Tandem mass spectrometry, also known as MS/MS, is an analytical technique to measure the mass-to-charge ratio of charged ions and widely used in genomics, proteomics and metabolomics areas. There are two types of automatic ways to interpret tandem mass spectra: de novo methods and database searching methods. Both of them need to use massive computational resources and complicated comparison algorithms. The real-time peptide-spectrum matching (RT-PSM) algorithm is a database searching method to interpret tandem mass spectra with strict time constraints. Restricted by the hardware and architecture of an individual workstation the RT-PSM algorithm has to sacrifice the level of accuracy in order to provide prerequisite processing speed. The peptide-spectrum similarity scoring module is the most time-consuming part out of four modules in the RT-PSM algorithm, which is also the core of the algorithm. In this study, a multi-core computing algorithm is developed for individual workstations. Moreover, a distributed computing algorithm is designed for a cluster. The improved algorithms can achieve the speed requirement of RT-PSM without sacrificing the accuracy. With some expansion, this distributed computing algorithm can also support different PSM algorithms. Simulation results show that compared with the original RT-PSM, the parallelization version achieves 25 to 34 times speed-up based on different individual workstations. A cluster with 240 CPU cores could accelerate the similarity score module 210 times compare with the single-thread similarity score module and the whole peptide identification process 85 times compare with the single-thread peptide identification process.

<p>Soft matter systems exhibiting spatially modulated patterns on a mesoscale are characterized by many long-lived metastable phases for which relaxation to equilibrium is difficult and a satisfactory thermodynamic description is missing. Current dynamical theories suffer as well, because they mostly rely on an understanding of the underlying equilibrium behavior. This thesis relates the study of two canonical examples of modulated systems: microphase and cluster crystal formers. Microphases are the counterpart to gas-liquid phase separation in systems with competing short-range attractive and long-range repulsive interactions. Periodic lamellae, cylinders, clusters, etc., are thus observed in a wide variety of physical and chemical systems, such as multiblock copolymers, oil-water surfactant mixtures, charged colloidal suspensions, and magnetic materials. Cluster crystals in which each lattice site is occupied by multiple particles are formed in systems with steep soft-core repulsive interactions. Dendrimers have been proposed as a potential experimental realization. In order to access and understand the equilibrium properties of modulated systems, we here develop novel Monte Carlo simulation methods. A thermodynamic integration scheme allows us to calculate the free energy of specific modulated phases, while a [N]pT ensemble simulation approach, in which both particle number and lattice spacing fluctuate, allows us to explore their phase space more efficiently. With these two methods, we solve the equilibrium phase behavior of five schematic modulated-phase-forming spin and particle models, including the axial next-nearest-neighbor Ising (ANNNI) model, the Ising-Coulomb (IC) model, the square-well linear (SWL) model, the generalized exponential model of index 4 (GEM-4) and the penetrable sphere model (PSM). Interesting new physics ensues. In the ANNNI layered regime, simple phases are not found to play a particularly significant role in the devil's flowers and interfacial roughening plays at most a small role. With the help of generalized order parameters, the paramagnetic-modulated critical transition of the ANNNI model is also studied. We confirm the XY universality of the paramagnetic-modulated transition and its isotropic nature. With our development of novel free energy minimization schemes, the determination of a first phase diagram of a particle-based microphase former SWL is possible. We identify the low temperature GEM-4 phase diagram to be hybrid between the Gaussian core model (GCM) and the PSM. The system additionally exhibits S-shaped doubly reentrant phase sequences as well as critical isostructural transitions between face-centered cubic (FCC) cluster solids of different integer occupancy. The fluid-solid coexistence in the PSM phase diagram presents a crossover behavior around T~0.1, below which the system approaches the hard sphere limit. Studying this regime allows us to correct and reconcile prior DFT and cell theory work around this transition.</p> / Dissertation

