A Hybrid Test Optimization Framework - Coupling Genetic Algorithm with Local Search Technique

Quality of test cases is determined by their ability to uncover as many errors as possible in the software code. In our approach, we applied Hybrid Genetic Algorithm (HGA) for improving the quality of test cases. This improvement can be achieved by analyzing both mutation score and path coverage of each test case. Our approach selects effective test cases that have higher mutation score and path coverage from a near infinite number of test cases. Hence, the final test set size is reduced which in turn reduces the total time needed in testing activity. In our proposed framework, we included two improvement heuristics, namely RemoveTop and LocalBest, to achieve near global optimal solution. Finally, we compared the efficiency of the test cases generated by our approach against the existing test case optimization approaches such as Simple Genetic Algorithm (SGA) and Bacteriologic Algorithm (BA) and concluded that our approach generates better quality test cases

Survey on Mutation-based Test Data Generation

The critical activity of testing is the systematic selection of suitable test cases, which be able to reveal highly the faults. Therefore, mutation coverage is an effective criterion for generating test data. Since the test data generation process is very labor intensive, time-consuming and error-prone when done manually, the automation of this process is highly aspired. The researches about automatic test data generation contributed a set of tools, approaches, development and empirical results. In this paper, we will analyse and conduct a comprehensive survey on generating test data based on mutation. The paper also analyses the trends in this field

Test data generation for testing mapreduce systems

Orientador : Prof. Dr. Eduardo C. de AlmeidaDissertação (mestrado) - Universidade Federal do Paraná, Setor de Ciências Exatas, Programa de Pós-Graduação em Informática. Defesa: Curitiba, 14/11/2011Bibliografia: fls. 47-49Resumo: 1.1 Motivação. MapReduce [13] tornou-se o padrão de industrial para processamento paralelo de grandes conjuntos de dados. Grandes companhias e institutos de pesquisa utilizam esse framework para processarem seus dados. Como para qualquer outro software, teste pode ser utilizado para avaliar a qualidade de aplicações MapReduce, chamadas jobs. Porém, jobs MapReduce trabalham com grandes quantidades de dados, e gerar dados de teste relevantes que possam revelar problemas na qualidade desses jobs é uma grande dificuldade. Algumas ferramentas de teste para jobs MapReduce estão disponíveis [1, 2, 18]. Entretanto, nenhuma delas gera dados de teste. 1.2 Contribuíção. O trabalho apresentado aqui contribui para o estabelecimento de técnicas sistemáticas de teste para jobs MapReduce, atráves das seguintes propostas: modelos de falha que focam em problemas de design em separar uma tarefa entre funções Map e Reduce; uma técnica automática de busca para gerar dados de teste que objetivam essas falhas; uma série de experimentos que ilustram a dificuldade de detectar essas falhas e a capacidade da nossa solução em gerar dados de teste relevantes.Abstract: MapReduce is a framework for parallel processing large data sets, which is largely adopted for complex web applications and data processing. The framework proposes a simple interface, based on two high-order functions, allowing the rapid development of large-scale distributed software. Among the many aspects of MapReduce software development, producing reliable, correct and efficient software is an obvious target. We present an automatic test data generation and qualification approach for MapReduce applications, also called jobs. This approach uses an evolutionary algorithm to generate the test data and proposes domain-specific mutation operators to evaluate the quality of the data through mutation analysis. We validated this framework through implementation and experimentation on different MapReduce jobs

Extrapulmonary tuberculosis in Pakistan: Challenges in diagnosis and detection of drug resistance

