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Aerosols show type-specific characteristics, which depend on intensive aerosol optical and microphysical properties that influence the radiation processes in the atmosphere in several ways. There are still large uncertainties in the calculation of the aerosol direct radiative effect. The classification of aerosols and the characterization of the vertical aerosol distribution is needed in order to provide more accurate information for radiative-transfer simulations. In the framework of the present thesis, the vertical and spatial distribution as well as optical properties of atmospheric aerosols over the European continent were investigated based on lidar measurements. Possibilities for an aerosol classification or so-called aerosol typing were presented and major aerosol types were specified. Former studies about the classification of aerosols were summarized and representative values for aerosol-type-dependent parameters were given. Case studies were used to demonstrate how observations of the European lidar network EARLINET from 2008 until 2010 were analyzed for aerosol layers and how model simulations and auxiliary data including the assessment of meteorological conditions were applied to determine the origin of each single aerosol layer. Thus, aerosol-type dependent parameters were evaluated and a novel method for the typing of aerosols was developed, which can be used, e.g., within algorithms of satellite data retrievals. Additionally, conversion factors were determined, which are needed for the harmonization of satellite data of present and upcoming missions. Furthermore, findings of the aerosol typing based on EARLINET data were compared to results of the aerosol classification scheme for satellite-borne lidar measurements onboard CALIPSO. It could be shown that deficient classifications of the aerosol type emerged systematically within the automated CALIPSO algorithm. Those wrong classification leads to an underestimation of the single-scattering albedo and hence to an overestimation of the warming effect of the respective aerosol layer. This overestimated warming effect has to be kept in mind for simulations of the global aerosol radiative effect based on CALIPSO data. / Die Bestimmung des direkten Strahlungsantriebs von Aerosolen ist mit großen Unsicherheiten behaftet. Inwiefern Aerosole die Strahlungsprozesse in der Atmosphäre beeinflussen ist abhängig von ihren optischen und mikrophysikalischen Eigenschaften. Zur Optimierung von Strahlungstransfersimulationen werden daher ergänzende Informationen über typspezifische Aerosoleigenschaften sowie die vertikale Aerosolverteilung benötigt. Im Rahmen der vorliegenden Arbeit wurden anhand von Lidarmessungen die vertikale und räumliche Verteilung atmosphärischer Aerosole über Europa analysiert sowie deren optische Eigenschaften ermittelt. Einleitend werden Möglichkeiten der Aerosolklassifizierung erläutert und Aerosoltypen spezifiziert, die über Europa beobachtet werden können. Vorherige Studien zur Aerosolklassifizierung sind in einer Literaturübersicht zusammengefasst. Anhand von Fallstudien wurde zunächst die Analyse von Beobachtungen des europäischen Lidarnetzwerkes EARLINET von 2008 bis 2010 auf das Vorhandensein von Aerosolschichten verdeutlicht. Die Herkunft jeder einzelnen Aerosolschicht wurde anschließend unter Verwendung von Modellrechnungen sowie weiteren Informationen bestimmt und aerosoltypspezifische Kenngrößen berechnet. Mit Hilfe dieser Kenngrößen ist es möglich, den Typ des Aerosols abzuleiten. Daraus wurde eine neuartige Methode zur Typisierung von Aerosolen entwickelt, die z.B. in Algorithmen zur Verarbeitung von Satellitendaten verwendet werden kann. Zusätzlich wurden Umrechnungsfaktoren bestimmt, die zur Zusammenführung und zum Vergleich von Daten aktueller und zukünftiger Satellitenmissionen benötigt werden. Die Ergebnisse der Aerosoltypisierung auf Basis von EARLINET-Daten wurden anschließend mit Ergebnissen der automatischen Typisierung weltraumbasierter Lidarmessungen des CALIPSO-Satelliten verglichen. Es konnte gezeigt werden, dass innerhalb des CALIPSO-Algorithmus systematisch fehlerhafte Klassifizierungen des Aerosoltyps auftreten. Diese falsche Klassifizierung führt zu einer Unterschätzung der Einfachstreualbedo und zu einer Überschätzung der erwärmenden Wirkung der betreffenden Aerosolschicht. Die überschätzte Wärmewirkung hat wiederum fehlerhafte Ergebnisse bei Strahlungstransferrechnungen, die auf CALIPSO-Daten basieren, zur Folge.

