Primary screening of blood donors by nat testing for HCV-RNA: development of an "in-house" method and results

An "in-house" RT-PCR method was developed that allows the simultaneous detection of the RNA of the Hepatitis C Virus (HCV) and an artificial RNA employed as an external control. Samples were analyzed in pools of 6-12 donations, each donation included in two pools, one horizontal and one vertical, permitting the immediate identification of a reactive donation, obviating the need for pool dismembering. The whole process took 6-8 hours per day and results were issued in parallel to serology. The method was shown to detect all six HCV genotypes and a sensitivity of 500 IU/mL was achieved (95% hit rate). Until July 2005, 139,678 donations were tested and 315 (0.23%) were found reactive for HCV-RNA. Except for five false-positives, all 310 presented the corresponding antibody as well, so the yield of NAT-only donations was zero, presenting a specificity of 99.83%. Detection of a window period donation, in the population studied, will probably demand testing of a larger number of donations. International experience is showing a rate of 1:200,000 - 1:500,000 of isolated HCV-RNA reactive donations.

Implementação de um modelo de Data Warehouse para o Serviço Nacional de Avisos Agrícolas

Trabalho de Projecto apresentado como requisito parcial para obtenção do grau de Mestre em Estatística e Gestão de Informação.

Training and discovering corpus-based data driven exercices in english teaching (L2/FL) to native speakers of portuguese (L1)

Project submitted as part requirement for the degree of Masters in English teaching,

Candida bloodstream infection: data from a teaching hospital in Mato Grosso do Sul, Brazil

The incidence of Candida bloodstream infection has increased over the past years. In the Center-West region of Brazil, data on candidemia are scarce. This paper reports a retrospective analysis of 96 cases of Candida bloodstream infection at a Brazilian tertiary-care teaching hospital in the state of Mato Grosso do Sul, from January 1998 to December 2006. Demographic, clinical and laboratory data were collected from medical records and from the hospital's laboratory database. Patients' ages ranged from three days to 92 years, with 53 (55.2%) adults and 43 (44.8%) children. Of the latter, 25 (58.1%) were newborns. The risk conditions most often found were: long period of hospitalization, utilization of venous central catheter, and previous use of antibiotics. Fifty-eight (60.4%) patients died during the hospitalization period and eight (13.7%) of them died 30 days after the diagnosis of candidemia. Candida albicans (45.8%) was the most prevalent species, followed by C. parapsilosis (34.4%), C. tropicalis (14.6%) and C. glabrata (5.2%). This is the first report of Candida bloodstream infection in the state of Mato Grosso do Sul and it highlights the importance of considering the possibility of invasive Candida infection in patients exposed to risk factors, particularly among neonates and the elderly.

Single operation multiple data - paralelismo de dados ao nível da sub-rotina

Dissertação para obtenção do Grau de Mestre em Engenharia Informática

On the analysis of data emerging in non-linear and complex systemscomparison of two X-Ray prony spectra

New arguments proving that successive (repeated) measurements have a memory and actually remember each other are presented. The recognition of this peculiarity can change essentially the existing paradigm associated with conventional observation in behavior of different complex systems and lead towards the application of an intermediate model (IM). This IM can provide a very accurate fit of the measured data in terms of the Prony's decomposition. This decomposition, in turn, contains a small set of the fitting parameters relatively to the number of initial data points and allows comparing the measured data in cases where the “best fit” model based on some specific physical principles is absent. As an example, we consider two X-ray diffractometers (defined in paper as A- (“cheap”) and B- (“expensive”) that are used after their proper calibration for the measuring of the same substance (corundum a-Al2O3). The amplitude-frequency response (AFR) obtained in the frame of the Prony's decomposition can be used for comparison of the spectra recorded from (A) and (B) - X-ray diffractometers (XRDs) for calibration and other practical purposes. We prove also that the Fourier decomposition can be adapted to “ideal” experiment without memory while the Prony's decomposition corresponds to real measurement and can be fitted in the frame of the IM in this case. New statistical parameters describing the properties of experimental equipment (irrespective to their internal “filling”) are found. The suggested approach is rather general and can be used for calibration and comparison of different complex dynamical systems in practical purposes.

Measuring data transfer in heterogeneous IoT environments

Dissertação para obtenção do Grau de Mestre em Engenharia Electrotécnica e de Computadores

E.D.I.: electronic data interchange

O presente trabalho tem como tema a Troca Electrónica de Dados (Electronic Data Interchange – EDI) transferência de dados estruturados, respeitando mensagens normalizadas estabelecidas, computador a computador, por meios electrónicos. Trocas entre computadores refere-se a trocas entre aplicações informáticas: por exemplo o sistema de encomendas envia ordens ao sistema central de controlo da produção, o qual então fará o envio da respectiva factura. O EDI aberto faz a troca electrónica de dados entre parceiros autónomos que se associaram para fazerem trocas de dados estruturados que são destinados a serem processados por programas de aplicações.

A score test for non-nested hypotheses with applications to discrete data models

This paper suggests that a convenient score test against non-nested alternatives can be constructed from the linear combination of the likelihood functions of the competing models. It is shown that this procedure is essentially a test for the correct specification of the conditional distribution of the variable of interest.

