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Matrix assisted laser desorption/ionization imaging has greatly improved our understanding of spatial biology, however a robust bioinformatic pipeline for data analysis is lacking. Here, we demonstrate the application of high-dimensionality reduction/spatial clustering and histopathological annotation of matrix assisted laser desorption/ionization imaging datasets to assess tissue metabolic heterogeneity in human lung diseases. Using metabolic features identified from this pipeline, we hypothesize that metabolic channeling between glycogen and N-linked glycans is a critical metabolic process favoring pulmonary fibrosis progression. To test our hypothesis, we induced pulmonary fibrosis in two different mouse models with lysosomal glycogen utilization deficiency. Both mouse models displayed blunted N-linked glycan levels and nearly 90% reduction in endpoint fibrosis when compared to WT animals. Collectively, we provide conclusive evidence that lysosomal utilization of glycogen is required for pulmonary fibrosis progression. In summary, our study provides a roadmap to leverage spatial metabolomics to understand foundational biology in pulmonary diseases., (© 2023. The Author(s).)

Neutralizing antibodies (nAbs) are a critical part of coronavirus disease 2019 (COVID-19) research as they are used to gain insight into the immune response to severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) infections. Among the technologies available for generating nAbs, DNA-based immunization methods are an alternative to conventional protocols. In this pilot study, we investigated whether DNA-based immunization by needle injection in rabbits was a viable approach to produce a functional antibody response. We demonstrated that three doses of DNA plasmid carrying the gene encoding the full-length spike protein (S) or the receptor binding domain (RBD) of SARS-CoV-2 induced a time-dependent increase in IgG antibody avidity maturation. Moreover, the IgG antibodies displayed high cross neutralization by live SARS-CoV-2 and pseudoviruses neutralization assays. Thus, we established a simple, low cost and feasible DNA-based immunization protocol in rabbits that elicited high IgG avidity maturation and nAbs production against SARS-CoV-2, highlighting the importance of DNA-based platforms for developing new immunization strategies against SARS-CoV-2 and future emerging epidemics.

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., (© 2022. The Author(s).)

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., (© 2022. The Author(s).)

The parabasalid Pentatrichomonas hominis is generally considered to represent a symbiotic component of the gastrointestinal microbiota in a wide variety of vertebrate hosts including humans. Nevertheless, a limited number of studies have raised the possibility that it may act as a pathogen of humans, dogs, and pigs and that some human infections may have a zoonotic origin. Data from North America revealed an association between P. hominis and the bovine urogenital tract, principally in bulls and rarely in cows. The importance of this observation is linked to possible interference in the accurate diagnosis of the economically important venereal pathogen Tritrichomonas foetus. The current study employed culture-based and molecular methods to examine the preputial cavities of four breeding bulls, raised in open pasture in southeastern Brazil, for the presence of trichomonads. Motile protozoa were isolated from three of the bulls and were definitively identified as P. hominis based on nucleotide sequencing of polymerase chain reaction (PCR) amplicons derived from the ribosomal RNA operon (ITS1-5.8S rDNA-ITS2) of the parasite. The potential implications of these findings for bovine and human health are discussed.

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., (© 2022. The Author(s).)

The objective of this study was to characterize the prevalence of viral encephalitis due to arbovirus infection of the Togaviridae and Flaviviridae families in São Paulo, Brazil. A total of 500 cerebrospinal fluid (CSF) samples collected between August 2012 and January 2013, from patients with symptoms of acute encephalitis were analyzed. Findings suggestive of viral encephalitis-elevations in cell concentration, glucose and total protein-were observed in 234 (46.8%) samples, designated as Group 1. The remaining 266 samples comprised Group 2. All samples were tested for Flaviviruses (dengue virus 1, 2, 3 and 4, yellow fever virus and West Nile virus), Alphavirus (NS5 region) and enterovirus by RT- PCR and for herpesviruses and enteroviruses using CLART-Entherpex. A presumptive viral etiological agent was detected in 26 samples (5.2%), 18 (8.0%) in Group 1 and 8 (3.0%) in Group 2. In Group 1 human herpesviruses were detected in 9 cases, enteroviruses in 7 cases, dengue viruses (DENV) in 2 CSFs and St. Louis encephalitis virus (SLEV) in one case. In Group 2 there were 3 CSFs positive for human herpesviruses, 2 for enteroviruses, 2 for DENV and 1 for SLEV. Detection of arboviruses, even though present in a minority of infected patients, identifies these viruses as a probable etiological agent of encephalitis. This is of special concern in regions where this class of viruses is endemic and has been linked to other recent epidemics., Competing Interests: The authors have declared that no competing interests exist.