Base Teórica: O câncer de mama é provavelmente o mais temido pelas mulheres devido a sua alta freqüência e, sobretudo, pelos seus efeitos psicológicos que afetam a percepção da sexualidade e a própria imagem pessoal. Ele é relativamente raro antes dos 35 anos de idade, mas acima desta faixa etária sua incidência cresce rápida e progressivamente. Estudos indicam que fatores genéticos e ambientais são responsáveis pela incidência do câncer de mama, sendo que a hereditariedade provavelmente tenha participação restrita no desenvolvimento deste tipo de tumor. Os principais genes associados ao desenvolvimento do câncer de mama, BRCA1 e BRCA2, são responsáveis por cerca de 80% desses casos, conferindo um risco de 71 a 85% de chance de desenvolver a neoplasia em alguma fase da vida. Mutações nesses genes, classificados como supressores tumorais, demonstram que a perda de suas funções não pára o ciclo celular, não permite a ação do sistema de reparo, e não estimula a apoptose (morte celular programada), culminando em replicação anormal e câncer. A observação epidemiológica de que mulheres judias de origem Ashkenazi parecem ser mais vulneráveis ao câncer de mama está sendo explicada através de estudos moleculares dos genes BRCA1 e BRCA2, onde encontramos a prevalência de três mutações específicas: 185delAG e 5382insC, no gene BRCA1 e 6174delT, no gene BRCA2. Métodos: Utilizou-se um banco de DNA pré-existente, extraído de 209 mulheres da comunidade judaica Ashkenazi da cidade de Porto Alegre. A amplificação do DNA foi realizada por PCR, através da técnica PSM (PCR Mediated site-direct) seguida de digestão dos produtos de PCR com enzimas de restrição. Os objetivos foram verificar se as freqüências das mutações 185delAG e 5382insC, no gene BRCA1 são significativas nesta população e compará-las com demais freqüências encontradas. Resultados: Foram encontradas três pacientes com a mutação 185delAG e duas pacientes com a mutação 5382insC, com as freqüências de 1,435% (95% IC: 0,366; 3,856) e 0,957% (95% IC: 0,161; 3,125), respectivamente. / Introduction: Breast cancer is probably the worst diagnosed cancer for women due to its high frequency and furthermore by its psychological problems that affect the perception of sexuality and the self image. It is relatively rare before 35 years of age, but beyond this age its incidence increases rapidly and progressively. Studies show that genetic and environmental factors are responsible for breast cancer incidence, but heredity may play a restrict role in the development of this kind of tumor. The main genes associated to the development of breast cancer, BRCA1 and BRCA2, are responsible for almost 80% of these cases, reaching a chance between 71 and 85% of developing the disease at any life stage. Mutations in these genes, classified as tumor suppressors, do not allow the repair mechanisms of DNA to perform its action and do not stimulate apoptosis, culminating in abnormal replication and cancer. The epidemiological observation in which Ashkenazi Jewish women seems to be more vulnerable to breast cancer is explained through molecular studies of BRCA1 and BRCA2 genes, where three specific mutations have been found (185delAG and 5382insC, in the BRCA1 gene and 6174delT, in the BRCA2 gene). Methods: A pre-existent bank of DNA extracted from 209 women of the Ashkenazi Jewish community of Porto Alegre city has been used. The DNA amplification was performed through PCR, using the PSM (PCR Mediated Site-Direct) technique followed by the digestion of PCR products with restriction enzymes. The objectives of this study was to identify the frequencies of mutations 185delAG and 5382insC at the BRCA1 gene and verify if they are significantly different in this population when compared to frequencies found in other studies. Results: We found three patients with 185delAG mutation and two patients with 5382insC mutation, with frequencies of 1.435% (95% CI: 0,366; 3,856) and 0,957% (95% IC: 0,161; 3,125), respectively.

