symptoms. Antibiotics very frequently prescribed, especially early, were not correlated with outcome, suggesting that bacterial infections may not be important in determining prognosis. There were no differences between age groups.

CONCLUSIONS

In conclusion, we achieved an important result in the area of Artificial Intelligence, as we were able to establish a correlation between concrete variables in a real and extremely complex environment of clinical data from COVID-19. Our results are an initial and promising contribution in decision-making and real-time environments to support resource management and forecasting prognosis of patients with COVID-19.

Annotation and functional characterization of long noncoding RNAs deregulated in pancreatic adenocarcinoma

PURPOSE

Transcriptome analysis of pancreatic ductal adenocarcinoma (PDAC) has been useful to identify gene expression changes that sustain malignant phenotypes. Yet, most studies examined only tumor tissues and focused on protein-coding genes, leaving long non-coding RNAs (lncRNAs) largely underexplored.

METHODS

We generated total RNA-Seq data from patient-matched tumor and nonmalignant pancreatic tissues and implemented a computational pipeline to survey known and novel lncRNAs. siRNA-mediated knockdown in tumor cell lines was performed to assess the contribution of PDAC-associated lncRNAs to malignant phenotypes. Gene co-expression network and functional enrichment analyses were used to assign deregulated lncRNAs to biological processes and molecular pathways.

RESULTS

We detected 9,032 GENCODE lncRNAs as well as 523 unannotated lncRNAs, including transcripts significantly associated with patient outcome. Aberrant expression of a subset of novel and known lncRNAs was confirmed in patient samples and cell lines. siRNA-mediated knockdown of a subset of these lncRNAs (LINC01559, LINC01133, CCAT1, LINC00920 and UCA1) reduced cell proliferation, migration and invasion. Gene co-expression network analysis associated PDAC-deregulated lncRNAs with diverse biological processes, such as cell adhesion, protein glycosylation and DNA repair. Furthermore, UCA1 knockdown was shown to specifically deregulate co-expressed genes involved in DNA repair and to negatively impact DNA repair following damage induced by ionizing radiation.

CONCLUSIONS

Our study expands the repertoire of lncRNAs deregulated in PDAC, thereby revealing novel candidate biomarkers for patient risk stratification. It also provides a roadmap for functional assays aimed to characterize novel mechanisms of action of lncRNAs in pancreatic cancer, which could be explored for therapeutic development.

Validation of physician certified verbal autopsy using conventional autopsy: a large study of adult non-external causes of death in a metropolitan area in Brazil

Background

Reliable mortality data are essential for the development of public health policies. In Brazil, although there is a well-consolidated universal system for mortality data, the quality of information on causes of death (CoD) is not even among Brazilian regions, with a high proportion of ill-defined CoD. Verbal autopsy (VA) is an alternative to improve mortality data. This study aimed to evaluate the performance of an adapted and reduced version of VA in identifying the underlying causes of non-forensic deaths, in São Paulo, Brazil. This is the first time that a version of the questionnaire has been validated considering the autopsy as the gold standard.

Methods

The performance of a physician-certified verbal autopsy (PCVA) was evaluated considering conventional autopsy (macroscopy plus microscopy) as gold standard, based on a sample of 2060 decedents that were sent to the Post-Mortem Verification Service (SVOC-USP). All CoD, from the underlying to the immediate, were listed by both parties, and ICD-10 attributed by a senior coder. For each cause, sensitivity and chance corrected concordance (CCC) were computed considering first the underlying causes attributed by the pathologist and PCVA, and then any CoD listed in the death certificate given by PCVA. Cause specific mortality fraction accuracy (CSMF-accuracy) and chance corrected CSMF-accuracy were computed to evaluate the PCVA performance at the populational level.