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., Competing Interests: The authors have declared that no competing interests exist.

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.

Purpose:: To evaluate whether undergraduate students feel motivated to develop surgical skills and know their impression about the importance of having a surgical technique discipline in the curriculum of a medical school., Methods:: A prospective study including three classes in a row, from the 8th period (n = 265) evaluated the knowledge acquired at the Center of Experimental Surgery, Department of Surgery, School of Medicine of Federal University of Rio de Janeiro (UFRJ). The importance of the discipline for medical training as a way of encouragement to arouse and deepen the interest in surgical technique was emphasized. The questions were scored from 1 to 5 (worst to best grade) ., Results:: Concerning the importance of the discipline for medical training, 78% and 18% of the students assigned a score 5 and 4, respectively. Regarding the stimulus to improve their surgical technical skills, 40% and 32% attributed the score 5 and 4, respectively., Conclusion:: Undergraduate students from the Medical School of UFRJ effectively shared the understanding that the operative technique bases improve the formative process with significant impact, not only in the development of skills, but also to arouse vocations and stimulate new attitudes aimed to knowledge acquirement in the field of Surgery.

Purpose:: To critically analyze and standardize the rat pancreatectomy nomenclature variants., Methods:: It was performed a review of indexed manuscripts in PUBMED from 01/01/1945 to 31/12/2015 with the combined keywords "rat pancreatectomy" and "rat pancreas resection". The following parameters was considered: A. Frequency of publications; B. Purpose of the pancreatectomy in each article; C. Bibliographic references; D. Nomenclature of techniques according to the pancreatic parenchyma resection percentage., Results:: Among the 468, the main objectives were to surgically induce diabetes and to study the genes regulations and expressions. Five rat pancreatectomy technique references received 15 or more citations. Twenty different terminologies were identified for the pancreas resection: according to the resected parenchyma percentage (30 to 95%); to the procedure type (total, subtotal and partial); or based on the selected anatomical region (distal, longitudinal and segmental). A nomenclature systematization was gathered by cross-checking information between the main surgical techniques, the anatomic parameters descriptions and the resected parenchyma percentages., Conclusion:: The subtotal pancreatectomy nomenclature for parenchymal resection between 80 and 95% establishes a surgical parameter that also defines the total and partial pancreatectomy limits and standardizes these surgical procedures in rats.

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., (Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/)

Purpose: To track the regeneration process of lateral gastrocnemius due to a muscle laceration in rats, and to treatment with plateletrich plasma (PRP)., Methods: Ultrasound (40 MHz) images were used for measuring pennation angle (PA), muscle thickness (MT) and mean pixel intensity, along with claudication scores, of treated (PRPG) and non-treated (NTG) groups of rats., Results: NTG showed a PA increase for the non-injured leg (p<0.05) and a tendency of MT to increase, whereas for PRPG there were no differences. There was a progressive reduction of the claudication score for the PRPG group throughout the entire period, with an immediate difference after seven days (p<0.05), whereas the NTG had a significant reduction only at day 28 (p<0.05)., Conclusion: It was observed a compensatory hypertrophic response due to the overload condition imposed to healthy leg for NTG that did not occur in PRPG, suggesting an accelerated repair process of the injured leg due to treatment, anticipating its 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.

The authors present an evidence-based case report of a patient with agenesis or pseudoagenesis of the dorsal pancreas.

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.

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.

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.

The present study aimed to compare two different methods of extracting RNA from formalin-fixed paraffin-embedded (FFPE) specimens of diffuse large B-cell lymphoma (DLBCL). We further aimed to identify possible influences of variables--such as tissue size, duration of paraffin block storage, fixative type, primers used for cDNA synthesis, and endogenous genes tested--on the success of amplification from the samples. Both tested protocols used the same commercial kit for RNA extraction (the RecoverAll Total Nucleic Acid Isolation Optimized for FFPE Samples from Ambion). However, the second protocol included an additional step of washing with saline buffer just after sample rehydration. Following each protocol, we compared the RNA amount and purity and the amplification success as evaluated by standard PCR and real-time PCR. The results revealed that the extra washing step added to the RNA extraction process resulted in significantly improved RNA quantity and quality and improved success of amplification from paraffin-embedded specimens.

Over time, data warehouse (DW) systems have become more difficult to develop because of the growing heterogeneity of data sources. Despite advances in research and technology, DW projects are still too slow for pragmatic results to be generated. Here, we address the following question: how can the complexity of DW development for integration of heterogeneous transactional information systems be reduced? To answer this, we proposed methodological guidelines based on cycles of conceptual modeling and data analysis, to drive construction of a modular DW system. These guidelines were applied to the blood donation domain, successfully reducing the complexity of DW development.