Bakgrunn: Pakistan er blant de fem landene med høyest forekomst av tuberkulose (TB) og legemiddelresistent TB. Ekstrapulmonær TB (EPTB) utgjør 20% av alle registrerte TB-pasienter, men det er lite informasjon om sykdomsmanifestasjon, bakteriologiske diagnoser og forekomst av legemiddelresistens i EPTB. Mål: Det overordnede målet var å studere EPTB i Pakistan og evaluere nytten av konvensjonelle og nye diagnostiske verktøy for å diagnostisere og oppdage legemiddelresistens hos pasienter med EPTB. Hovedmålet med den første studien var å beskrive sykdomstegnene blant pasienter med EPTB. Målet med den andre studien var å vurdere den diagnostiske ytelsen av en rask molekylær analyse, Xpert MTB/RIF (Xpert), og histologisk undersøkelse for tuberkuløs lymfadenitt. Målet med den tredje studien var å studere forekomsten av rifampicin og annen legemiddelresistens mot TB hos nye pasienter med EPTB, og den fjerde studien hadde som mål å vurdere forekomsten og den genetiske profilen til isoniazidresistens samt tilhørende resistens mot fluorokinolon og pyrazinamid. Materiale og metoder: I studie 1 ble det utført deskriptiv analyse av en retrospektiv kohort av TB-pasienter registrert nasjonalt i 2016. Studie 2 og 3 ble utført på en prospektiv kohort av pasienter med antatt EPTB ved et tertiært sykehus. I studie 2 ble personer som ikke hadde fått TB-behandling og hadde forstørrede lymfeknuter inkludert, og vevsprøver fra eksisjonsbiopsier ble undersøkt med histologi, Xpert og dyrkning. I studie 3 ble pasienter med pleural effusjon i tillegg til personene i studie 2 med forstørrede lymfeknuter, inkludert. Pleuravæske ble undersøkt for syrefastestaver (AFB)-mikroskopi, Xpert MTB/RIF og dyrkning. Fenotypisk legemiddelsusceptibilitetstesting (DST) ble utført ved bruk av automatisert flytende DST (MGIT 960), og genotypisk DST ble utført ved hjelp av line-probe-undersøkelser (LPA). I studie 4 ble et fem års retrospektiv DST-datasett analysert for pasienter som ble testet ved det nasjonale TB-referanselaboratoriet ved hjelp av både fenotypiske og genotypiske DST-metoder. Resultater: I studie 1 ble individuelle pasientdata samlet inn fra 54 092 registrerte TB-tilfeller i 2016. Blant disse hadde 15 790 pasienter EPTB. De tre vanligste formene for EPTB var pleural (29,6 %), lymfatisk (22,7%) og abdominal TB (21,0%). Pleural TB var den vanligste blant voksne (34,2%), mens abdominal TB var mest utbredt blant barn (38,4%). Sannsynligheten for å ha EPTB var 1,1 ganger høyere for kvinner, 2,0 ganger høyere for barn og 3,3 ganger høyere for innbyggere i provinsene nordvest i landet. Behandlingssuksessraten for alle typer EPTB som var inkludert i studien, var høy, bortsett fra for TB-meningitt. I studie 2 ble ytelsen til diagnostiske verktøy analysert i en kohort på 390 pasienter med forstørrede lymfeknuter. Blant disse var 11 (2,8%) positive ved AFB-mikroskopi, 124 (31,8%) ved Xpert, 137 (35,1%) ved dyrkning, og histopatologi viste TB hos 208 (53,3%). Ved bruk av kombinerte resultater ble lymfeknutetuberkulose diagnostisert hos 228 pasienter, hvorav 78% ble bekreftet ved bakteriologiske tester. Sammenlignet med Xpert hadde histopatologi høyere sensitivitet (93% mot 62%), men lavere spesifisitet (68% mot 83%), og i undergruppeanalyser var sensitiviteten til Xpert høyere hos pasienter med kort klinisk historie. I studie 3 ble bakteriologisk diagnose og forekomst av legemiddelresistens analysert hos 671 studiepersoner. TB ble bekreftet bakteriologisk hos 255, og DST-resultater var tilgjengelige for 72,5% (n = 185) av pasientene med EPTB. Multidrug resistant -TB ble rapportert hos 2,2% (95% CI, 0,6–5,4), resistens mot rifampicin hos 2,7% (95% CI, 0,9–6,2), isoniazid hos 7,6% (95% CI, 4,1–12,4), ethambutol hos 1,1% (95% CI, 0,1–3,9), pyrazinamid hos 2,2% (95% CI, 0,9–5,5) og fluorokinoloner hos 6,0% (95% CI, 3,0–10,4). Sensitiviteten og spesifisiteten til LPA-DST var henholdsvis 100% og 98,8% for rifampicin, isoniazid og fluorokinolon. DST-resultater for rifampicin var tilgjengelige for 82 pasienter ved alle tre metoder og av disse ble fem rapportert som rifampicinresistente ved Xpert, men bare én ble bekreftet ved LPA, og ingen ble bekreftet ved fenotypisk DST. I studie 4 ble et retrospektivt DST-datasett med 11 045 TB-pasienter analysert. Både fenotypiske og genotypiske DST-resultater var tilgjengelige for 80 % av tilfellene. Det ble rapportert en betydelig forskjell mellom resistens som ble påvist ved fenotypisk og genotypisk DST-metoder, med en uoverensstemmelse på 16% for rifampicin og isoniazid. Blant nye EPTB-pasienter med rifampicinsensitivitet ble isoniazidresistens påvist hos 6,8%, sammenlignet med 9,8% hos pasienter med PTB. Den genetiske profilen for isoniazidresistens var lik for PTB og EPTB, men forskjellen var statistisk signifikant mellom rifampicinresistente og rifampicinsensitive populasjoner når det gjaldt påviste mutasjoner knyttet til isoniazidresistens, med 87% mot 71,6% og forekomsten av katG-mutasjoner på 76,1% mot 41,2% og inhA-mutasjoner på 7,6% mot 30,2%, henholdsvis. Det ble observert en signifikant høyere forekomst av levofloxacinresistens i forbindelse med isoniazidresistens. Konklusjoner: Pleural- og lymfatisk TB utgjorde til sammen 50% av alle registrerte tilfeller av EPTB. TB ble diagnostisert ved kun hjelp av Xpert i 54% av tilfellene, mens kombinasjonen av Xpert og histopatologi bekreftet diagnosen i over 95% av alle tilfeller med TB i lymfeknuter. Forekomsten av rifampicin- og isoniazidresistens var lavere blant nye EPTB-pasienter