Results

There was substantial variability of the sensitivities and CCC across the causes. Well-known chronic diseases with accurate diagnoses that had been informed by physicians to family members, such as various cancers, had sensitivities above 40% or 50%. However, PCVA was not effective in attributing Pneumonia, Cardiomyopathy and Leukemia/Lymphoma as underlying CoD. At populational level, the PCVA estimated cause specific mortality fractions (CSMF) may be considered close to the fractions pointed by the gold standard. The CSMF-accuracy was 0.81 and the chance corrected CSMF-accuracy was 0.49.

Conclusions

The PCVA was efficient in attributing some causes individually and proved effective in estimating the CSMF, which indicates that the method is useful to establish public health priorities.

Beneficial effects of benznidazole in Chagas disease: NIH SaMi-Trop cohort study

BACKGROUND

The effectiveness of anti-parasite treatment with benznidazole in the chronic Chagas disease (ChD) remains uncertain. We evaluated, using data from the NIH-sponsored SaMi-Trop prospective cohort study, if previous treatment with benznidazole is associated with lower mortality, less advanced cardiac disease and lower parasitemia in patients with chronic ChD.

METHODS

The study enrolled 1,959 ChD patients and abnormal electrocardiogram (ECG) from in 21 remote towns in Brazil. A total of 1,813 patients were evaluated at baseline and after two years of follow-up. Those who received at least one course of benznidazole were classified as treated group (TrG = 493) and those who were never treated as control group (CG = 1,320). The primary outcome was death after two-year follow-up; the secondary outcomes were presence at the baseline of major ChD-associated ECG abnormalities, NT-ProBNP levels suggestive of heart failure, and PCR positivity.

RESULTS

Mortality after two years was 6.3%; it was lower in the TrG (2.8%) than the CG (7.6%); adjusted OR: 0.37 (95%CI: 0.21;0.63). The ECG abnormalities typical for ChD and high age-adjusted NT-ProBNP levels suggestive of heart failure were lower in the TrG than the CG, OR: 0.35 [CI: 0.23;0.53]. The TrG had significantly lower rates of PCR positivity, OR: 0.35 [CI: 0.27;0.45].

CONCLUSION

Patients previously treated with benznidazole had significantly reduced parasitemia, a lower prevalence of markers of severe cardiomyopathy, and lower mortality after two years of follow-up. If used in the early phases, benznidazole treatment may improve clinical and parasitological outcomes in patients with chronic ChD.

TRIAL REGISTRATION

ClinicalTrials.gov, Trial registration: NCT02646943.

Desambiguação de nomes de autores para a identificação automática de perfis acadêmicos

A desambiguação de nomes é uma atividade fundamental em estudos bibliométricos, em particular naqueles que utilizam diferentes fontes de informação. O objetivo deste trabalho é propor e testar uma estratégia de desambiguação de nomes de autores de forma a possibilitar a identificação automática do perfil do Google Acadêmico de docentes. A estratégia proposta é baseada na busca pelos perfis dos docentes no Google Acadêmico, seguida por um processo de casamento de nomes. Adicionalmente são comparadas as publicações acadêmicas que estão cadastradas no currículo Lattes do docente e no perfil do Google Acadêmico. Por fim, a resolução de nomes ocorre, verificando-se entre os perfis compatíveis aquele que apresenta maiores evidências de pertencer ao respectivo docente. Um estudo de caso envolvendo os docentes da Universidade de São Paulo foi realizado, e o sistema automático foi capaz de identificar, de maneira correta, 4.283 perfis do Google Acadêmico. Uma análise de cobertura mostrou que o sistema foi capaz de encontrar cerca de 95% dos perfis dos docentes que possuem essa informação, e nenhum falso-positivo foi identificado.

Mortality among blood donors seropositive and seronegative for Chagas disease (1996-2000) in São Paulo, Brazil: A death certificate linkage study

Background

Individuals in the indeterminate phase of Chagas disease are considered to have mortality rates similar to those of the overall population. This study compares mortality rates among blood donors seropositive for Chagas disease and negative controls in the city of São Paulo, Brazil.