Background: Recent medical and biological technology advances have stimulated the development of new testing systems that have been providing huge, varied amounts of molecular and clinical data. Growing data volumes pose significant challenges for information processing systems in research centers. Additionally, the routines of genomics laboratory are typically characterized by high parallelism in testing and constant procedure changes., Results: This paper describes a formal approach to address this challenge through the implementation of a genetic testing management system applied to human genome laboratory. We introduced the Human Genome Research Center Information System (CEGH) in Brazil, a system that is able to support constant changes in human genome testing and can provide patients updated results based on the most recent and validated genetic knowledge. Our approach uses a common repository for process planning to ensure reusability, specification, instantiation, monitoring, and execution of processes, which are defined using a relational database and rigorous control flow specifications based on process algebra (ACP). The main difference between our approach and related works is that we were able to join two important aspects: 1) process scalability achieved through relational database implementation, and 2) correctness of processes using process algebra. Furthermore, the software allows end users to define genetic testing without requiring any knowledge about business process notation or process algebra., Conclusions: This paper presents the CEGH information system that is a Laboratory Information Management System (LIMS) based on a formal framework to support genetic testing management for Mendelian disorder studies. We have proved the feasibility and showed usability benefits of a rigorous approach that is able to specify, validate, and perform genetic testing using easy end user interfaces.

Objective: To evaluate the results obtained with curative resection of Borrmann IV gastric adenocarcinoma (B IV) through the analysis of clinical, surgical and pathological data, identifying which of these prognostic factors were associated with survival., Methods: We retrospectively analyzed 123 patients with B IV gastric adenocarcinoma undergoing surgical treatment at the Department of the pelvic-abdominal surgeries of the National Cancer Institute (INCA) from January 1997 to December 2005. The group undergoing curative resection was examined for various prognostic factors regarding overall survival., Results: Of the 123 patients studied, 68 underwent gastrectomy, 52 (42.3%) with curative intent and 16 (13%) palliative resection, while 55 (44.7%) had disease not subject to resection. Three postoperative deaths followed the curative resection, constituting a mortality rate of 5.76%. In nine (17.3%) patients there were technical complications, and esophagojejunal fistula seven cases, the most frequent. All technical complications and deaths occurred after total gastrectomy, which was the most commonly performed curative resection type in this series. The most common pattern of recurrence was peritoneal carcinomatosis. The location of the tumor, lymph node metastasis, lymphatic invasion and pathological staging were considered significant prognostic factors. The median survival time was 29 months, with a rate of five-year survival of 33% in patients undergoing curative resection., Conclusion: The curative resection of B IV gastric adenocarcinoma had a positive impact on survival of patients with the disease in stages IB, II and III, with up to 15 lymph nodes (pN2) and localized type.

In a previous article, we used Hartree-Fock (HF) theory to study the piezoelectricity in BaTiO₃. In this paper, we applied the Douglas-Kroll-Hess second order scalar relativistic method to investigate the possible piezoelectric properties in the perovskite YFeO₃ structure, which has not yet been studied experimentally. The 30s20p13d and 31s21p17d Gaussian basis sets for the Fe (⁵D) and Y (²D) atoms, respectively, were built with the Generator Coordinate HF method. After contraction to [13s7p5d] and [13s8p7d], in combination with the 20s14p/6s4p basis set for the O (³P) atom from literature, they had their quality evaluated using calculations of the total and the orbital energies for the ²FeO⁺¹ and ¹YO⁺¹ fragments. The dipole moment, the total energy, and the total atomic charges in YFeO₃ in C(s) space group were calculated. The results and the analysis lead us to believe that the perovskite YFeO₃ does not present piezoelectric properties.

Purpose: The aim of this study was to describe an experimental surgical technique to be used in the evaluation of bone grafts in rabbits., Methods: The operative technique was performed in jaws, with external approach from the labial commissure to the last molar tooth. An incision about 1cm extended forward to the alveolar ridge, followed by a exposing the cervical region of the alveolar bone and dental elements was done. Thus, after extraction of first molar with forceps, the tooth socket left was filled with hydroxyapatite. The bone gain was analyzed by histopathological studies., Results: The histological analyses indicated formed bone surrounding the biomaterial., Conclusion: The experimental model using the tooth socket of the rabbit molar is a feasible procedure for studies of bone grafts.

