Denna rapport beskriver ett projekt vars syfte är att underlätta valet av bakteri- estammar till testpaneler som används av Q-lineas instrument ASTar®. ASTar® är ett automatiserat instrument för snabb antibiotikasensitivitetstestning (AST). Med testpanel menas en uppsättning av bakteriestammar som används för träning av den algoritm som används av ASTar®. De huvudsakliga målen med detta projekt är att ta fram indikatorer som kan användas för att utvärdera en testpanel samt att skapa verktyg för visualisering av en testpanel. Indikatorerna återspeglar en pa- nels spridning, täckning och redundans. Spridning är hur många olika MIC-värden en testpanel innefattar för varje antibiotikum och hur utspridda de är, täckning är antalet MIC-värden som varje antibiotikum har i en testpanel och redundans är kopplat till hur unikt varje MIC-värde på panelen är. Med MIC-värden menas den minsta koncentration av antibiotika som hämmar en bakteries tillväxt. I detta projekt har indikatorer tagits fram för att kunna kvantifiera en panels spridning, täckning och redundans, och enkelt kunna jämföra olika testpaneler utifrån dessa aspekter. Ett skript compare.py har skrivits i programmeringsspråket Python för att skapa en visualisering som jämför de kvantitativa indikatorvärdena för olika paneler i relation till de högsta möjliga värdena. Ytterligare ett skript, master_vis.py har skrivits för att generera olika visualiseringar av en panel och dess täckning, sprid- ning och redundans. Sex olika grafer och två tabeller kan genereras med detta skript. Dessa visualiseringar och tabeller visar bland annat hur utspridda MIC-värdena är på en panel, hur många känsliga, intermediära och resistenta MIC-värden som finns för varje antibiotikum på en panel och hur många unika MIC-värden som finns för varje stam på panelen. Slutligen har även ett tredje skript skrivits, kallat isola- te_selection.py. Detta skript utgår från de framtagna kvantitativa indikatorerna för att välja ett specificerat antal stammar till en panel och utvecklades för att under- söka hur indikatorerna skulle kunna användas för att påverka stamvalet. Möjligen skulle en liknande implementering kunna göras i Q-lineas nuvarande stamvalsskript. Samtliga skript, visualiseringar och beräkningsmetoder som har arbetats fram i det- ta projekt är tänkta att kunna användas av Q-linea för att underlätta deras fram- tagning och utvärdering av testpaneler.

No description available.

No description available.

No description available.

No description available.

No description available.