Thesis (MScMedSc (Pathology. Medical Microbiology))--University of Stellenbosch, 2010. / ENGLISH ABSTRACT: S. aureus causes serious infections in the hospital and community settings. The rate of MRSA infections are rapidly increasing worldwide. Currently, at Tygerberg hospital, approximately a third of S. aureus isolates are MRSA. This was the first epidemiological study of S. aureus conducted at Tygerberg Hospital that included prospective clinical data on patients with S. aureus bacteraemia together with spa typing of strains and the detection of the mecA and pvl genes in a multiplex PCR. Clonal cluster groups of S. aureus isolates were obtained by BURP analysis and compared to international important clones. The molecular epidemiology of hospital acquired (HA), health-care associated (HCA) and community acquired (CA) S. aureus bacteraemic strains at this hospital was examined. Lastly, repeat isolates of patients were collected to analyse any possible organism-related factors associated with persistent and recurrent bacteraemia. We investigated a total number of 113 S. aureus strains from 104 patients (70% MSSA, 30% MRSA). Repeat strains consisted of nine isolates (from 5 patients). All isolates were obtained from blood cultures collected during the period March 2008 to May 2009. Phenotypic and genotypic detection of methicillin resistance correlated well. According to the literature, most CA-MRSA strains are distinguishable from HA-MRSA strains based upon the presence of the PVL toxin. However, no CA-MRSA was detected in our study, therefore the association between HA-MRSA versus CA-MRSA strains could not be analysed. In this study, CA-MSSA was identified in 22% of all MSSA isolates versus 0% CA-MRSA. PVL positive strains were found in 22.7% of all MSSA isolates with no detection in MRSA isolates. It was noted that MRSA strains clustered in spa CC-701 and CC-012, whereas CC-002 only contained MSSA strains. Likewise HA-strains representing the majority of MRSA strains also clustered in spa CC-701 and CC-012. Forty nine spa types were identified in 89.3% of all isolates, whereas 9.7% of these strains were non-typeable. Five novel spa types were revealed. We detected a diverse number of spa-types that correlated to international clones. The most predominant spa type found in our setting was t037 (only in MRSA), followed by t891. According to the literature, t037 is associated to the Brazilian/Hungarian clone (SCCmec type III; ST 239). Our findings, as well as other South African studies, indicate that t037 has been identified in clinical strains from numerous provinces in South Africa. Interestingly, all isolates from spa type t891 were PVL positive MSSA. Bacteraemia cases were predominantly related to catheter sepsis, followed by skin and soft tissue infections (SSTI). Only one persistent bacteraemia case was identified related to a HA-SSTI. Recurrent bacteraemia cases were found in patients on dialysis for chronic renal failure and in burns patients related to intravascular catheter infections. The local epidemiology of S. aureus and the prevalence rate of different strains are important to investigate. The information provided contributes to the epidemiology of staphylococcal strains causing bacteraemia in our setting. These insights are useful for optimal diagnostic and therapeutic measures. The techniques developed can be used to identify outbreaks and recurrent