An alternative genotyping method using dye-labeled universal primer to reduce unspecific amplifications

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Tumores da glandula tireoide. Estudo retrospectivo de 130 casos com enfase especial em biopsia aspirativa, biopsia de congelacao e exame histopatologico

The authors studied retrospectively 130 patients with thyroid tumors comparing the histopathologic diagnoses with fine needle aspirate (FNA) and frozen section results. FNA was performed in 118 patients with the following results: 75 (63.6%) benign, 21 (17.8%) malignant and 22 (18.6%) not conclusives. In seven cases false-negative result was obtained and there were six false-positive. These data reveals some drawbacks of this procedure. These results indicated that frozen as well as FNA are useful diagnostic procedure in helping to choose the most appropriate therapy in patients with thyroid tumors. On the other hand, traditional methods seems to be also important methods, such as scintilography, in the evaluation of thyroid diseases.

RAPD optimization for genetic studies with Citrulus lanatus and Sesamum indicum genotypes

The Random Amplified Polymorphic DNA (RAPD) technique is powerful for DNA polymorphism determinations and is widely used in research involving different organisms, but it is known that RAPD can be affected by many factors that may result in false positive bands and non-reproducible assays. In this study, we analyzed the effect of several factors such as DNA template, primer and Taq DNA polymerase concentrations to optimize and standardize the RAPD technique for further genetic studies with Citrulus lanattus and Sesamum indicum L. The best combination of DNA, Taq DNA polymerase enzyme and primer concentrations in RAPD amplification procedures for sesame and watermelon genotypes was established.

Clonagem, análise estrutural e imunológica do alérgeno antígeno 5 do veneno da vespa Polybia paulista (Hymenoptera : Vespidae)

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Busca de parceiros físicos por duplo-híbrido das proteínas ADAM23 e MX1, codificadas por genes metilados em câncer de cabeça e pescoço

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Leishmaniose visceral canina-LVC, em Campina Grande-PB/Brasil: avalição epidemiológica e diagnóstica

Pós-graduação em Doenças Tropicais - FMB

Avaliação do teste do anel na vigilância epidemiológica da brucelose bovina em rebanhos e laticínios

Pós-graduação em Medicina Veterinária - FMVZ

False positivity of gamma-glutamyl transpeptidase measurement in urine

Although enzymuria tends to be associated to renal injury, there are no studies that have evaluated the presence of the enzyme gamma-glutamyl transpeptidase (GGT) spectrophotometry in the urine using a non-nephrotoxic agent (Nerium oleander) in order to evaluate the possibility of false positive results. The urinary GGT/urinary creatinine concentration ratio (uGGT/uCr) of 10 healthy dogs was calculated and posteriorly confronted with data from clinical evaluation, hematological and serum biochemical profiles, creatinine clearance (CrC), urinalysis, urine protein/creatinine ratio (UPC), electrocardiogram, systemic blood pressure (SBP) and light and electron microscopy. The results for kidney histology, SBP, UPC and CrC were not significantly different in any of the time-points analyzed. However, uGGT/uCr was significantly higher when measured 4 hours and 24 hours after administration of N. oleander. The measurement of the urinary GGT enzyme, as performed in many studies, yielded false positive results in dogs poisoned by a non-nephrotoxic agent.

Métodos diagnóstico de Hiperadrenocorticismo canina

The Hyperadrenocorticism is a disease that occur in dogs between mead to old age, is associated with the higher level of glucocorticoid that result in a corporal reaction. To make a diagnostic of this disease is necessary have a good history and physical examination, the principals complains of the proprietary are polyuria, polydipsia and polyphagia, in some times abdominal enlargement and lethargy. In the physical examination is observed this abdominal enlargement, hepatomegaly, alopecia, in some cases pyoderma and difficult respiratory. From this documents is possible determinate the differential diagnostics and with the tests find the diagnostic of the disease that the animal have. The base methods are hemogram, biochemical, urinalysis, radiographs and ultrasonography it’s possible do tomography and magnetic resonance too. There are confirmation methods too, they are very important, because the others not have documents necessary for the final diagnostic. Those are Urine cortisol to creatinine ratio, dexamethasone suppression test with high dose or low dose and ACTH stimulation test. Despite those tests have high sensibility and specificity, they can result in false positive or false negative, this is one of the causes to do the base methods and together make the veterinary doctor find the solution of the diagnostic and do the adequate treatment

Segmentation of Cell Nuclei Regions in Epithelium of Prostate Glands

This paper proposes a method for segmentation of cell nuclei regions in epithelium of prostate glands. This structure provides information to diagnosis and prognosis of prostate cancer. In the initial step, the contrast stretching technique was applied in image in order to improve the contrast between regions of interest and other regions. After, the global thresholding technique was applied and the value of threshold was defined empirically. Finally, the false positive regions were removed using the connected components technique. The performance of the proposed method was compared with the Otsu technique and statistical measures of accuracy were calculated based on reference images (gold standard). The result of the mean value of accuracy of proposed method was 93% ± 0.07.