Methodology/principal findings

This is a retrospective cohort study of blood donors from 1996 to 2000: 2842 seropositive and 5684 seronegative for Chagas disease. Death status was ascertained by performing probabilistic record linkage (RL) with the Brazil national mortality information system (SIM). RL was assessed in a previous validation study. Cox Regression was used to derive hazard ratios (HR), adjusting for confounders. RL identified 159 deaths among the 2842 seropositive blood donors (5.6%) and 103 deaths among the 5684 seronegative (1.8%). Out of the 159 deaths among seropositive donors, 26 had the 10th International Statistical Classification of Diseases and Related Health Problems (ICD-10) indicating Chagas disease as the underlying cause of death (B57.0/B57.5), 23 had ICD-10 codes (I42.0/I42.2/I47.0/I47.2/I49.0/I50.0/I50.1/ I50.9/I51.7) indicating cardiac abnormalities possibly related to Chagas disease listed as an underlying or associated cause of death, with the others having no mention of Chagas disease in part I of the death certificate. Donors seropositive for Chagas disease had a 2.3 times higher risk of death due to all causes (95% Confidence Interval (95% CI), 1.8–3.0) than seronegative donors. When considering deaths due to Chagas disease or those that had underlying causes of cardiac abnormalities related to Chagas disease, seropositive donors had a risk of death 17.9 (95% CI, 6.3–50.8) times greater than seronegative donors.

Conclusions/significance

There is an excess risk of death in donors seropositive blood for Chagas disease compared to seronegative donors. Chagas disease is an under-reported cause of death in the Brazilian mortality database.

Chagas disease is classified as one of the 17 most important neglected diseases by the World Health Organization (WHO). The majority of infected individuals live in 21 countries of Central and South America. Estimates of mortality attributable to Chagas disease vary considerably (between 0.2% and 19.2% annually). To improve the measurement of disease burden and policy decision-making in regard to treatment availability, more accurate estimates of mortality, especially among otherwise asymptomatic seropositive individuals are needed,. This study compares mortality rates and causes of death of asymptomatic blood donors who tested seropositive for Chagas disease and seronegative for all screening tests conducted in Brazil. Mortality status was ascertained by linking donor names with the Brazilian national mortality information system (SIM). The study found that donors who tested Chagas disease seropositive had risk of death from all causes 2.3 (95% CI, 1.8–3.0) times greater than seronegative ones. The data also suggest that the SIM may underestimate the total number of deaths attributable to Chagas disease in Brazil.

Longitudinal study of patients with chronic Chagas cardiomyopathy in Brazil (SaMi-Trop project): a cohort profile

PURPOSE

We have established a prospective cohort of 1959 patients with chronic Chagas cardiomyopathy to evaluate if a clinical prediction rule based on ECG, brain natriuretic peptide (BNP) levels, and other biomarkers can be useful in clinical practice. This paper outlines the study and baseline characteristics of the participants.

PARTICIPANTS

The study is being conducted in 21 municipalities of the northern part of Minas Gerais State in Brazil, and includes a follow-up of 2 years. The baseline evaluation included collection of sociodemographic information, social determinants of health, health-related behaviours, comorbidities, medicines in use, history of previous treatment for Chagas disease, functional class, quality of life, blood sample collection, and ECG. Patients were mostly female, aged 50-74 years, with low family income and educational level, with known Chagas disease for >10 years; 46% presented with functional class >II. Previous use of benznidazole was reported by 25.2% and permanent use of pacemaker by 6.2%. Almost half of the patients presented with high blood cholesterol and hypertension, and one-third of them had diabetes mellitus. N-terminal of the prohormone BNP (NT-ProBNP) level was >300 pg/mL in 30% of the sample.