infections. / AFRIKAANSE OPSOMMING: S. aureus veroorsaak ernstige infeksies in die hospitaalomgewing en in die gemeenskap. Wêreldwyd, neem metisillien-weerstandige S. aureus (MRSA) infeksies vinnig toe. Huidiglik by Tygerberg hospitaal is ongeveer ‘n derde van S. aureus isolate MRSA. Hierdie is die eerste epidemiologiese studie by Tygerberg hospitaal wat prospektiewe kliniese data van pasiënte met S. aureus bakteremie saam met spa tipering en aantoning van die mecA en pvl gene in ‘n multipleks PKR insluit. Klonale groepe (spa-CC) van MRSA en MSSA isolate is deur BURP analise verkry, en vergelyk met internasionaal belangrike klone. Die molekulêre epidemiologie van hospitaalverworwe (HA), gesondheidsorgverworwe (HCA) en gemeenskapsverworwe (CA) S. aureus bakteremie by hierdie hospitaal is ondersoek. Laastens, oorspronklike en daaropvolgende herhaal isolate is gekollekteer om moontlike organisme- faktore geassosieerd met persisterende en herhalende bakteremiese episodes te analiseer. Ons het in totaal 113 S. aureus isolate van 104 pasiënte ondersoek (70% MSSA, 30% MRSA). Nege isolate (van 5 pasiënte) was herhaal isolate. Alle isolate was afkomstig vanaf bloedkulture wat gedurende die periode Maart 2008 tot Mei 2009 gekollekteer is. Fenotipiese en genotipiese aantoning van metisillien weerstandigheid het goed gekorreleer. Volgens die literatuur kan die meeste CA-MRSA isolate van HA-MRSA isolate onderskei word op grond van die teenwoordigheid van die PVL toksien. Geen CA-MRSA is egter in ons studie gevind nie, dus kon die assosiasie tussen HA-MRSA en CA-MRSA isolate nie ondersoek word nie. CA-MSSA was in 22% van alle MSSA geidentifiseer teenoor 0% CA-MRSA. PVL is in MSSA isolate gevind (22.7% van alle MSSA) maar glad nie in MRSA nie. Dit is opgemerk dat MRSA isolate hoofsaaklik in spa CC 701 en CC-012 kloongroepe voorkom, teenoor kloongroep CC-002 wat slegs MSSA isolate bevat het. Soortgelyk het HA-isolate wat die meerderheid van MRSA isolate verteenwoordig het ook in kloongroepe 1 & 2 gegroepeer. Nege-en-veertig spa tipes is geïdentifiseer in 89.3% of alle isolate en 9.7% was nie-tipeerbaar. Vyf nuwe spa tipes is getoon. Ons het ‘n diverse aantal spa-tipes geïdentifiseer wat met internasionale klone gekorreleer het. Die mees dominante spa tipe in ons omgewing was t037 (slegs in MRSA), gevolg deur t891. Volgens die literatuur word t037 met die Brasiliaanse/Hongaarse kloon geassosieer (SCCmec tipe III; ST 239). Ons bevindings, asook ander Suid Afrikaanse studies, dui aan dat t037 in kliniese isolate vanaf talle provinsies in Suid-Afrika aangetoon is. Van belang is dat al die isolate van spa tipe t891 MSSA en PVL positief was. Bakteremiese gevalle was hoofsaaklik geassosieer met kateter-sepsis, gevolg deur vel en sagteweefsel infeksies (SSTI). Slegs een persisterende bakteremiese geval was geïdentifiseer geassosieer met HA-SSTI. Herhalende bakteremiese episodes is in pasiënte op dialise vir kroniese nierversaking en in brandwonde pasiënte met intra-vaskulêre kateter infeksies aangetoon. Die lokale epidemiologie van S. aureus en die prevalensie koers van verskillende stamme is van belang. Hierdie inligting dra by tot kennis van die epidemiologie van stafilokokkale stamme wat in ons omgewing bakteremie veroorsaak. Hierdie insigte is nuttig vir optimale diagnostiese en terapeutiese riglyne. Die tegnieke wat ontwikkel is, kan gebruik word om uitbrake en herhalende infeksies te identifiseer.

