Column-based databases: estudo exploratório no âmbito das bases de dados NoSQL

O aumento da quantidade de dados gerados que se tem verificado nos últimos anos e a que se tem vindo a dar o nome de Big Data levou a que a tecnologia relacional começasse a demonstrar algumas fragilidades no seu armazenamento e manuseamento o que levou ao aparecimento das bases de dados NoSQL. Estas estão divididas por quatro tipos distintos nomeadamente chave/valor, documentos, grafos e famílias de colunas. Este artigo é focado nas bases de dados do tipo column-based e nele serão analisados os dois sistemas deste tipo considerados mais relevantes: Cassandra e HBase.

Column-based databases: estudo exploratório no âmbito das bases de dados NoSQL

Dissertação de mestrado integrado em Engenharia e Gestão de Sistemas de Informação

Document-based databases: estudo comparativo no âmbito das bases de dados NoSql

Dissertação de mestrado integrado em Engenharia e Gestão de Sistemas de Informação

Improved column-based radiochemical processing of the generator produced 68Ga

An improved chemical strategy for processing of the generator produced 68Ga was developed based on processing of the original 68Ge/68Ga generator eluate on a micro-column. Direct pre-concentration and purification of the eluted 68Ga is performed on a cation-exchange resin in hydrochloric acid/acetone media. A supplementary step based on a second micro-column filled with a second resin allows direct re-adsorption of 68Ga eluted from the cation exchanger. 68Ga is finally striped from the second resin with a small volume of pure water. For this purpose a strong anion exchanger and a novel extraction chromatographic resin based on tetraalkyldiglycolamides are characterized. The strategy allows online pre-concentration and purification of 68Ga from the original generator eluate. The supplementary column allows transferring 68Ga with high radionuclide and chemical quality in the aqueous solution with small volume and low acidity useful for direct radiolabeling reactions.

Induction of protective T-helper 1 immune responses against Echinococcus granulosus in mice by a multi-T-cell epitope antigen based on five proteins

In this study, we designed an experiment to predict a potential immunodominant T-cell epitope and evaluate the protectivity of this antigen in immunised mice. The T-cell epitopes of the candidate proteins (EgGST, EgA31, Eg95, EgTrp and P14-3-3) were detected using available web-based databases. The synthesised DNA was subcloned into the pET41a+ vector and expressed in Escherichia coli as a fusion to glutathione-S-transferase protein (GST). The resulting chimeric protein was then purified by affinity chromatography. Twenty female C57BL/6 mice were immunised with the antigen emulsified in Freund's adjuvant. Mouse splenocytes were then cultured in Dulbecco's Modified Eagle's Medium in the presence of the antigen. The production of interferon-γ was significantly higher in the immunised mice than in the control mice (> 1,300 pg/mL), but interleukin (IL)-10 and IL-4 production was not statistically different between the two groups. In a challenge study in which mice were infected with 500 live protoscolices, a high protectivity level (99.6%) was demonstrated in immunised BALB/C mice compared to the findings in the control groups [GST and adjuvant (Adj) ]. These results demonstrate the successful application of the predicted T-cell epitope in designing a vaccine against Echinococcus granulosus in a mouse model.

Controlled oxidative protein refolding using an ion-exchange column

Column-based refolding of complex and highly disulfide-bonded proteins simplifies protein renaturation at both preparative and process scale by integrating and automating a number of operations commonly used in dilution refolding. Bovine serum albumin (BSA) was used as a model protein for refolding and oxido-shuffling on an ion-exchange column to give a refolding yield of 55 % after 40 Ih incubation. Successful on-column refolding was conducted at protein concentrations of up to 10 mg/ml and refolded protein, purified from misfolded forms, was eluted directly from the column at a concentration of 3 mg/ml. This technique integrates the dithiothreitol removal, refolding, concentration and purification steps, achieving a high level of process simplification and automation, and a significant saving in reagent costs when scaled. Importantly, the current result suggests that it is possible to controllably refold disulfide-bonded proteins using common and inexpensive matrices, and that it is not always necessary to control protein-surface interactions using affinity tags and expensive chromatographic matrices. Moreover, it is possible to strictly control the oxidative refolding environment once denatured protein is bound to the ion-exchange column, thus allowing precisely controlled oxido-shuffling. (c) 2005 Elsevier B.V. All rights reserved.

