Packaging controlled experiments using an evolutionary approach based on ontology

A body of knowledge in Software Engineering requires experiments replications. The knowledge generated by a study is registered in the so-called lab package, which, must be reviewed by an eventual research group with the intention to replicate it. However, researchers face difficulties reviewing the lab package, what leads to problems in share knowledge among research groups. Besides that, the lack of standardization is an obstacle to the integration of the knowledge from an isolated study in a common body of knowledge. In this sense, ontologies can be applied, since they can be seen as a standard that promotes the shared understanding of the experiment information structure. In this paper, we present a workflow to generate lab packages based on EXPEiiQntology, an ontology of controlled experiments domain. In addition, by means of lab packages instantiation, it is possible to evolve the ontology, in order to deal with new concepts that may appear in different lab packages. The iterative ontology evolution aims at achieve a standard that is able to accommodate different lab packages and, hence, facilitate to review and understand their content.

Proposta de abordagem metodológica para avaliação de desempenho na cadeia de valores aplicado em uma empresa de médio porte

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Modelagem direta de dados de eletrorresistividade 3-D

Dentre os métodos geofísicos, o da Eletrorresistividade é um dos mais tradicionais, com o seu desenvolvimento ocorrido há mais de 80 anos. Durante esse tempo o seu uso acompanhou o avanço no poder de processamento numérico e mais recentemente, a modelagem e inversão tridimensional tornou-se uma possibilidade para o geofísico. Apresentamos, neste trabalho, a técnica de elementos finitos aplicada ao método da eletrorresistividade 3-D, através do cálculo do potencial secundário. Para o desenvolvimento da metodologia, simulamos o levantamento do método da eletrorresistividade 3-D com os arranjos Dipolo-Dipolo e Schlumberger, visando medir as variações laterais e verticais da resistividade aparente do solo. Estes arranjos consistem na injeção de corrente elétrica na superfície e de medidas de diferenças de potencial elétrico, resultante da interação da corrente elétrica com o solo. Sendo que, as fontes e receptores são localizados de acordo com os arranjos escolhidos para o levantamento. Neste trabalho, as curvas de sondagem e as pseudo-secções de resistividade aparente, são obtidas através da modelagem de eletrorresistividade 3-D, usando malha de elementos finitos regular. Para efeito de validação, os resultados são comparados com a resposta 3-D obtida a partir dos potenciais totais.

Melhorias dos processos no setor de expedição em uma transportadora de cargas fracionadas

The transport market has forced organizations reduce the cost of services and processes, resulting from the highly competitive and, for such waste at all levels and processes are a focus of study for its elimination. This study refers to carrier fractional loads, located in the municipality of Itapecerica da Serra Layout and headquartered in São Paulo, which requires a rapid development throughout its structure, because its expansion was not accompanied by an evolution of effective processes. The need to increase efficiency in delivery with a reduced cost of transport forced the company to hire a logistics consulting to help identify potential bottlenecks in processes, suggest improvements with greater impact and implementation at the end of a critical analysis of results. This work focuses on the Layout of the warehouse shipping area of this organization and we used the method of action research to the consultant and involved could reach this conclusion collaboratively, as well as interviews with those involved in the process and also visual observation. Tools such as Key Performance Indicator, Mapping Workflow, Analytic Hierarchy Process, Applied Statistics and Standard Operating Procedure were used to assist in the identification, analysis and implementation of the proposed improvements

Sistema de cálculo para determinação do tempo de exposição em radioterapia veterinária

Radiotherapy in veterinary practice is already known and widely distributed in large specialized centers of developed countries. In early 2000, there were about 30 radiotherapy equipment specifically designed for the veterinary clinic in the United States. In Brazil, the veterinary radiotherapy is still confined to research in universities, where most of the procedures is radiation therapy performed with superficial x-ray machines, with a voltage between 50 and 150 kVp, focus-distance surface (DFS) between 20,0cm and 40,0cm. As that occurs in human medicine, new research strengthens the development and prospects for the use of radiotherapy as a safe option for treating cancer in animals. This paper presents a methodology for calculating the exposure time for superficial radiotherapy procedures in veterinary medicine for small animals (dogs and cats). The dosimetric parameters of X-rays are determined using a spreadsheet tool for Microsoft Office Excel, developed in this paper for a device Dermopan 2, Veterinary Hospital of UNESP in Araçatuba. Using the worksheet helps the veterinarian to determine the time of exposure to radiation determined for each clinical case, optimize the workflow for professionals in veterinary radiotherapy procedures, which often lack the medical physics in team and at the time of radiotherapy. The correct use of spreadsheet decreases the chances of errors in dose rates of radiation, providing a higher quality of care