Modelo de Resposta à Intervenção (RTI) para desenvolvimento das habilidades fonológicas com tutoria instrucional em contexto escolar: elaboração e controle de eficácia

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Accuracy of positron emission tomography/computed tomography and clinical assessment in the detection of complete rectal tumor regression after neoadjuvant chemoradiation Long-Term Results of a Prospective Trial (National Clinical Trial 00254683)

BACKGROUND: Neoadjuvant chemoradiation (CRT) therapy may result in significant tumor regression in patients with rectal cancer. Patients who develop complete tumor regression have been managed by treatment strategies that are alternatives to standard total mesorectal excision. Therefore, assessment of tumor response with positron emission tomography/computed tomography (PET/CT) after neoadjuvant treatment may offer relevant information for the selection of patients to receive alternative treatment strategies. METHODS: Patients with clinical T2 (cT2) through cT4NxM0 rectal adenocarcinoma were included prospectively. Neoadjuvant therapy consisted of 54 grays of radiation and 5-fluorouracil-based chemotherapy. Baseline PET/CT studies were obtained before CRT followed by PET/CT studies at 6 weeks and 12 weeks after the completion of CRT. Clinical assessment was performed at 12 weeks after CRT completion. PET/CT results were compared with clinical and pathologic data. RESULTS: In total, 99 patients were included in the study. Twenty-three patients were complete responders (16 had a complete clinical response, and 7 had a complete pathologic response). The PET/CT response evaluation at 12 weeks indicated that 18 patients had a complete response, and 81 patients had an incomplete response. There were 5 false-negative and 10 false-positive PET/CT results. PET/CT for the detection of residual cancer had 93% sensitivity, 53% specificity, a 73% negative predictive value, an 87% positive predictive value, and 85% accuracy. Clinical assessment alone resulted in an accuracy of 91%. PET/CT information may have detected misdiagnoses made by clinical assessment alone, improving overall accuracy to 96%. CONCLUSIONS: Assessment of tumor response at 12 weeks after CRT completion with PET/CT imaging may provide a useful additional tool with good overall accuracy for the selection of patients who may avoid unnecessary radical resection after achieving a complete clinical response. Cancer 2012;35013511. (C) 2011 American Cancer Society.

Design and implementation of bioinformatics tools for large scale genome annotation

The continuous increase of genome sequencing projects produced a huge amount of data in the last 10 years: currently more than 600 prokaryotic and 80 eukaryotic genomes are fully sequenced and publically available. However the sole sequencing process of a genome is able to determine just raw nucleotide sequences. This is only the first step of the genome annotation process that will deal with the issue of assigning biological information to each sequence. The annotation process is done at each different level of the biological information processing mechanism, from DNA to protein, and cannot be accomplished only by in vitro analysis procedures resulting extremely expensive and time consuming when applied at a this large scale level. Thus, in silico methods need to be used to accomplish the task. The aim of this work was the implementation of predictive computational methods to allow a fast, reliable, and automated annotation of genomes and proteins starting from aminoacidic sequences. The first part of the work was focused on the implementation of a new machine learning based method for the prediction of the subcellular localization of soluble eukaryotic proteins. The method is called BaCelLo, and was developed in 2006. The main peculiarity of the method is to be independent from biases present in the training dataset, which causes the over‐prediction of the most represented examples in all the other available predictors developed so far. This important result was achieved by a modification, made by myself, to the standard Support Vector Machine (SVM) algorithm with the creation of the so called Balanced SVM. BaCelLo is able to predict the most important subcellular localizations in eukaryotic cells and three, kingdom‐specific, predictors were implemented. In two extensive comparisons, carried out in 2006 and 2008, BaCelLo reported to outperform all the currently available state‐of‐the‐art methods for this prediction task. BaCelLo was subsequently used to completely annotate 5 eukaryotic genomes, by integrating it in a pipeline of predictors developed at the Bologna Biocomputing group by Dr. Pier Luigi Martelli and Dr. Piero Fariselli. An online database, called eSLDB, was developed by integrating, for each aminoacidic sequence extracted from the genome, the predicted subcellular localization merged with experimental and similarity‐based annotations. In the second part of the work a new, machine learning based, method was implemented for the prediction of GPI‐anchored proteins. Basically the method is able to efficiently predict from the raw aminoacidic sequence both the presence of the GPI‐anchor (by means of an SVM), and the position in the sequence of the post‐translational modification event, the so called ω‐site (by means of an Hidden Markov Model (HMM)). The method is called GPIPE and reported to greatly enhance the prediction performances of GPI‐anchored proteins over all the previously developed methods. GPIPE was able to predict up to 88% of the experimentally annotated GPI‐anchored proteins by maintaining a rate of false positive prediction as low as 0.1%. GPIPE was used to completely annotate 81 eukaryotic genomes, and more than 15000 putative GPI‐anchored proteins were predicted, 561 of which are found in H. sapiens. In average 1% of a proteome is predicted as GPI‐anchored. A statistical analysis was performed onto the composition of the regions surrounding the ω‐site that allowed the definition of specific aminoacidic abundances in the different considered regions. Furthermore the hypothesis that compositional biases are present among the four major eukaryotic kingdoms, proposed in literature, was tested and rejected. All the developed predictors and databases are freely available at: BaCelLo http://gpcr.biocomp.unibo.it/bacello eSLDB http://gpcr.biocomp.unibo.it/esldb GPIPE http://gpcr.biocomp.unibo.it/gpipe