Determination of beta-artemether and its main metabolite dihydroartemisinin in plasma employing liquid-phase microextraction prior to liquid chromatographic-tandem mass spectrometric analysis

A method for the determination of artemether (ART) and its main metabolite dihydroartemisinin (DHA) in plasma employing liquid-phase microextraction (LPME) for sample preparation prior to liquid chromatography-tandem mass spectrometry (LC-MS-MS) was developed. The analytes were extracted from 1 nil, of plasma utilizing a two-phase LPME procedure with artemisinin as internal standard. Using the optimized LPME conditions, mean absolute recovery rates of 25 and 32% for DHA and ART, respectively, were achieved using toluene-n-octanol (1:1, viv) as organic phase with an extraction time of 30 min. After extraction, the analytes were resolved within 5 min using a mobile phase consisting of methanol-ammonium acetate (10 mmol L(-1) pH 5.0, 80:20. v/v) on a laboratory-made column based on poly(methyltetradecylsiloxane) attached to a zirconized-silica support. MS-MS detection was employed using an electrospray interface in the positive ion mode. The method developed was linear over the range of 5-1000 ng mL(-1) for both analytes. Precision and accuracy were within acceptable levels of confidence (<15%). The assay was applied to the determination of these analytes in plasma from rats treated with ART. The two-phase LPME procedure is affordable and the solvent consumption was very low compared to the traditional methods of sample preparation. (C) 2010 Elsevier B.V. All rights reserved.

Computational methods for prediction of T-cell epitopes - a framework for modelling, testing, and applications

Computational models complement laboratory experimentation for efficient identification of MHC-binding peptides and T-cell epitopes. Methods for prediction of MHC-binding peptides include binding motifs, quantitative matrices, artificial neural networks, hidden Markov models, and molecular modelling. Models derived by these methods have been successfully used for prediction of T-cell epitopes in cancer, autoimmunity, infectious disease, and allergy. For maximum benefit, the use of computer models must be treated as experiments analogous to standard laboratory procedures and performed according to strict standards. This requires careful selection of data for model building, and adequate testing and validation. A range of web-based databases and MHC-binding prediction programs are available. Although some available prediction programs for particular MHC alleles have reasonable accuracy, there is no guarantee that all models produce good quality predictions. In this article, we present and discuss a framework for modelling, testing, and applications of computational methods used in predictions of T-cell epitopes. (C) 2004 Elsevier Inc. All rights reserved.

Multicentre validation study of nucleic acids extraction from FFPE tissues.

In most pathology laboratories worldwide, formalin-fixed paraffin embedded (FFPE) samples are the only tissue specimens available for routine diagnostics. Although commercial kits for diagnostic molecular pathology testing are becoming available, most of the current diagnostic tests are laboratory-based assays. Thus, there is a need for standardized procedures in molecular pathology, starting from the extraction of nucleic acids. To evaluate the current methods for extracting nucleic acids from FFPE tissues, 13 European laboratories, participating to the European FP6 program IMPACTS (www.impactsnetwork.eu), isolated nucleic acids from four diagnostic FFPE tissues using their routine methods, followed by quality assessment. The DNA-extraction protocols ranged from homemade protocols to commercial kits. Except for one homemade protocol, the majority gave comparable results in terms of the quality of the extracted DNA measured by the ability to amplify differently sized control gene fragments by PCR. For array-applications or tests that require an accurately determined DNA-input, we recommend using silica based adsorption columns for DNA recovery. For RNA extractions, the best results were obtained using chromatography column based commercial kits, which resulted in the highest quantity and best assayable RNA. Quality testing using RT-PCR gave successful amplification of 200 bp-250 bp PCR products from most tested tissues. Modifications of the proteinase-K digestion time led to better results, even when commercial kits were applied. The results of the study emphasize the need for quality control of the nucleic acid extracts with standardised methods to prevent false negative results and to allow data comparison among different diagnostic laboratories.

Annual Report Of the State Geologist, March 2012

What we do: Since 1892, the Iowa Geological and Water Survey (IGWS) has provided earth, water, and mapping science to all Iowans. We collect and interpret information on subsurface geologic conditions, groundwater and surface water quantity and quality, and the natural and built features of our landscape. This information is critical for: Predicting the future availability of economic water supplies and mineral resources. Assuring proper function of waste disposal facilities. Delineation of geologic hazards that may jeopardize property and public safety. Assessing trends and providing protection of water quality and soil resources. Applied technical assistance for economic development and environmental stewardship. Our goal: Providing the tools for good decision making to assure the long-term vitality of Iowa’s communities, businesses, and quality of life. Information and technical assistance are provided through web-based databases, comprehensive Geographic Information System (GIS) tools, predictive groundwater models, and watershed assessments and improvement grants. The key service we provide is direct assistance from our technical staff, working with Iowans to overcome real-world challenges. This report describes the basic functions of IGWS program areas and highlights major activities and accomplishments during calendar year 2011. More information on IGWS is available at http://www.igsb.uiowa.edu/.