Thesis (MSc)--Stellenbosch University, 2012. / Background: While Selection of reverse transcriptase (RT) mutation has been reported frequently, protease (PR) mutations on antiretroviral therapy (ART) including boosted Protease inhibitor (PI) have not been reported as much in Zambia. Affordable in-house genotyping assays can been used to expand the number of patients receiving drug resistance geno-typing, which can aid in determining prevalence of RT/PI emerging mutations. Methods: A previously published drug resistance genotyping assay was modified and used to genotype RT and PR genes. 19 patients virologically failing first-line regimen and 24 failing second-line regimen were studied to determine resistance patterns. Virological failure was defined as failing to maintain <1000 copies/mL during ART. Only major and minor RT and PR mutations (IAS-USA 2010) were considered for analysis. The in-house assay was validated by comparing sequence data of 7 previously ViroSeq tested samples and 5 randomly selected samples to determine reproducibility. Results: The in-house assay efficiently amplified all 12 validation samples with the lowest sample scoring 99.4% sequence homology. The most common RT mutation was M184V (79% n=19) and (71% n=24) first and second-line respectively. No significant differences were reported in all the other RT mutations between first-line and secondline regimens. Drug resistant PI mutations (I54V, M46I and V82A all present 20.8%) were only found in the second-line regimen and were insignificant, p= 0.0562. Conclusion: The in-house assays can be used as alternatives for commercial kits to genotype HIV-1C in Zambia without compromising test quality. The insignificant PI drug resistant mutations which were found, despite virological failure in patients, could indicate a possibility of other mutations within the HIV-1 genome that could reduce PI susceptibility.

The aim of this study was to design a resolution typing system for the HLA-B gene. This technique involves a one-step PCR reaction utilizing genomic DNA and sequence-specific primers to determine the specificity of each allele and to produce a larger primer data base ideal for serological analysis. The application of this technique to serological analysis can improve serology detection which is currently hindered by antibody cross-reactivity and the unavailability of useful typing reagents.

Pyrolysis-capillary gas chromatography combined with FID, ECD and MS detection were used to characterize refuse-derived fuel and aquatic fulvic acids. Different pyrolysis methods and programs were evaluated. Pyrolysis temperatures of 700-800°C produced the strongest signal for organics present in RDF and fulvic acid. Cellulose and fatty acids pyrolyzates were identifiable by GC-MS following preparative pyrolysis fractionation. At organic chloride content of 0.023%, only three halogenated compounds were detected in the GC-MS of the fractions. None of the priority pollutants were detected at lower detection limit of 0.72 to 24 mg/ kg RDF. Selective solvent extraction improves the reproduciblities of the technique and allows the detection of polymeric structures. Pyrograms of polyvinyl chloride and regular typing paper showed some common peaks that are present in the RDF pyrogram. About 65% of the peaks in the RDF pyrogram might be of paper origin. The organic chloride content of the RDF was evaluated by ion chromatography of the trapped pyrolyzates in 2% NaOH trap and it was found to be 221 mg Cl/ kg dry RDF. Pyrolysis conditions and temperature programs for FA were systematically evaluated. Samples included purified FA, methylated FA and HPLC separated fractions. Characteristic pyrograms were developed. Profiles of benzene, toluene, phenol, m-cresol and biphenyl from FA were evaluated. The production of phenol was the largest at 800°C, at concentration of 1.61 mg per gram of FA pyrolyzed. The profiles of benzene and toluene followed the same pathways. Both pyrolyzates had at least two precursors. HPLC fractions of FA showed some regular retention patterns characteristic of polymeric material. DL-proline, seriene and vanillic acid pyrograms showed some peaks with the same retention times as those in FA pyrogram under the same conditions. A reproducibility of 6% relative standard deviation was achieved in the pyrolysis of RDF and 0.91% in the case of FA.