Objectives: Systemic antibiotics are generally recognized as providing a beneficial impact in treatment of both aggressive and chronic periodontitis. Since strains of periodontal pathogens among periodontitis patients may vary in their antibiotic drug resistance, the American Academy of Periodontology recommends antimicrobial susceptibility testing of suspected periodontal pathogens prior to administration of systemic periodontal antibiotic therapy, to reduce the risk of a treatment failure due to pathogen antibiotic resistance. E-test and MIC Test Strip assays are two in vitro antimicrobial susceptibility testing systems employing plastic- and paper-based, respectively, carriers loaded with predefined antibiotic gradients covering 15 two-fold dilutions. To date, no performance evaluations have been carried out comparing the Etest and MIC Test Strip assays in their ability to assess the in vitro antimicrobial susceptibility of periodontal bacterial pathogens. As a result, the purpose of this study was to compare the in vitro performance of E-test and MIC Test Strip assays in assessing minimal inhibitory concentration (MIC) values of four antibiotics frequently utilized in systemic periodontal antibiotic therapy against 11 fresh clinical subgingival isolates of the putative periodontal pathogen, Prevotella intermedia/ nigrescens, and to compare the distribution of P. intermedia/ nigrescens strains identified with interpretative criteria as "susceptible" and "resistant" to each of the four antibiotics using MIC values determined by the two antimicrobial susceptibility testing methods. Methods: Standardized cell suspensions, equivalent to a 2.0 McFarland turbidity standard, were prepared with 11 fresh clinical isolates of P. intermedia/nigrescens, each recovered from the subgingival microbiota of United States chronic periodontitis subjects, and plated onto to the surfaces of culture plates containing enriched Brucella blood agar. After drying, pairs of antibiotic-impregnated, quantitative, gradient diffusion strips from two manufacturers (E-test, bioMérieux, Durham, NC, USA, and MIC Test Strip, Liofilchem s.r.l., Roseto degli Abruzzi, Italy) for amoxicillin, clindamycin, metronidazole, and doxycycline were each placed apart from each other onto the inoculated enriched Brucella blood agar surfaces, so that an antibiotic test strip from each manufacturer was employed per plate against each P. intermedia/ nigrescens clinical isolate for antibiotic susceptibility testing. After 48-72 hours anaerobic jar incubation, individual MIC values for each antibiotic test strip against P. intermedia/nigrescens were read in μg/ml at the point where the edge of the bacterial inhibition ellipse intersected with the antibiotic test strip. MIC50, MIC90, and MIC range were calculated and compared for each of the test antibiotics, with essential agreement (EA) values determined per test antibiotic for the level of outcome agreement between two antimicrobial susceptibility testing methods. In addition, the identification of antibiotic "susceptible" and "resistant" strains among the P. intermedia/nigrescens clinical isolates was determined for each test antibiotic using MIC interpretative criteria from the MIC interpretative standards developed by the European Committee on Antimicrobial Susceptibility Testing (EUCAST) for gram-negative anaerobic bacteria for amoxicillin, clindamycin, and metronidazole findings, and from the French Society of Microbiology breakpoint values for anaerobic disk diffusion testing for doxycycline data. Results: For amoxicillin, higher MIC50 and MIC90 values against the P. intermedia/ nigrescens strains were found with the MIC Test Strip assay than with E-test strips, resulting in a relatively low EA value of 45.5% between the two susceptibility testing methods. A higher percentage of amoxicillin "resistant" P. intermedia/nigrescens strains (72.7%) were identified by MIC Test Strips as compared to E-test strips (54.5%), although both methods found the same proportion of amoxicillin "susceptible" strains (27.3%). For clindamycin, both susceptibility testing methods provided identical MIC values (EA value = 100%), and exactly the same distributions of "susceptible" and "resistant" strains of P. intermedia/nigrescens. For metronidazole, only very poor agreement (EA value = 9.1%) was found between the two susceptibility testing methods, with MIC Test Strips exhibiting markedly higher MIC50 and MIC90 values against P. intermedia/nigrescens as compared to E-test strips. However, the distribution of "susceptible" and "resistant" P. intermedia/ nigrescens were identical between the two susceptibility testing methods. For doxycycline, relatively good agreement (EA value = 72.7%) was found in MIC concentrations between the two susceptibility testing methods, although generally lower MIC values were associated with MIC Test Strips. In addition, identical distributions of "susceptible" and "resistant" P. intermedia/nigrescens were provided by both susceptibility testing methods. Conclusions: Relative to MIC values measured against periodontal strains of P. intermedia/nigrescens, MIC Test Strips gave higher MIC values with amoxicillin and metronidazole, equal MIC values with clindamycin, and lower MIC values with doxycycline, as compared to MIC values measured with the E-test assay. Relative to the identification of antibiotic "susceptible" periodontal P. intermedia/ nigrescens strains, both susceptibility testing methods provided identical findings, suggesting that both methods appear to be interchangeable for clinical decision making in regard to identification of antibiotic-sensitive strains of periodontal P. intermedia/nigrescens. However, for epidemiologic surveillance of drug susceptibility trends, where exact MIC values are important to track over time, the relatively higher proportion of non-exact MIC differences between the two susceptibility testing methods argues against using them interchangeably. Instead, one or the other method should be used consistently for such studies. Further comparative studies of the E-test and MIC Test Strip assays are indicated using other periodontopathic bacterial species besides P. intermedia/ nigrescens, and to assess the reproducibility of MIC values provided by both in vitro susceptibility testing methods over time. / Oral Biology

An effective tool used by planners and policy makers in public health, such as Center for Disease Control (CDC), to curtail spread of infectious diseases over a given population is contagion diffusion simulations. These simulations model the relevant characteristics of the population (age, gender, income etc.) and the disease (attack rate, etc.) and compute the spread under various configuration and plausible intervention strategies (such as vaccinations, school closure, etc.). Hence, the model and the computation form a complex agent based system and are highly compute and resource intensive. In this work, we design a benchmark consisting of several kernels which capture the essential compute, communication, and data access patterns for such applications. For each kernel, the benchmark provides different evaluation strategies. The goal is to (a) derive alternative implementations for computing the contagion by combining different implementation of the kernels, and (b) evaluate which combination of implementation, runtime, and hardware is most effective in running large scale contagion diffusion simulations. Our proposed benchmark is designed using C++ generic programming primitives and lifting sequential strategies for parallel computations. Together, these lead to a succinct description of the benchmark and significant code reuse when deriving strategies for new hardware. For the benchmark to be effective, this aspect is crucial, because the potential combination of hardware and runtime are growing rapidly thereby making infeasible to write optimized strategy for the complete contagion diffusion from ground up for each compute system. / Master of Science