FINDINGS TO DATE

Clinical and laboratory markers predictive of severe and progressive Chagas disease were identified as high NT-ProBNP levels, as well as symptoms of advanced heart failure. These results confirm the important residual morbidity of Chagas disease in the remote areas, thus supporting political decisions that should prioritise in addition to epidemiological surveillance the medical treatment of chronic Chagas cardiomyopathy in the coming years. The São Paulo-Minas Gerais Tropical Medicine Research Center (SaMi-Trop) represents a major challenge for focused research in neglected diseases, with knowledge that can be applied in primary healthcare.

FUTURE PLANS

We will continue following this patients' cohort to provide relevant information about the development and progression of Chagas disease in remotes areas, with social and economic inequalities.

TRIAL REGISTRATION NUMBER

NCT02646943; Pre-results.

The Virological and Immunological Characteristics of the HIV-1-Infected Population in Brazil: From Initial Diagnosis to Impact of Antiretroviral Use

Background

Immunological and virological status of HIV-infected individuals entering the Brazilian public system over time was analyzed. We evaluated the impact of ART on virological, immunological and antiretroviral resistance over time.

Methods

CD4+ T cell counts, viral loads and genotypes from patients over 13 years old from 2001–2011 were analyzed according to demographic data. We compared groups using parametric t-tests and linear regression analysis in the R statistical software language.

Results

Mean baseline CD4+ T cell counts varied from 348 (2003) to 389 (2009) and was higher among women (p = 1.1 x 10⁻⁸), lower in older patients (p< 1 x 10⁻⁸) and lower in less developed regions (p = 1.864 x 10⁻⁵). Percentage of treated patients with undetectable viral loads increased linearly from 46% (2001) to 77% (2011), was lower among women (p = 2.851 x 10⁻⁶), younger ages (p = 1 x 10⁻³), and in less developed regions (p = 1.782 x 10⁻⁴). NRTI acquired resistance was 86% in 2001–3 and decreased over time. NNRTI resistance increased from 2001-3(50%) to 2006–9 (60%), PI resistance decreased from 2001–3 (60%) to 2009 (40%), and 3-class resistance was stable over time around 25%. Subtype prevalence comprised B (75.3%), B/F recombinants (12.2%), C (5.7%), F (5.3%) and B/C recombinants (1.5%), with regional variations. Three-class resistance was 26.5% among Bs, 22.4% among Fs and 17.2% among Cs.

Conclusions

HIV diagnosis occurs late, especially among elderly Brazilians. Younger individuals need special attention due to poor virological response to treatment. Antiretroviral Resistance profile is subtype related.

Accuracy of a probabilistic record-linkage methodology used to track blood donors in the Mortality Information System database

The probabilistic record linkage (PRL) is based on a likelihood score that measures the degree of similarity of several matching variables. Screening test results for different diseases are available for the blood donor population. In this paper, we describe the accuracy of a PRL process used to track blood donors from the Fundação Pró-Sangue (FPS) in the Mortality Information System (SIM), in order that future studies might determine the blood donor's cause of death. The databases used for linkage were SIM and the database made up of individuals that were living (200 blood donors in 2007) and dead (196 from the Hospital das Clinicas de São Paulo that died in 2001-2005). The method consists of cleaning and linking the databases using three blocking steps comparing the variables "Name/Mother's Name/ Date of Birth" to determine a cut-off score. For a cut-off score of 7.06, the sensitivity and specificity of the method is 94.4% (95%CI: 90.0-97.0) and 100% (95%CI: 98.0-100.0), respectively. This method can be used in studies that aim to track blood donors from the FPS database in SIM.

Data-intensive analysis of HIV mutations

BACKGROUND

In this study, clustering was performed using a bitmap representation of HIV reverse transcriptase and protease sequences, to produce an unsupervised classification of HIV sequences. The classification will aid our understanding of the interactions between mutations and drug resistance. 10,229 HIV genomic sequences from the protease and reverse transcriptase regions of the pol gene and antiretroviral resistant related mutations represented in an 82-dimensional binary vector space were analyzed.