Recent sex role research suggested that androgynous subjects demonstrated better adjustment than sex-typed subjects. Fundamentalist religious belief, however, has strongly supported sex role differentiation. This study hypothesized that the effect of appropriate sex role typing or androgyny on self-esteem would depend on religious belief. Although this hypothesis was not supported, a main effect on sex roles for females was obtained; androgynous females had a higher self-esteem level than feminine females. In addition, males in this study had a higher self-esteem level than females.

Chronic infection with P. aeruginosa is expected in patients with cystic fibrosis (CF), but the ability to delay, prevent, or better manage infection with multiply-resistant P. aeruginosa (MRPA) can potentially increase quality of life and extend survival. The Texas Children’s Hospital CF Care Center has identified an endemic MRPA strain (dominant clone), and this study aimed to identify risk factors for acquisition of the clone as well as determine differences in patient outcome associated with subsequent infection with the clone. The study included 71 patients with CF with documented MRPA infection. Designation of patients as members of the dominant clone or a non-dominant clone group was based on molecular typing by rep-PCR of MRPA isolates from respiratory cultures. Patient data was collected from Port CF, the national patient registry of the CF Foundation. Patient demographic information and clinical parameters prior to MRPA infection were analyzed by logistic regression as potential risk factors. Differences in patient outcome including change in BMI, change in FEV1, and hospitalization rate were evaluated by MANOVA. Recent hospitalization (< 90 days) was a statistically significant (p = 0.035) risk factor for acquisition of the dominant clone. Patients hospitalized < 90 days prior to MRPA diagnosis were four times more likely to be infected with the dominant clone, and patients hospitalized 91-180 days prior were almost three times more likely. Increased hospitalization rates were seen in the dominant clone group both pre- (11 more days/year) and post-infection (14 more days/year) as compared to the non-dominant clone group. Patients infected with the endemic strain exhibited poorer outcomes in terms of nutritional status (3.73% decrease/year in BMI %ile) and lung function (3.7% decrease/year in FEV1 %ile). Significant overlap in hospitalization episodes of patients known to be infected with the dominant clone and patients subsequently infected with the dominant clone was observed. Recent hospitalization was a significant risk factor for infection with the dominant MRPA clone, and following infection, patients infected with the endemic strain exhibited declines in nutritional status and lung function and increased hospitalization rates. The results suggest potentially increased virulence and transmissibility of the endemic MRPA strain.

Doctor en Ciencias, Mención Computación / Gradual Typing permite a un programador aplicar tipos estáticos a ciertas partes de un programa, dejando el resto dinámicamente tipeado. Sin embargo, esto viene con un costo en el rendimiento. Una razón es que el runtime tiene que realizar siempre un casteo en el borde entre tipos estáticos y dinámicos. Otra razón es que el borde puede ser creado accidentalmente. Esto también trae un efecto lateral de reducir la fiabilidad del código estático, porque ahora el programador no puede garantizar que su código no arrojará errores de tipo en tiempo de ejecución. En este trabajo de tesis, mejoramos el rendimiento y la fiabilidad de los programas gradualmente tipeados. Para esto, desarrollamos un lenguaje gradualmente tipeado, Gradualtalk, y luego presentamos dos novedosas ideas: hybrid strategy y Confined Gradual Typing. La hybrid strategy es una nueva forma de insertar los casts al invocar métodos que combina dos estrategias existentes, permitiendo obtener el mejor rendimiento de ambas. Validamos esta afirmación con benchmarks. Confined Gradual Typing refina gradual typing con anotaciones para prohibir explícitamente ciertos cruces de frontera entre el código estáticamente y dinámicamente tipeado. Nosotros desarrollamos formalmente dos variantes de CGT que capturan diferentes compromisos entre flexibilidad/garantías. Probamos que CGT es type sound y que las anotaciones ofrecen las garantías esperadas.