Readout architectures for hybrid pixel detector readout chips

The original contribution of this thesis to knowledge are novel digital readout architectures for hybrid pixel readout chips. The thesis presents asynchronous bus-based architecture, a data-node based column architecture and a network-based pixel matrix architecture for data transportation. It is shown that the data-node architecture achieves readout efficiency 99% with half the output rate as a bus-based system. The network-based solution avoids “broken” columns due to some manufacturing errors, and it distributes internal data traffic more evenly across the pixel matrix than column-based architectures. An improvement of > 10% to the efficiency is achieved with uniform and non-uniform hit occupancies. Architectural design has been done using transaction level modeling (TLM) and sequential high-level design techniques for reducing the design and simulation time. It has been possible to simulate tens of column and full chip architectures using the high-level techniques. A decrease of > 10 in run-time is observed using these techniques compared to register transfer level (RTL) design technique. Reduction of 50% for lines-of-code (LoC) for the high-level models compared to the RTL description has been achieved. Two architectures are then demonstrated in two hybrid pixel readout chips. The first chip, Timepix3 has been designed for the Medipix3 collaboration. According to the measurements, it consumes < 1 W/cm^2. It also delivers up to 40 Mhits/s/cm^2 with 10-bit time-over-threshold (ToT) and 18-bit time-of-arrival (ToA) of 1.5625 ns. The chip uses a token-arbitrated, asynchronous two-phase handshake column bus for internal data transfer. It has also been successfully used in a multi-chip particle tracking telescope. The second chip, VeloPix, is a readout chip being designed for the upgrade of Vertex Locator (VELO) of the LHCb experiment at CERN. Based on the simulations, it consumes < 1.5 W/cm^2 while delivering up to 320 Mpackets/s/cm^2, each packet containing up to 8 pixels. VeloPix uses a node-based data fabric for achieving throughput of 13.3 Mpackets/s from the column to the EoC. By combining Monte Carlo physics data with high-level simulations, it has been demonstrated that the architecture meets requirements of the VELO (260 Mpackets/s/cm^2 with efficiency of 99%).

Vancomycin-resistant enterococcus outbreak in a pediatric intensive care unit: report of successful interventions for control and prevention

The objective of this study is to retrospectively report the results of interventions for controlling a vancomycin-resistant enterococcus (VRE) outbreak in a tertiary-care pediatric intensive care unit (PICU) of a University Hospital. After identification of the outbreak, interventions were made at the following levels: patient care, microbiological surveillance, and medical and nursing staff training. Data were collected from computer-based databases and from the electronic prescription system. Vancomycin use progressively increased after March 2008, peaking in August 2009. Five cases of VRE infection were identified, with 3 deaths. After the interventions, we noted a significant reduction in vancomycin prescription and use (75% reduction), and the last case of VRE infection was identified 4 months later. The survivors remained colonized until hospital discharge. After interventions there was a transient increase in PICU length-of-stay and mortality. Since then, the use of vancomycin has remained relatively constant and strict, no other cases of VRE infection or colonization have been identified and length-of-stay and mortality returned to baseline. In conclusion, we showed that a bundle intervention aiming at a strict control of vancomycin use and full compliance with the Hospital Infection Control Practices Advisory Committee guidelines, along with contact precautions and hand-hygiene promotion, can be effective in reducing vancomycin use and the emergence and spread of vancomycin-resistant bacteria in a tertiary-care PICU.