Diagnostic accuracy of coronary in-stent restenosis using 64-slice computed tomography: comparison with invasive coronary angiography

OBJECTIVES: This study sought to evaluate the diagnostic accuracy of coronary binary in-stent restenosis (ISR) with angiography using 64-slice multislice computed tomography coronary angiography (CTCA) compared with invasive coronary angiography (ICA). BACKGROUND: A noninvasive detection of ISR would result in an easier and safer way to conduct patient follow-up. METHODS: We performed CTCA in 81 patients after stent implantation, and 125 stented lesions were scanned. Two sets of images were reconstructed with different types of convolution kernels. On CTCA, neointimal proliferation was visually evaluated according to luminal contrast attenuation inside the stent. Lesions were graded as follows: grade 1, none or slight neointimal proliferation; grade 2, neointimal proliferation with no significant stenosis (<50%); grade 3, neointimal proliferation with moderate stenosis (> or =50%); and grade 4, neointimal proliferation with severe stenosis (> or =75%). Grades 3 and 4 were considered binary ISR. The diagnostic accuracy of CTCA compared with ICA was evaluated. RESULTS: By ICA, 24 ISRs were diagnosed. Sensitivity, specificity, positive predictive value, and negative predictive value were 92%, 81%, 54%, and 98% for the overall population, whereas values were 91%, 93%, 77%, and 98% when excluding unassessable segments (15 segments, 12%). For assessable segments, CTCA correctly diagnosed 20 of the 22 ISRs detected by ICA. Six lesions without ISR were overestimated as ISR by CTCA. As the grade of neointimal proliferation by CTCA increases, the median value of percent diameter stenosis increased linearly. CONCLUSIONS: Binary ISR can be excluded with high probability by CTCA, with a moderate rate of false-positive results.

Investigating the potential of reported cattle mortality data in Switzerland for syndromic surveillance

Systems for the identification and registration of cattle have gradually been receiving attention for use in syndromic surveillance, a relatively recent approach for the early detection of infectious disease outbreaks. Real or near real-time monitoring of deaths or stillbirths reported to these systems offer an opportunity to detect temporal or spatial clusters of increased mortality that could be caused by an infectious disease epidemic. In Switzerland, such data are recorded in the "Tierverkehrsdatenbank" (TVD). To investigate the potential of the Swiss TVD for syndromic surveillance, 3 years of data (2009-2011) were assessed in terms of data quality, including timeliness of reporting and completeness of geographic data. Two time-series consisting of reported on-farm deaths and stillbirths were retrospectively analysed to define and quantify the temporal patterns that result from non-health related factors. Geographic data were almost always present in the TVD data; often at different spatial scales. On-farm deaths were reported to the database by farmers in a timely fashion; stillbirths were less timely. Timeliness and geographic coverage are two important features of disease surveillance systems, highlighting the suitability of the TVD for use in a syndromic surveillance system. Both time series exhibited different temporal patterns that were associated with non-health related factors. To avoid false positive signals, these patterns need to be removed from the data or accounted for in some way before applying aberration detection algorithms in real-time. Evaluating mortality data reported to systems for the identification and registration of cattle is of value for comparing national data systems and as a first step towards a European-wide early detection system for emerging and re-emerging cattle diseases.