RESULTS

A new cluster representation was proposed using an image inspired by microarray data, such that the rows in the image represented the protein sequences from the genotype data and the columns represented presence or absence of mutations in each protein position.The visualization of the clusters showed that some mutations frequently occur together and are probably related to an epistatic phenomenon.

CONCLUSION

We described a methodology based on the application of a pattern recognition algorithm using binary data to suggest clusters of mutations that can easily be discriminated by cluster viewing schemes.

[Not Available]

The Retrovirus Epidemiology Donor Study (REDS) program was established in the United States in 1989 with the purpose of increasing blood transfusion safety in the context of the HIV/AIDS and human T-lymphotropic virus epidemics. REDS and its successor, REDS-II were at first conducted in the US, then expanded in 2006 to include international partnerships with Brazil and China. In 2011, a third wave of REDS renamed the Recipient Epidemiology and Donor Evaluation Study-III (REDS-III) was launched. This seven-year research program focuses on both blood banking and transfusion medicine research in the United States of America, Brazil, China, and South Africa. The main goal of the international programs is to reduce and prevent the transmission of HIV/AIDS and other known and emerging infectious agents through transfusion, and to address research questions aimed at understanding global issues related to the availability of safe blood. This article describes the contribution of REDS-II to transfusion safety in Brazil. Articles published from 2010 to 2013 are summarized, including database analyses to characterize blood donors, deferral rates, and prevalence, incidence and residual risk of the main blood-borne infections. Specific studies were developed to understand donor motivation, the impact of the deferral questions, risk factors and molecular surveillance among HIV-positive donors, and the natural history of Chagas disease. The purpose of this review is to disseminate the acquired knowledge and briefly summarize the findings of the REDS-II studies conducted in Brazil as well as to introduce the scope of the REDS-III program that is now in progress and will continue through 2018.

© 2014 Associação Brasileira de Hematologia, Hemoterapia e Terapia Celular. All rights reserved.

Demographic, risk factors and motivations among blood donors with reactive serologic tests for syphilis in São Paulo, Brazil

OBJECTIVE

To identify the demographic characteristics, risk factors and motivations for donating among blood donors with reactive serologic tests for syphilis.

BACKGROUND

Post-donation interviews with syphilis seropositive blood donors improve recruitment and screening strategies.

METHODS

This case-control study compares 75 Venereal Disease Research Laboratory (VDRL) > 8, EIA+ (enzyme immunoassay) and FTA-ABS+ (fluorescent treponemal antibody); 80 VDRL-, EIA+ and FTA-ABS+; and 34 VDRL- and EIA- donors between 2004 and 2009. Donors were assessed by their demographic characteristics, sexual behaviour, history of alcohol and illicit drugs use, and motivations to donate.

RESULTS

Donors with VDRL > 8 were more likely to be divorced [AOR = 12·53; 95% confidence interval (CI) 1·30-120·81], to have had more than six sexual partners (AOR=7·1; 95% CI 1·12-44·62) and to report male-male-sex in the past 12 months (AOR=8·18; 95% CI 1·78-37·60). Donors with VDRL-, EIA+ and FTA-ABS+ were less likely to be female (AOR=0·26; 95% CI 0·07-0·96), more likely to be older (AOR=10·2; 95% CI 2·45-42·58 ≥ 39 and <60 years old) and to have had more than six sexual partners in the past 12 months (AOR = 8·37; 95% CI 1·49-46·91). There was no significant difference among groups regarding illicit drugs use; 30·7% (VDRL > 8) and 12·5% (VDRL-, EIA+ and FTA-ABS+) of donors reported that they had been at risk for HIV infection (P = 0·004). One-third of donors came to the blood bank to help a friend or a relative who needed blood.

CONCLUSION

Although donors exposed to syphilis reported and recognised some high risk behaviour, most were motivated by direct appeal to donate blood. Monitoring the risk profile of blood donors can benefit public health and improve blood safety.