Classificação de workflows baseados em web services

Over the last decades changes have occurred in communication within and between enterprises, made easier by technologies suchas E-commerce, Internet, ERP systems and remote meetings and there was a rapid progress in network technology, which has changed the way business is done. A standardized way to offer services over the internet is using web services. Web services are a kind of remote procedure call and are generally used to integrate systems, independent of language, both client and server. It is common to use several web services run in sequence to perform a business process. To this type of process, gives the name of workflow. Thus, Web services are the primary components of workflows. A tool that provides a way of visualizing the behavior of a workflow can assist the administrator and is required. The present work presents the development of a tool that allows the administrator to classify visually services components and evaluate their importance in the final performance of a workflow. As proof of concept we used several virtual servers and computers where each computer has received a set of web services. A proxy was added between each call of workflows collecting relevant information and storing them in a database for later analysis. The analysis was based on Quality of Service parameters

Estudo da deposição de energia das radiofrequências através do método das diferenças finitas dependentes do tempo Monografia

Radiotherapy in veterinary practice is already known and widely distributed in large specialized centers of developed countries. In early 2000, there were about 30 radiotherapy equipment specifically designed for the veterinary clinic in the United States. In Brazil, the veterinary radiotherapy is still confined to research in universities, where most of the procedures is radiation therapy performed with superficial x-ray machines, with a voltage between 50 and 150 kVp, focus-distance surface (DFS) between 20,0cm and 40,0cm. As that occurs in human medicine, new research strengthens the development and prospects for the use of radiotherapy as a safe option for treating cancer in animals. This paper presents a methodology for calculating the exposure time for superficial radiotherapy procedures in veterinary medicine for small animals (dogs and cats). The dosimetric parameters of X-rays are determined using a spreadsheet tool for Microsoft Office Excel, developed in this paper for a device Dermopan 2, Veterinary Hospital of UNESP in Araçatuba. Using the worksheet helps the veterinarian to determine the time of exposure to radiation determined for each clinical case, optimize the workflow for professionals in veterinary radiotherapy procedures, which often lack the medical physics in team and at the time of radiotherapy. The correct use of spreadsheet decreases the chances of errors in dose rates of radiation, providing a higher quality of care

Empacotamento de experimentos controlados em engenharia de software: uma abordagem baseada em ontologia

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

Apoio à execução de experimentos controlados usando uma ontologia para empacotamento: a ferramenta OntoExpTool

Pós-graduação em Ciência da Computação - IBILCE

High precision and selectivity for quantitation of enrofloxacin and ciprofloxacin in five chicken tissues using solid phase extraction and ESI LC-MS/MS for application in monitoring residues

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

De novo transcriptome assembly for a non-model species, the blood-sucking bug Triatoma brasiliensis, a vector of Chagas disease

High throughput sequencing (HTS) provides new research opportunities for work on non-model organisms, such as differential expression studies between populations exposed to different environmental conditions. However, such transcriptomic studies first require the production of a reference assembly. The choice of sampling procedure, sequencing strategy and assembly workflow is crucial. To develop a reliable reference transcriptome for Triatoma brasiliensis, the major Chagas disease vector in Northeastern Brazil, different de novo assembly protocols were generated using various datasets and software. Both 454 and Illumina sequencing technologies were applied on RNA extracted from antennae and mouthparts from single or pooled individuals. The 454 library yielded 278 Mb. Fifteen Illumina libraries were constructed and yielded nearly 360 million RNA-seq single reads and 46 million RNA-seq paired-end reads for nearly 45 Gb. For the 454 reads, we used three assemblers, Newbler, CAP3 and/or MIRA and for the Illumina reads, the Trinity assembler. Ten assembly workflows were compared using these programs separately or in combination. To compare the assemblies obtained, quantitative and qualitative criteria were used, including contig length, N50, contig number and the percentage of chimeric contigs. Completeness of the assemblies was estimated using the CEGMA pipeline. The best assembly (57,657 contigs, completeness of 80 %, < 1 % chimeric contigs) was a hybrid assembly leading to recommend the use of (1) a single individual with large representation of biological tissues, (2) merging both long reads and short paired-end Illumina reads, (3) several assemblers in order to combine the specific advantages of each.

Imputation of microsatellite alleles from dense SNP genotypes for parentage verification across multiple Bos taurus and Bos indicus breeds

To assist cattle producers transition from microsatellite (MS) to single nucleotide polymorphism (SNP) genotyping for parental verification we previously devised an effective and inexpensive method to impute MS alleles from SNP haplotypes. While the reported method was verified with only a limited data set (N = 479) from Brown Swiss, Guernsey, Holstein, and Jersey cattle, some of the MS-SNP haplotype associations were concordant across these phylogenetically diverse breeds. This implied that some haplotypes predate modern breed formation and remain in strong linkage disequilibrium. To expand the utility of MS allele imputation across breeds, MS and SNP data from more than 8000 animals representing 39 breeds (Bos taurus and B. indicus) were used to predict 9410 SNP haplotypes, incorporating an average of 73 SNPs per haplotype, for which alleles from 12 MS markers could be accurately be imputed. Approximately 25% of the MS-SNP haplotypes were present in multiple breeds (N = 2 to 36 breeds). These shared haplotypes allowed for MS imputation in breeds that were not represented in the reference population with only a small increase in Mendelian inheritance inconsistancies. Our reported reference haplotypes can be used for any cattle breed and the reported methods can be applied to any species to aid the transition from MS to SNP genetic markers. While ~91% of the animals with imputed alleles for 12 MS markers had ≤1 Mendelian inheritance conflicts with their parents' reported MS genotypes, this figure was 96% for our reference animals, indicating potential errors in the reported MS genotypes. The workflow we suggest autocorrects for genotyping errors and rare haplotypes, by MS genotyping animals whose imputed MS alleles fail parentage verification, and then incorporating those animals into the reference dataset.