Fossils recovered from limestones of the lower Cambrian (Stage 2-3) Yanjiahe Formation in Hubei Province, South China, recovered using acetic acid maceration, fracturing, and thin sectioning techniques were examined using a combination of analytical techniques, including energy dispersive spectroscopic (EDS) elemental mapping and micro-focus X-ray computed tomography (micro-CT). One important fossil recovered and analyzed with these techniques is a fossilized embryo. Fossilized animal embryos from lower Cambrian rocks provide a rare opportunity to study the ontogeny and developmental biology of early animals during the Cambrian explosion. The fossil embryos in this study exhibit a phosphatized outer envelope (interpreted as the chorion) that encloses a multicelled blastula-like embryo or a calcitized embryo marked by sets of grooves on its surface. The arrangement of these grooves resembles annulations found on the surface of the Cambrian-Ordovician fossil embryo Markuelia. Previously described late-stage Markuelia embryos exhibit annulations and an introvert ornamented by scalids, suggesting a scalidophoran affinity. In the Yanjiahe fossils illustrated herein, however, the phosphatized chorions and blastulas are not taxonomically or phylogenetically diagnostic, and the late-stage embryo is secondarily calcitized and thus poorly preserved, with only vague grooves indicative of Markuelia-type annulations. Consequently, their taxonomic assignment to the genus Markuelia is uncertain. If they indeed belong to the genus Markuelia, they are the oldest known Markuelia fossils from China, and represent both a new occurrence and possibly a new species. / Master of Science

O potencial farmacológico de espécies do gênero Lippia no tratamento de infecções é conhecido popularmente, assim foi considerado o estudo da atividade da Lippia salviaefolia nativa do cerrado brasileiro. O objetivo do trabalho foi avaliar a atividade antimicrobiana de extratos de Lippia salviaefolia Cham. e sua citotoxicidade, visando aplicação como conservante natural em formulações cosméticas. O ensaio antimicrobiano foi realizado através do método de difusão em placa e determinação do CMI por de microdiluição em microplacas, utilizando os microrganismos: P. aeruginosa ATCC 9027, S. aureus ATCC 6538, E. coli ATCC 8739, C. albicans ATCC 10231. Desenvolveu-se e avaliou-se a estabilidade acelerada de cremes, geis e xampus contendo o extrato de Lippia salviaefolia. As formulações de melhor desempenho quanto à estabilidade foram submetidas ao teste de eficácia de conservante. Avaliou-se segurança das formulações in vitro, em substituto cutâneo dermo-epidérmico por meio de estudos histológicos e o teste de citotoxicidade em cultura de queratinócitos humanos. No teste de atividade antimicrobiana verificou-se que a fração de acetato de etila e a fração de clorofórmio foram frações mais ativas com CMI de 0,2 % para bactérias e fungos. Os testes de eficácia de conservante das formulações contendo fr. ac. etila de L. salviaefolia apresentaram atividade antimicrobiana para bactérias e C. albicans em creme, gel e xampu, para A. niger apresentaram atividade adequada somente em xampu. No teste de citoxicidade foi verificado segurança em concentrações a partir de 0,05 %. Sendo que na concentração de 0,2 %, correspondente ao CMI, se atinge a faixa de segurança apenas com meia hora de contato. Os resultados sugerem que a fração de acetato de etila da Lippia salviaefolia Cham. pode ser utilizada como conservante natural em produtos cosméticos. / The pharmacological potential of species of the Lippia in the treatment of infections has been known popularly, thus was considered the study of the activity of the native salviaefolia Lippia of the Brazilian Cerrado. The purpose of the work was to evaluate the antimicrobial activity of extracts of Lippia salviaefolia Cham. and its citotoxicy aiming the application as natural preservative in cosmetic formulations. The assay antimicrobial was carried through the method of diffusion in plate and determination of the MIC by microdilution, having used the microorganisms: P.aeruginosa ATCC 9027, S. aureus ATCC 6538, E. coli ATCC 8739, C. albicans ATCC 10231. It has developed and evaluated the stability of creams, gels and xampus with the extract of Lippia salviaefolia Cham. The formulations of the best stability performance have submitted to preservative efficacy test. The safe of the formulations has histological evaluated by in vitro. In the test of antimicrobial activity it has verified that the ethyl acetate and the chloroform fraction have been the most active and with CMI of 0.2 % for bacteria and fungus. The tests of effectiveness of preservatives have showed of the formulations contend the ethyl acetate fraction presented antimicrobial activity for bacteria and C. albican in cream, gel and shampoo. On the other hand, against A.niger it has been suitable activity in shampoo. In the citotoxity test, the 0,05 % ethyl acetate fraction has presented interval of security. And in the concentration of 0,2%, corresponding to CMI, safety\'s strip is just reached with half hour of contact. The results have suggested that the ethyl acetate extract of the Lippia salviaefolia Cham. should be used as natural preservative in cosmetic products.