Prevalence of serologic markers for hepatitis B and C viruses in Brazilian blood donors and incidence and residual risk of transfusion transmission of hepatitis C virus

BACKGROUND

We evaluate the current prevalence of serologic markers for hepatitis B virus (HBV) and hepatitis C virus (HCV) in blood donors and estimated HCV incidence and residual transfusion-transmitted risk at three large Brazilian blood centers.

STUDY DESIGN AND METHODS

Data on whole blood and platelet donations were collected from January through December 2007, analyzed by center; donor type; age; sex; donation status; and serologic results for hepatitis B surface antigen (HBsAg), antibody to hepatitis B core antigen (anti-HBc), and anti-HCV. HBV and HCV prevalence rates were calculated for all first-time donations. HCV incidence was derived including interdonation intervals that preceded first repeat donations given during the study, and HCV residual risk was estimated for transfusions derived from repeat donors.

RESULTS

There were 307,354 donations in 2007. Overall prevalence of concordant HBsAg and anti-HBc reactivity was 289 per 100,000 donations and of anti-HCV confirmed reactivity 191 per 100,000 donations. There were significant associations between older age and hepatitis markers, especially for HCV. HCV incidence was 3.11 (95% confidence interval, 0.77-7.03) per 100,000 person-years, and residual risk of HCV window-phase infections was estimated at 5.0 per million units transfused.

CONCLUSION

Improvement in donor selection, socioeconomic conditions, and preventive measures, implemented over time, may have helped to decrease prevalence of HBV and HCV, relative to previous reports. Incidence and residual risk of HCV are also diminishing. Ongoing monitoring of HBV and HCV markers among Brazilian blood donors should help guide improved recruitment procedures, donor selection, laboratory screening, and counseling strategies.

Human immunodeficiency virus prevalence, incidence, and residual risk of transmission by transfusions at Retrovirus Epidemiology Donor Study-II blood centers in Brazil

BACKGROUND

In Brazil nationally representative donor data are limited on human immunodeficiency virus (HIV) prevalence, incidence, and residual transfusion risk. The objective of this study was to analyze HIV data obtained over 24 months by the Retrovirus Epidemiology Donor Study-II program in Brazil.

STUDY DESIGN AND METHODS

Donations reactive to third- and fourth-generation immunoassays (IAs) were further confirmed by a less-sensitive (LS) IA algorithm and Western blot (WB). Incidence was calculated for first-time (FT) donors using the LS-EIA results and for repeat donors with a model developed to include all donors with a previous negative donation. Residual risk was projected by multiplying composite FT and repeat donor incidence rates by HIV marker-negative infectious window periods.

RESULTS

HIV prevalence among FT donors was 92.2/10(5) donations. FT and repeat donor and composite incidences were 38.5 (95% confidence interval [CI], 25.6-51.4), 22.5 (95% CI, 17.6-28.0), and 27.5 (95% CI, 22.0-33.0) per 100,000 person-years, respectively. Male and community donors had higher prevalence and incidence rates than female and replacement donors. The estimated residual risk of HIV transfusion transmission was 11.3 per 10(6) donations (95% CI, 8.4-14.2), which could be reduced to 4.2 per 10(6) donations (95% CI, 3.2-5.2) by use of individual-donation nucleic acid testing (NAT).

CONCLUSION

The incidence and residual transfusion risk of HIV infection are relatively high in Brazil. Implementation of NAT will not be sufficient to decrease transmission rates to levels seen in the United States or Europe; therefore, other measures focused on decreasing donations by at-risk individuals are also necessary.

Number of recent sexual partners among blood donors in Brazil: associations with donor demographics, donation characteristics, and infectious disease markers

BACKGROUND

Brazilian blood centers ask candidate blood donors about the number of sexual partners in the past 12 months. Candidates who report a number over the limit are deferred. We studied the implications of this practice on blood safety.