sammenlignet med PTB, men forskjellen var ikke statistisk signifikant. Den genetiske profilen for isoniazidresistens og tilhørende resistens mot fluorokinolon og pyrazinamid var sammenlignbar mellom EPTB og PTB.Background: Pakistan is among the top five high-burden countries for tuberculosis (TB) and drug-resistant TB. Extrapulmonary TB (EPTB) accounts for 20% of all notified TB patients but there is little information on disease manifestations, bacteriological diagnoses, and prevalence of anti-TB drug resistance in EPTB. Objective: The overall objective was to study EPTB in Pakistan, and evaluate the usefulness of conventional and new diagnostic tools in diagnosing and detecting drug resistance in EPTB patients. The first study primarily aimed to describe the disease manifestations among EPTB patients notified in Pakistan. The second study aimed to assess the performance of a rapid molecular assay, Xpert MTB/RIF (Xpert), and histological examination in the diagnoses of tuberculous lymphadenitis. The third study aimed to determine the prevalence of rifampicin and other anti-TB drug resistance in new EPTB patients and the fourth study aimed to assess the prevalence and genetic profile of isoniazid resistance and associated resistance to fluoroquinolone and pyrazinamide. Material and Methods: In study-1, descriptive analysis was performed on a retrospective cohort of TB patients notified nationwide in 2016. Studies 2 and 3 were performed on a prospective cohort of patients presumed to have EPTB in a tertiary care hospital. In study-2, TB treatment naïve people with enlarged lymph nodes were included and excision biopsy specimens were tested by histology, Xpert, and culture. In study-3, patients with pleural effusion in addition to people in study-2 with enlarged lymph nodes were included. Pleural fluid sediments were tested for smear, Xpert MTB/RIF, and culture. Phenotypic drug susceptibility testing (DST) was performed using automated liquid DST (MGIT 960) and genotypic DST by line-probe assays (LPA). For study-4, a five-year retrospective DST data set was analyzed of TB patients tested in the National TB reference laboratory by phenotypic and/or genotypic DST methods. Results: In study-1, individual patient data was collected of 54092 TB cases notified in 2016. Among 15790 EPTB patients included, the three most common forms of EPTB were pleural (29.6%), lymphatic (22.7%), and abdominal TB (21.0%). Pleural TB was the most common among adults (34.2%) and abdominal TB in children (38.4%). The likelihood of having EPTB, was 1.1 times high for females, 2.0 times for children, and 3.3 times for residents of provinces in the Northwest. The treatment success rate for all types of EPTB included in the study was high except for TB meningitis. In study-2, the performance of diagnostic tools in a cohort of 390 patients with enlarged lymph nodes was analyzed and among these 11 (2.8%) were positive by AFB microscopy, 124 (31.8%) by Xpert, 137 (35.1%) by culture, and histopathology was consistent with TB in 208 (53.3%). Using composite results, lymph node TB was diagnosed in 228 of which 78% were bacteriologically confirmed. Histopathology compared to Xpert had higher sensitivity (93 vs. 62%) but lower specificity (68 vs.83%) and in sub-group analysis, the sensitivity of Xpert was higher in patients with short clinical history. In study-3, bacteriological diagnosis and prevalence of drug resistance was analyzed in 671 study participants. Bacteriologically confirmed TB was diagnosed in 255 and DST results were available for 72.5% (n=185) of EPTB patients. MDR-TB was reported in 2.2% (95% CI, 0.6–5.4)., resistance to rifampicin in 2.7% (95% CI, 0.9–6.2), isoniazid in 7.6% (95% CI, 4.1–12.4), ethambutol in 1.1% (95% CI, 0.1–3.9), pyrazinamide in 2.2% (95%CI, 0.9–5.5) and fluoroquinolones in 6.0% (95% CI, 3.0–10.4). The sensitivity and specificity of LPA-DST was 100% and 98.8% respectively for rifampicin, isoniazid, and fluoroquinolone. Rifampicin results were available by all three methods for 82 patients and of these five were reported rifampicin resistant by Xpert and only one was confirmed by LPA and none by phenotypic DST. In study-4, a retrospective DST data set of 11045 TB patients was analyzed. Both phenotypic and genotypic DST results were available for 80% of cases. A significant difference was reported between resistance detected by phenotypic and genotypic DST methods with 16% discordance in rifampicin and isoniazid. Among rifampicin-sensitive new EPTB, isoniazid resistance was 6.8% compared to 9.8% in PTB. The genetic profile of isoniazid resistance was similar in PTB and EPTB but the difference was statistically significant between rifampicin-resistant and sensitive populations for isoniazid-resistant conferring mutations detected in 87% vs 71.6%, the prevalence of katG mutations in 76.1% vs 41.2% and inhA in 7.6% vs 30.2% respectively. A significantly higher levofloxacin resistance was seen associated with isoniazid resistance. Conclusions: Pleural and lymphatic TB collectively comprised 50% of all notified EPTB cases. TB was diagnosed by Xpert alone in 54%, while in combination with histopathology in more than 95% of all TB lymph node cases. Rifampicin and isoniazid resistance was lower in the new EPTB compared to PTB; the difference was not statistically significant. The genetic profile of isoniazid resistance and associated fluoroquinolone and pyrazinamide resistance in EPTB was comparable with PTB.Doktorgradsavhandlin