O Brasil é o maior exportador de carne de frango e o terceiro maior produtor desta carne. O consumo desta fonte de proteína tem aumentado bastante nos últimos anos, tendo passado de 23,2 Kg/habitante em 1995 para 35,5 Kg/habitante em 2005. O mercado internacional tem se tornado cada vez mais exigente com relação aos padrões microbiológicos destes produtos. Pela importância das aves para a economia brasileira e por Listeria monocytogenes apresentar alta taxa de mortalidade, além de ser facilmente encontrada em carne de aves, decidiu-se verificar a ocorrência deste patógeno em dois matadouros, um com evisceração automática (Planta A) e outro com evisceração manual (Planta M), e traçar as possíveis rotas da disseminação do microrganismo na linha de processamento. Do total de 851 amostras coletadas de produtos, das superfícies de contato e de não contato com o produto, das mãos dos manipuladores e da água utilizada durante o processo de abate, 423 amostras foram da Planta A e 428 da Planta M. O teste VIP&#174; Listeria foi utilizado para a triagem das amostras, sendo que aquelas positivas foram submetidas à caracterização fenotípica (provas bioquímicas e ágar cromogênico). A identificação e a tipagem das cepas foi realizada por técnicas moleculares (BAX® System, multiplex-PCR 16S rRNA, multiplex-PCR, ribotipagem e PFGE). L. monocytogenes foi isolada de 20,1% das amostras da Planta A, sendo 61,6% pertencentes ao sorogrupo 4b, 4d ou 4e; 19,2% ao sorogrupo 1/2a ou 3a; 15,2% ao sorogrupo 1/2c ou 3c; e 4,0% ao sorogrupo 1/2b, 3b ou 7. Na Planta M, 16,4% das amostras foram positivas para L. monocytogenes, havendo predomínio do sorogrupo 1/2a ou 3a (72,9%), seguido do sorogrupo 4b, 4d ou 4e (27,1%). Baseado nos resultados dos testes para caracterização fenotípica e genotípica, verificou-se que L. monocytogenes presente no produto final apresentou características semelhantes àquelas presentes na planta, e não no animal. Apenas uma cepa foi isolada na zona suja da Planta A, piso da seção de depenagem, e todas as demais foram isoladas da zona limpa de ambas as plantas. / Brazil is the first exporter of chicken meat and the third producer of this kind of meat in the world. The consumption of this protein source in Brazil has been increasing, having passed from 23.2 Kg/inhabitant in 1995 to 35.5 Kg/inhabitant in 2005. The international market has become more demanding for safety of these products. Because of the importance of this food commodity to Brazilian economy and because of Listeria monocytogenes importance as a foodborne pathogen this study was conducted. The presence of the pathogen in two facilities, one with automatic evisceration (Plant A) and another with manual evisceration (Plant M), was evaluated to identify possible routes of microorganism dissemination in the processing line. From a total of 851 collected samples of products, food contact and non-food contact surfaces, workers\' hands and water used in the process, 423 samples were from Plant A and 428 from Plant M. VIP&#174; Listeria was used for the samples screening, positive ones were plated and suspected characteristic colonies submitted to biochemical characterization. Selected strains were submitted to identification and typing by molecular techniques (BAX® System, multiplex-PCR 16S rRNA, multiplex-PCR, ribotyping and PFGE). L. monocytogenes was isolated in 20.1% of the samples from Plant A with 61.6% belonging to serogroup 4b, 4d or 4e; 19.2% to serogroup 1/2a or 3a; 15.2% to serogroup 1/2c or 3c; and 4.0% to serogroup 1/2b, 3b or 7. From Plant M 16.4% of the samples were positive for L. monocytogenes, with predominance of serogroup 1/2a or 3a (72.9%) followed by serogroup 4b, 4d or 4e (27.1%). Based on the results of phenotypic and genotypic characterization, it was verified that L. monocytogenes present in the final product had similar characteristics to those isolated in the plant, and not in the animals. Only one strain was isolated in the dirty zone of Plant A, on the floor of defeathering section, and all others were isolated in the clean zone of both plants.