A zinc hydroxide nitrate (ZHN), Zn5(OH)8(NO3)2.2H2O, and a layered double hydroxide (LDH), Zn/Al-NO3 were doped with 0.2 mol% of Cu2+ during alkaline chemical precipitation. Both compounds were intercalated with adipate ((-)OOC(CH2)4COO(-)), azelate ((-)OOC(CH2)7COO(-)), and benzoate (C6H5COO(-)) ions through ion exchange reactions. Solid state 13C nuclear magnetic resonance spectroscopy showed only one signal of carboxylic carbon for adipate and azelate intercalated into LDH, indicating that the carboxylic ends of both acids were equivalent, whereas the signal split when the intercalation was into the ZHN matrix. The electron paramagnetic resonance (EPR) spectrum of copper in octahedral cation sites of LDH layers showed a Hamiltonian parameter ratio g ||/A ||=170 cm and, after intercalation of adipate, the change was not significant: g ||/A ||=174 cm. This result indicates that the carboxylate ions did not coordinate with copper centers. Nonetheless, the intercalation of azelate increased the ratio to g ||/A ||=194 cm, similar to the spectra of ZHN modified with adipate, g ||/A ||=199 cm, and azelate, g ||/A ||=183 and 190 cm, which are associated with the coordination of copper by weak carboxylate anion ligands. Copper occupies octahedral or tetrahedral sites in ZHN layers, and the EPR spectra indicate that the dicarboxylate anions reacted preferentially with octahedral sites, whereas benzoate reacted with both sites.

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.

Purpose: To test the use of intraluminal protection in colonic anastomosis without intestinal cleansing. The intraluminal liner was fashioned from porcine submucosa preserved in glycerin and then fixed 10 cm anteriorly to the anastomotic site. This technique was compared with the one used in termino-terminal colonic anastomosis without intraluminal protection., Methods: Twenty-eight dogs were divided into two groups of fourteen animals each. Clinical and histopathological tests were performed on the fourth and twenty-first postoperative days., Results: The morbidity and mortality rates were higher in animals that did not receive the intraluminal liner. Histopathological examinations in animals in which the intraluminal liner was used showed better healing, characterized by milder inflammation and increased amount of collagen., Conclusion: It can be concluded that the use of intraluminal protection decreases complication rates in colonic anastomosis and promotes better healing.

We developed a database system for collaborative HIV analysis (DBCollHIV) in Brazil. The main purpose of our DBCollHIV project was to develop an HIV-integrated database system with analytical bioinformatics tools that would support the needs of Brazilian research groups for data storage and sequence analysis. Whenever authorized by the principal investigator, this system also allows the integration of data from different studies and/or the release of the data to the general public. The development of a database that combines sequences associated with clinical/epidemiological data is difficult without the active support of interdisciplinary investigators. A functional database that securely stores data and helps the investigator to manipulate their sequences before publication would be an attractive tool for investigators depositing their data and collaborating with other groups. DBCollHIV allows investigators to manipulate their own datasets, as well as integrating molecular and clinical HIV data, in an innovative fashion.

Background: We analyzed rates of drug resistance mutations in antiretroviral-naive São Paulo blood donors with recently acquired or established HIV-1 infections and characterized clade diversity in this population., Methods: Six hundred forty-eight seropositive blood donor specimens were identified at the Blood Center of São Paulo between July 1998 and March 2002. To discriminate recent infections, samples were subjected to the standardized testing algorithm for recent HIV seroconversion (less-sensitive enzyme immunoassay) testing algorithm. There were 531 samples with a sufficient volume of serum to attempt polymerase chain reaction (PCR) and viral sequencing; 341 (64%) samples yielded a PCR product that could be sequenced for the reverse transcriptase and protease genes. Mutations were analyzed using the 2005 International AIDS Society mutation list., Results: Of 341 specimens successfully analyzed, 21 (6.3%; 95% confidence interval [CI]: 3.9% to 9.3%) had drug-resistant mutations. The proportion of resistant strains was 12.7% (95% CI: 5.2% to 24.5%) among recently infected individuals compared with 5.0% (95% CI: 2.8% to 8.2%) among those with long-standing infections (P = 0.03). No change in the proportion of drug-resistant strains was observed among recently infected donor samples from the first half of the study period (4 of 32 samples) as compared with the second half (3 of 23 samples; P = 0.95). Of the 341 samples, 277 (81.2%) were classified as subtype B, 25 (7.3%) as subtype F1, 13 (3.8%) as subtype C, and 26 (7.6%) as recombinant strains. The distribution of HIV-1 subtypes was similar among recent and long-standing infected individuals and over time., Conclusions: The prevalence of drug-resistant mutations among newly diagnosed persons in São Paulo city is low and similar to what has been described in Europe and the United States. Although HIV-1 subtype B remains predominant, subtypes F and C and recombinant forms are present in substantial proportions in infected donors.