Metamodel Instance Generation: A systematic literature review

Modelling and thus metamodelling have become increasingly important in Software Engineering through the use of Model Driven Engineering. In this paper we present a systematic literature review of instance generation techniques for metamodels, i.e. the process of automatically generating models from a given metamodel. We start by presenting a set of research questions that our review is intended to answer. We then identify the main topics that are related to metamodel instance generation techniques, and use these to initiate our literature search. This search resulted in the identification of 34 key papers in the area, and each of these is reviewed here and discussed in detail. The outcome is that we are able to identify a knowledge gap in this field, and we offer suggestions as to some potential directions for future research.Comment: 25 page

Dominant Role of Nucleotide Substitution in the Diversification of Serotype 3 Pneumococci over Decades and during a Single Infection

Streptococcus pneumoniae of serotype 3 possess a mucoid capsule and cause disease associated with high mortality rates relative to other pneumococci. Phylogenetic analysis of a complete reference genome and 81 draft sequences from clonal complex 180, the predominant serotype 3 clone in much of the world, found most sampled isolates belonged to a clade affected by few diversifying recombinations. However, other isolates indicate significant genetic variation has accumulated over the clonal complex’s entire history. Two closely related genomes, one from the blood and another from the cerebrospinal fluid, were obtained from a patient with meningitis. The pair differed in their behaviour in a mouse model of disease and in their susceptibility to antimicrobials, with at least some of these changes attributable to a mutation that upregulated the patAB efflux pump. This indicates clinically important phenotypic variation can accumulate rapidly through small alterations to the genotype

An empirical investigation into branch coverage for C programs using CUTE and AUSTIN

Automated test data generation has remained a topic of considerable interest for several decades because it lies at the heart of attempts to automate the process of Software Testing. This paper reports the results of an empirical study using the dynamic symbolic-execution tool. CUTE, and a search based tool, AUSTIN on five non-trivial open source applications. The aim is to provide practitioners with an assessment of what can be achieved by existing techniques with little or no specialist knowledge and to provide researchers with baseline data against which to measure subsequent work. To achieve this, each tool is applied 'as is', with neither additional tuning nor supporting harnesses and with no adjustments applied to the subject programs under test. The mere fact that these tools can be applied 'out of the box' in this manner reflects the growing maturity of Automated test data generation. However, as might be expected, the study reveals opportunities for improvement and suggests ways to hybridize these two approaches that have hitherto been developed entirely independently. (C) 2010 Elsevier Inc. All rights reserved

Salmonella infection in healthy pet reptiles: Bacteriological isolation and study of some pathogenic characters

The fecal samples from 213 captive reptiles were examined, and 29 (13.61%) Salmonella enterica isolates were detected: 14/62 (22.58%) from chelonians, 14/135 (10.37%) from saurians, and 1/16 (6.25%) from ophidians. The isolates were distributed among 14 different serotypes: Miami, Ebrie, Hermannsweder, Tiergarten, Tornov, Pomona, Poona, Goteborg, Abaetetube, Nyanza, Kumasi, Typhimurium, 50:b:z6, 9,12:z29:1,5, and a non-motile serotype with antigenic formula 1,4,[5],12:-:-. Salmonella typhimurium and 50:b:z6 isolates showed the spv plasmid virulence genes, responsible of the capability to induce extra-intestinal infections. In some cases, pulsed field gel electrophoresis revealed different profiles for the strains of the same serotypes, showing different origins, whereas a common source of infection was supposed when one pulsotype had been observed for isolates of a serovar. Twenty-seven (93.10%) isolates showed resistance to one or more antibiotics. Ceftazidime was active to all the tested isolates, whereas the highest percentages of strains were no susceptible to tigecycline (93.10%), streptomycin (89.66%), and sulfonamide (86.21%)