Indicadores del desempeño clínico fisioterapéutico en el manejo hospitalario temprano del accidente

Las oportunidades conocidas de intervenciones tempranas en los accidentes cardiocerebrovasculares (ACV) desde el punto de vista médico y de rehabilitación hacen necesario avanzar en la formulación de indicadores del desempeño clínico en el manejo fisioterapéutico hospitalario de una persona con ACV. Objetivo: identificar los indicadores de desempeño clínico fisioterapéutico en el manejo hospitalario temprano de personas sobrevivientes de ACV. Materiales y métodos: se trata de un estudio exploratorio descriptivo que indaga sobre las pruebas y prácticas fisioterapéuticas existentes, la evidencia científica sobre indicadores clínicos en ACV, los indicadores estándar y los posibles indicadores clínicos en el escenario. Se llevó a cabo una revisión sistemática de estudios descriptivos, guías de práctica clínica, revisiones sistemáticas, estudio de casos clínicos basados en la evidencia en bases de datos como Pubmed, Proquest, Pedro y en revistas electrónicas, además del análisis de datos epidemiológicos de la prevalencia del ACV en Colombia y en Chile, en páginas web de la Organización Mundial de la Salud, Ministerio de Salud y Departamento AdministrativoNacional de cada país. Resultados: la evidencia señala que la rehabilitación temprana del ACV debe iniciarse durante la hospitalización, tan pronto como el diagnóstico se establezca y los problemas que ponen en riesgo la vida del paciente estén controlados. Las prioridades en la intervención fisioterapéutica en ACV son prevenir las complicaciones (trombosis venosa, infecciones y dolor) y facilitar la movilización temprana. Actualizaciones recientes de estas directrices incluyen la rehabilitación temprana, en particular la movilidad luego de las veinticuatro horas posteriores al ACV.Las pruebas que sustentan los indicadores de desempeño en rehabilitación para la atención en la etapa subaguda del ACV son escasas. Conclusiones: se hace notoria la importancia de la atención temprana fisioterapéutica en el proceso agudo del paciente con ACV, puesto que la evidencia disponible resalta un mejor pronóstico para pacientes que son intervenidos por el área dentro de las primeras veinticuatro horas posteriores al evento y la importancia de los indicadores de atención del paciente, como la calidad y el tiempo de atención, la periodicidad y el aprovechamiento de la intervención dentro de la ventana temporal aguda de recuperación del paciente.

O ensino de oncologia em enfermagem: um panorama do Brasil, Estados Unidos e outros países

The incidence of neoplasias has increased worldwide every year, and the training of qualified nurses for quality care provision to oncologic patients is necessary. This study aimed at identifying, in the literature, how oncology has been taught in the curricula of several undergraduate nursing programs in Brazil, the United States and other countries. The articles were located on Internet-based databases, namwly Lilacs and Scopus, from which 35 publications were found, and 18 articles were included. In Brazil, oncology is taught in undergraduate nursing programs in an isolated and punctual fashion, and it is not included in curricula. Parallelly, in the other countries included in the study, similarity was found as to this aspect; however, there is evidence of the implantation of elective and extracurricular courses. It is noteworthy that, in Brazil, there is evidence of government policies for oncology teaching and cancer control; nevertheless, such guidelines have not been concretized in curricula. The study showed a scenario in which oncology teaching in undergraduate nursing programs is insufficient or inexistent both in Brazil and in other countries, which compromises the training of future qualified professionals that will be attentive to that theme, since cancer is a frequent pathology, and the presence of nurses is fundamental for the care of such patients from diagnosis to cure, or even during occasional death

Vancomycin-resistant enterococcus outbreak in a pediatric intensive care unit: report of successful interventions for control and prevention

The objective of this study is to retrospectively report the results of interventions for controlling a vancomycin-resistant enterococcus (VRE) outbreak in a tertiary-care pediatric intensive care unit (PICU) of a University Hospital. After identification of the outbreak, interventions were made at the following levels: patient care, microbiological surveillance, and medical and nursing staff training. Data were collected from computer-based databases and from the electronic prescription system. Vancomycin use progressively increased after March 2008, peaking in August 2009. Five cases of VRE infection were identified, with 3 deaths. After the interventions, we noted a significant reduction in vancomycin prescription and use (75% reduction), and the last case of VRE infection was identified 4 months later. The survivors remained colonized until hospital discharge. After interventions there was a transient increase in PICU length-of-stay and mortality. Since then, the use of vancomycin has remained relatively constant and strict, no other cases of VRE infection or colonization have been identified and length-of-stay and mortality returned to baseline. In conclusion, we showed that a bundle intervention aiming at a strict control of vancomycin use and full compliance with the Hospital Infection Control Practices Advisory Committee guidelines, along with contact precautions and hand-hygiene promotion, can be effective in reducing vancomycin use and the emergence and spread of vancomycin-resistant bacteria in a tertiary-care PICU.