Unlabelled: Clinically non-functioning pituitary adenomas do not produce clinical signs of hormonal hypersecretion. Therefore, signs and symptoms will depend on the mass effect of these adenomas over the central nervous system. Their etiopathogeny is complex and their development is probably influenced by several factors, such as hypothalamic hormones (GHRH), growth factors (FGF), proliferation factors (PCNA, and KI-67), protein P53 and the proto-oncogene c-erb-B2., Objective: 1) Determining the clinical features of a population of 117 patients treated for clinically non-functioning pituitary adenoma (age, sex, tumor size, number of surgical procedures, development of hormonal deficiency and hyperprolactinemia). 2) Identifying, after the patients had been clinically characterized, those with clinically non-functioning adenomas with positive immunohistochemistry for hypophyseal hormones (PRL, LH, FSH, GH, TSH and ACTH). 3) Determining if the immunohistochemistry of this population was positive for the cellular proliferation factor Ki-67, protein P53 and protein C-erb-B2 and establishing a correlation with tumor size and tumor invasiveness. This will help in the evaluation of the prognostic value of these proliferation factors. 4) Confronting the results of immunohistochemistry using a standard block with the results of immunohistochemistry using a tissue micro-array., Method: Study of the clinical features of 117 patients with clinically non-functioning pituitary adenoma (age, sex, tumor size, number of surgical procedures, development of hormonal deficiency and hyperprolactinemia). Immunohistochemical study (H&E) of 39 patients for hypophyseal hormones, protein P53, protein C-erb-B2, Ki-67 to establish their correlation to tumor growth. The next step was a tissue micro-array of the 39 previously studied cases, using immunohistochemistry for hypophyseal hormones, protein P 53, protein C-erb-B2, Ki-67 to establish their correlation to tumor growth., Results: There was no statistically significant difference between males and females with regards to age, tumor size and number of surgical procedures (p=0.279, p=813, p=139 respectively). There is a statistically significant correlation between the size of the tumor, the number of surgical procedures and hormonal deficiency (p=0.032, p=0.223 respectively). There was no statistically significant correlation between a positive immunohistochemistry for protein P53, protein C-erb-B2, Ki-67 and tumor size (r=0.182, p=0.396; r=-0.181, p=0.397; r=0.272, p=0.199, respectively). The tissue micro-array also did not demonstrate a correlation between positive immunohistochemistry for Ki-67 and C-erb-B2 and tumor size, but it showed a statistically significant correlation between a positive immunohistochemistry for p53 and tumor size (r=-0.696; p=001)., Conclusion: The biological behavior of the clinically non-functioning adenoma is similar for both sexes. The larger the tumor the greater the number of surgical procedures needed. Hormonal deficiency also becomes more significant as the size of the tumor increases. This paper suggests that a positive immunohistochemistry for p53 is negatively correlated to tumor size, thus demonstrating that it has a predictor value. However, a positive immunohistochemistry for Ki-67 and protein C-erb-B2 does not seem to be a prognostic factor for clinically non-functioning pituitary adenomas, as is the case with other neoplasias.

The intercalation of ions derived from succinic, glutaric, and adipic acid into layered zinc hydroxide nitrate by ionic exchange reaction is reported. Different reaction conditions are investigated and the materials are characterized by powder X-ray diffraction, Fourier transform infrared spectroscopy, thermal analysis (simultaneous thermogravimetry and differential scanning calorimetry) and elemental analysis. The dicarboxylic acids can be grafted to the matrix slab by one carboxylate group and the second hydrated carboxylate group is hanging between the layers. Benzoate ions have also been intercalated by both ionic exchange reaction and stirring in acetonitrile. The two benzoate-intercalated materials exchange the organic moiety by sulfate ions if stirred in magnesium sulfate solution, but the sample obtained by anion exchange also allows the unusual incorporation of neutral magnesium sulfate in addition to free solvated sulfate ion. A schematic arrangement of the intercalated species between the layers is presented.

Sandbox experiments with different boundary conditions demonstrate that antiformal stacks result from a forward-breaking thrust sequence. An obstacle blocks forward thrust propagation and transfers the deformation back to the hinterland in a previously formed true duplex. In the hinterland, continued shortening causes faults to merge toward the tectonic transport direction until the older thrusts override the younger thrusts. In experiments using thin sand layers or high basal friction, shortening is accommodated by a cyclic process of thrusting, back rotation of the newly formed thrust combined with strong vertical strain, and nucleation of a new thrust. Continuous deformation produces an antiformal stack through progressive convergence of branch lines.