Base Teórica: O câncer de mama é provavelmente o mais temido pelas mulheres devido a sua alta freqüência e, sobretudo, pelos seus efeitos psicológicos que afetam a percepção da sexualidade e a própria imagem pessoal. Ele é relativamente raro antes dos 35 anos de idade, mas acima desta faixa etária sua incidência cresce rápida e progressivamente. Estudos indicam que fatores genéticos e ambientais são responsáveis pela incidência do câncer de mama, sendo que a hereditariedade provavelmente tenha participação restrita no desenvolvimento deste tipo de tumor. Os principais genes associados ao desenvolvimento do câncer de mama, BRCA1 e BRCA2, são responsáveis por cerca de 80% desses casos, conferindo um risco de 71 a 85% de chance de desenvolver a neoplasia em alguma fase da vida. Mutações nesses genes, classificados como supressores tumorais, demonstram que a perda de suas funções não pára o ciclo celular, não permite a ação do sistema de reparo, e não estimula a apoptose (morte celular programada), culminando em replicação anormal e câncer. A observação epidemiológica de que mulheres judias de origem Ashkenazi parecem ser mais vulneráveis ao câncer de mama está sendo explicada através de estudos moleculares dos genes BRCA1 e BRCA2, onde encontramos a prevalência de três mutações específicas: 185delAG e 5382insC, no gene BRCA1 e 6174delT, no gene BRCA2. Métodos: Utilizou-se um banco de DNA pré-existente, extraído de 209 mulheres da comunidade judaica Ashkenazi da cidade de Porto Alegre. A amplificação do DNA foi realizada por PCR, através da técnica PSM (PCR Mediated site-direct) seguida de digestão dos produtos de PCR com enzimas de restrição. Os objetivos foram verificar se as freqüências das mutações 185delAG e 5382insC, no gene BRCA1 são significativas nesta população e compará-las com demais freqüências encontradas. Resultados: Foram encontradas três pacientes com a mutação 185delAG e duas pacientes com a mutação 5382insC, com as freqüências de 1,435% (95% IC: 0,366; 3,856) e 0,957% (95% IC: 0,161; 3,125), respectivamente. / Introduction: Breast cancer is probably the worst diagnosed cancer for women due to its high frequency and furthermore by its psychological problems that affect the perception of sexuality and the self image. It is relatively rare before 35 years of age, but beyond this age its incidence increases rapidly and progressively. Studies show that genetic and environmental factors are responsible for breast cancer incidence, but heredity may play a restrict role in the development of this kind of tumor. The main genes associated to the development of breast cancer, BRCA1 and BRCA2, are responsible for almost 80% of these cases, reaching a chance between 71 and 85% of developing the disease at any life stage. Mutations in these genes, classified as tumor suppressors, do not allow the repair mechanisms of DNA to perform its action and do not stimulate apoptosis, culminating in abnormal replication and cancer. The epidemiological observation in which Ashkenazi Jewish women seems to be more vulnerable to breast cancer is explained through molecular studies of BRCA1 and BRCA2 genes, where three specific mutations have been found (185delAG and 5382insC, in the BRCA1 gene and 6174delT, in the BRCA2 gene). Methods: A pre-existent bank of DNA extracted from 209 women of the Ashkenazi Jewish community of Porto Alegre city has been used. The DNA amplification was performed through PCR, using the PSM (PCR Mediated Site-Direct) technique followed by the digestion of PCR products with restriction enzymes. The objectives of this study was to identify the frequencies of mutations 185delAG and 5382insC at the BRCA1 gene and verify if they are significantly different in this population when compared to frequencies found in other studies. Results: We found three patients with 185delAG mutation and two patients with 5382insC mutation, with frequencies of 1.435% (95% CI: 0,366; 3,856) and 0,957% (95% IC: 0,161; 3,125), respectively.

Base Teórica: O câncer de mama é provavelmente o mais temido pelas mulheres devido a sua alta freqüência e, sobretudo, pelos seus efeitos psicológicos que afetam a percepção da sexualidade e a própria imagem pessoal. Ele é relativamente raro antes dos 35 anos de idade, mas acima desta faixa etária sua incidência cresce rápida e progressivamente. Estudos indicam que fatores genéticos e ambientais são responsáveis pela incidência do câncer de mama, sendo que a hereditariedade provavelmente tenha participação restrita no desenvolvimento deste tipo de tumor. Os principais genes associados ao desenvolvimento do câncer de mama, BRCA1 e BRCA2, são responsáveis por cerca de 80% desses casos, conferindo um risco de 71 a 85% de chance de desenvolver a neoplasia em alguma fase da vida. Mutações nesses genes, classificados como supressores tumorais, demonstram que a perda de suas funções não pára o ciclo celular, não permite a ação do sistema de reparo, e não estimula a apoptose (morte celular programada), culminando em replicação anormal e câncer. A observação epidemiológica de que mulheres judias de origem Ashkenazi parecem ser mais vulneráveis ao câncer de mama está