Empacotamento de experimentos controlados com abordagem evolutiva baseada em ontologia

Um corpo de conhecimento em Engenharia de Software requer a replicação de experimentos controlados. O conhecimento gerado por um experimento é registrado no chamado pacote de laboratório, o qual deve ser revisado por um eventual grupo de pesquisa com a intenção de replicá-lo. Entretanto, pesquisadores enfrentam dificuldades ao revisar pacotes de laboratório, o que leva a problemas de compartilhamento de conhecimento entre grupos de pesquisa. Além disso, a falta de padronização é um obstáculo à integração de um estudo isolado em um corpo de conhecimento comum. Nesse contexto, é proposto um workflow para gerar pacotes de laboratório baseados na ExperOntology, uma ontologia do domínio de experimentos controlados, visando a contribuir na revisão e no entendimento de pacotes de laboratório.

Low-Cost Ultra-Wide Genotyping Using Roche/454 Pyrosequencing for Surveillance of HIV Drug Resistance

Background: Great efforts have been made to increase accessibility of HIV antiretroviral therapy (ART) in low and middle-income countries. The threat of wide-scale emergence of drug resistance could severely hamper ART scale-up efforts. Population-based surveillance of transmitted HIV drug resistance ensures the use of appropriate first-line regimens to maximize efficacy of ART programs where drug options are limited. However, traditional HIV genotyping is extremely expensive, providing a cost barrier to wide-scale and frequent HIV drug resistance surveillance. Methods/Results: We have developed a low-cost laboratory-scale next-generation sequencing-based genotyping method to monitor drug resistance. We designed primers specifically to amplify protease and reverse transcriptase from Brazilian HIV subtypes and developed a multiplexing scheme using multiplex identifier tags to minimize cost while providing more robust data than traditional genotyping techniques. Using this approach, we characterized drug resistance from plasma in 81 HIV infected individuals collected in Sao Paulo, Brazil. We describe the complexities of analyzing next-generation sequencing data and present a simplified open-source workflow to analyze drug resistance data. From this data, we identified drug resistance mutations in 20% of treatment naive individuals in our cohort, which is similar to frequencies identified using traditional genotyping in Brazilian patient samples. Conclusion: The developed ultra-wide sequencing approach described here allows multiplexing of at least 48 patient samples per sequencing run, 4 times more than the current genotyping method. This method is also 4-fold more sensitive (5% minimal detection frequency vs. 20%) at a cost 3-5 x less than the traditional Sanger-based genotyping method. Lastly, by using a benchtop next-generation sequencer (Roche/454 GS Junior), this approach can be more easily implemented in low-resource settings. This data provides proof-of-concept that next-generation HIV drug resistance genotyping is a feasible and low-cost alternative to current genotyping methods and may be particularly beneficial for in-country surveillance of transmitted drug resistance.

A palaeobiologist's guide to 'virtual' micro-CT preparation

This paper provides a brief but comprehensive guide to creating, preparing and dissecting a 'virtual' fossil, using a worked example to demonstrate some standard data processing techniques. Computed tomography (CT) is a 3D imaging modality for producing 'virtual' models of an object on a computer. In the last decade, CT technology has greatly improved, allowing bigger and denser objects to be scanned increasingly rapidly. The technique has now reached a stage where systems can facilitate large-scale, non-destructive comparative studies of extinct fossils and their living relatives. Consequently the main limiting factor in CT-based analyses is no longer scanning, but the hurdles of data processing (see disclaimer). The latter comprises the techniques required to convert a 3D CT volume (stack of digital slices) into a virtual image of the fossil that can be prepared (separated) from the matrix and 'dissected' into its anatomical parts. This technique can be applied to specimens or part of specimens embedded in the rock matrix that until now have been otherwise impossible to visualise. This paper presents a suggested workflow explaining the steps required, using as example a fossil tooth of Sphenacanthus hybodoides (Egerton), a shark from the Late Carboniferous of England. The original NHMUK copyrighted CT slice stack can be downloaded for practice of the described techniques, which include segmentation, rendering, movie animation, stereo-anaglyphy, data storage and dissemination. Fragile, rare specimens and type materials in university and museum collections can therefore be virtually processed for a variety of purposes, including virtual loans, website illustrations, publications and digital collections. Micro-CT and other 3D imaging techniques are increasingly utilized to facilitate data sharing among scientists and on education and outreach projects. Hence there is the potential to usher in a new era of global scientific collaboration and public communication using specimens in museum collections.