STUDY DESIGN AND METHODS

We analyzed demographic characteristics, number of heterosexual partners, and disease marker rates among 689,868 donations from three Brazilian centers between July 2007 and December 2009. Donors were grouped based on maximum number of partners allowed in the past 12 months for each center. Chi-square and logistic regression analysis were conducted to examine associations between demographic characteristics, number of sex partners, and individual and overall positive markers rates for human immunodeficiency virus (HIV), human T-lymphotropic virus Types 1 and 2, hepatitis B virus, hepatitis C virus, and syphilis.

RESULTS

First-time, younger, and more educated donors were associated with a higher number of recent sexual partners, as was male sex in São Paulo and Recife (p<0.001). Serologic markers for HIV and syphilis and overall were associated with multiple partners in São Paulo and Recife (p<0.001), but not in Belo Horizonte (p=0.05, p=0.94, and p=0.75, respectively). In logistic regression analysis, number of recent sexual partners was associated with positive serologic markers (adjusted odds ratio [AOR], 1.2-1.5), especially HIV (AOR, 1.9-4.4).

CONCLUSIONS

Number of recent heterosexual partners was associated with HIV positivity and overall rates of serologic markers of sexually transmitted infections. The association was not consistent across centers, making it difficult to define the best cutoff value. These findings suggest the use of recent heterosexual contacts as a potentially important deferral criterion to improve blood safety in Brazil.

Optimal clone identifier for genomic shotgun libraries: "OC Identifier tool"

In DNA microarray experiments, the gene fragments that are spotted on the slides are usually obtained by the synthesis of specific oligonucleotides that are able to amplify genes through PCR. Shotgun library sequences are an alternative to synthesis of primers for the study of each gene in the genome. The possibility of putting thousands of gene sequences into a single slide allows the use of shotgun clones in order to proceed with microarray analysis without a completely sequenced genome. We developed an OC Identifier tool (optimal clone identifier for genomic shotgun libraries) for the identification of unique genes in shotgun libraries based on a partially sequenced genome; this allows simultaneous use of clones in projects such as transcriptome and phylogeny studies, using comparative genomic hybridization and genome assembly. The OC Identifier tool allows comparative genome analysis, biological databases, query language in relational databases, and provides bioinformatics tools to identify clones that contain unique genes as alternatives to primer synthesis. The OC Identifier allows analysis of clones during the sequencing phase, making it possible to select genes of interest for construction of a DNA microarray.

Extense variant gene family repertoire overlap in Western Amazon Plasmodium falciparum isolates

In order to find a molecular basis for observations of relatively fast developing immunity to malarial infections in the Western Amazon region, the partial var, stevor and rif gene repertoires of nine different Plasmodium falciparum isolates collected in 1985 and 2000-2004 were evaluated. In contrast to previous results from South East Asia, the variant gene repertoire in Brazilian isolates is rather small and redundant. While the individual var repertoire sizes of Brazilian strains did not differ from Southeast Asian/African isolates, we found an over three times higher overlap of var sequence repertoires in Amazonian strains which was also conserved over time, suggesting the ongoing circulation of a similar var gene repertoire. Coincidently, almost 40% of the sequences identified herein showed the highest degree of similarity to var genes from either Brazilian or Venezuelan isolates, indicating a limited var repertoire of P. falciparum in the Amazon Basin as a whole. The intrastrain similarities of var genes were slightly but significantly lower than in Southeast Asian/African samples suggesting a higher selective pressure for diversification in Amazonian isolates. Despite of higher copy numbers per genome, rif genes also showed a significant repertoire overlap. stevor genes, which share the same predominant subtelomeric localization as var and rif genes, showed a still higher repertoire overlap and were highly similar to 3D7 stevor genes, indicating stronger functional conservation than var and rif genes. This is the first study that reveals that P. falciparum variant gene repertoires of certain areas can be limited. This has important implications for the strain-specific immunity against variant antigens occurring in these areas.