PIASA: A power and interference aware resource management strategy for heterogeneous workloads in cloud data centers

Cloud data centers have been progressively adopted in different scenarios, as reflected in the execution of heterogeneous applications with diverse workloads and diverse quality of service (QoS) requirements. Virtual machine (VM) technology eases resource management in physical servers and helps cloud providers achieve goals such as optimization of energy consumption. However, the performance of an application running inside a VM is not guaranteed due to the interference among co-hosted workloads sharing the same physical resources. Moreover, the different types of co-hosted applications with diverse QoS requirements as well as the dynamic behavior of the cloud makes efficient provisioning of resources even more difficult and a challenging problem in cloud data centers. In this paper, we address the problem of resource allocation within a data center that runs different types of application workloads, particularly CPU- and network-intensive applications. To address these challenges, we propose an interference- and power-aware management mechanism that combines a performance deviation estimator and a scheduling algorithm to guide the resource allocation in virtualized environments. We conduct simulations by injecting synthetic workloads whose characteristics follow the last version of the Google Cloud tracelogs. The results indicate that our performance-enforcing strategy is able to fulfill contracted SLAs of real-world environments while reducing energy costs by as much as 21%.

Analysis of correlation between cerebrospinal fluid and plasma HIV-1 RNA levels in patients with neurological opportunistic diseases

The question of whether HIV-1 RNA in cerebrospinal fluid (CSF) is derived from viral replication in the central nervous system or simply reflects the transit of infected lymphocytes from the blood compartment has long been a matter of debate. Some studies found no correlation between CSF and plasma viral load, whereas others did. The lack of a correlation between the two compartments suggests that the presence of HIV-1 RNA is not simply due to the passive passage of the virus from blood to CSF but rather due to intrathecal replication. To evaluate the correlation between plasma and CSF HIV-1 RNA levels and to identify situations in which there is no correlation between the two compartments, seventy patients were prospectively studied. The association between CSF and plasma viral load was evaluated in the total population and in subgroups of patients with similar characteristics. A correlation between the CSF and plasma compartments was observed for patients undergoing highly active antiretroviral therapy (HAART), those with a CD4 T lymphocyte count lower than 200 cells/mm³, and those with increased CSF protein content. On the other hand, no correlation was observed for patients without adequate virological control, who had a CD4 count higher than 200 cells/mm³ and who did not use HAART. The correlation between the two compartments observed in some patients suggests that CSF HIV-1 RNA levels may reflect plasma levels in these subjects. In contrast, the lack of a correlation between the two compartments in patients who were not on HAART and who had normal CSF proteins and a poor virological control possibly indicates compartmentalization of the virus in CSF and, consequently, plasma-independent intrathecal viral replication.

Publicação de linked data: o caso de uso Pordata

Dissertação para obtenção do Grau de Mestre em Lógica Computacional

Transoesophageal Echocardiography for Monitoring Liver Surgery: Data from a Pilot Study

A pilot study aimed to introduce intraoperative monitoring of liver surgery using transoesophageal echocardiography (TEE) is described. A set of TEE measurements was established as a protocol, consisting of left atrial (LA) dimension at the aortic valve plane; mitral velocity flow integral, calculation of stroke volume and cardiac output (CO); mitral annular plane systolic excursion; finally, right atrial area. A total of 165 measurements (on 21 patients) were performed, 31 occurring during hypotension. The conclusions reached were during acute blood loss LA dimension changed earlier than CVP, and, in one patient, a dynamic left ventricular (LV) obstruction was observed; in 3 patients a transient LV systolic dysfunction was documented. The comparison between 39 CO paired measurements obtained by TEE and PiCCO2 revealed a statistically significant correlation (P < 0.001, r = 0.83). In this pilot study TEE successfully answered the questions raised by the anesthesiologists. Larger cohort studies are needed to address this issue.

Genetic diversity and primary resistance among HIV-1-positive patients from Maringá, Paraná, Brazil

The objective of this study is to identify subtypes of Human Immunodeficiency Virus type 1 (HIV-1) and to analyze the presence of mutations associated to antiretroviral resistance in the protease (PR) and reverse transcriptase (RT) regions from 48 HIV-1 positive treatment naïve patients from an outpatient clinic in Maringá, Paraná, Brazil. Sequencing was conducted using PR, partial RT and group-specific antigen gene (gag) nested PCR products from retrotranscribed RNA. Transmitted resistance was determined according to the Surveillance Drug Resistance Mutation List (SDRM) algorithm. Phylogenetic and SimPlot analysis of concatenated genetic segments classified sequences as subtype B 19/48 (39.6%), subtype C 12/48 (25%), subtype F 4/48 (8.3%), with 13/48 (27.1%) recombinant forms. Most recombinant forms were B mosaics (B/F 12.5%, B/C 10.4%), with one C/F (2.1%) and one complex B/C/F mosaic (2.1%). Low levels of transmitted resistance were found in this study, 2/48 (2.1% to NRTIs and 2.1% for PI). This preliminary data may subsidize the monitoring of the HIV evolution in the region.

Acute respiratory viral infections in children in Rio de Janeiro and Teresópolis, Brazil

The frequency of viral pathogens causing respiratory infections in children in the cities of Rio de Janeiro and Teresópolis was investigated. Nasal swabs from children with acute respiratory illnesses were collected between March 2006 and October 2007. Specimens were tested for viral detection by conventional (RT)-PCR and/or real time PCR. Of the 205 nasal swabs tested, 64 (31.2%) were positive for at least one of the viral pathogens. Single infections were detected in 56 samples, 50 of those were caused by RNA viruses: 33 samples tested positive for rhinovirus, five for influenza A, five for metapneumovirus, four for coronavirus and, three for respiratory syncytial virus. For the DNA viruses, five samples were positive for bocavirus and one for adenovirus. Co-infections with these viruses were detected in eight samples. Our data demonstrate a high frequency of viral respiratory infections, emphasizing the need for a more accurate diagnosis particularly for the emerging respiratory viruses. The fact that the emerging respiratory viruses were present in 9.2% of the tested samples suggests that these viruses could be important respiratory pathogens in the country.