sendo explicada através de estudos moleculares dos genes BRCA1 e BRCA2, onde encontramos a prevalência de três mutações específicas: 185delAG e 5382insC, no gene BRCA1 e 6174delT, no gene BRCA2. Métodos: Utilizou-se um banco de DNA pré-existente, extraído de 209 mulheres da comunidade judaica Ashkenazi da cidade de Porto Alegre. A amplificação do DNA foi realizada por PCR, através da técnica PSM (PCR Mediated site-direct) seguida de digestão dos produtos de PCR com enzimas de restrição. Os objetivos foram verificar se as freqüências das mutações 185delAG e 5382insC, no gene BRCA1 são significativas nesta população e compará-las com demais freqüências encontradas. Resultados: Foram encontradas três pacientes com a mutação 185delAG e duas pacientes com a mutação 5382insC, com as freqüências de 1,435% (95% IC: 0,366; 3,856) e 0,957% (95% IC: 0,161; 3,125), respectivamente. / Introduction: Breast cancer is probably the worst diagnosed cancer for women due to its high frequency and furthermore by its psychological problems that affect the perception of sexuality and the self image. It is relatively rare before 35 years of age, but beyond this age its incidence increases rapidly and progressively. Studies show that genetic and environmental factors are responsible for breast cancer incidence, but heredity may play a restrict role in the development of this kind of tumor. The main genes associated to the development of breast cancer, BRCA1 and BRCA2, are responsible for almost 80% of these cases, reaching a chance between 71 and 85% of developing the disease at any life stage. Mutations in these genes, classified as tumor suppressors, do not allow the repair mechanisms of DNA to perform its action and do not stimulate apoptosis, culminating in abnormal replication and cancer. The epidemiological observation in which Ashkenazi Jewish women seems to be more vulnerable to breast cancer is explained through molecular studies of BRCA1 and BRCA2 genes, where three specific mutations have been found (185delAG and 5382insC, in the BRCA1 gene and 6174delT, in the BRCA2 gene). Methods: A pre-existent bank of DNA extracted from 209 women of the Ashkenazi Jewish community of Porto Alegre city has been used. The DNA amplification was performed through PCR, using the PSM (PCR Mediated Site-Direct) technique followed by the digestion of PCR products with restriction enzymes. The objectives of this study was to identify the frequencies of mutations 185delAG and 5382insC at the BRCA1 gene and verify if they are significantly different in this population when compared to frequencies found in other studies. Results: We found three patients with 185delAG mutation and two patients with 5382insC mutation, with frequencies of 1.435% (95% CI: 0,366; 3,856) and 0,957% (95% IC: 0,161; 3,125), respectively.

This paper is dedicated to the empirical analysis of the pilot trainee project Stáže ve firmách, which is considered as treatment in this analysis. The main objective of the empirical analysis is estimation of average treatment effect(ATE) and average treatment effect on treated(ATET) for characteristics like socioeconomic status and wage. Counterfactual methods for policy impact evaluation like Difference in Differences Estimator(DiD), First Differences Estimator(FD) and Propensity Score Matching(PSM) are used to estimation mentioned effects. This paper contains extension of Assignment Problem that is used for people matching purposes as alternative for PSM. This way of matching provides better control over creation of couples. Resulting pairs are more similar in selected characteristics due to better control during couples creation process.

<p dir="ltr">Plant secondary metabolites (PSMs) are specialized compounds produced in response to a range of insect herbivores and microbes, making them important in shaping tri-trophic interactions. However, despite being well-studied in the context of plant-insect coevolution, it is unclear how PSMs impact microbial communities associated with plants and the insect herbivores that feed on them. The overarching goal of this dissertation was to better understand how variation in plant defensive responses, particularly expression of PSMs, influences the composition and functional potential of microbial communities associated with plant tissues (roots and leaves) and insect herbivores. Monarchs (<i>Danaus plexippus</i>) and their milkweed hosts (<i>Asclepias spp.)</i> are well-studied for mechanisms of plant defense and insect counter defense, but little is known about the role of associated microbial communities in this iconic system. To address this knowledge gap, a combination of metabarcoding and metagenomics was used to characterize the taxonomic composition and functional gene profiles of bacterial communities associated with plant tissues (i.e., phyllosphere and rhizosphere) and monarch caterpillars fed on multiple milkweed species (<i>A. curassavica</i>, <i>A. syriaca</i>, and <i>A. tuberosa</i>). Findings show the composition of phyllosphere, rhizosphere, and monarch microbiomes vary across milkweed species in terms of diversity and relative abundance of bacterial taxa. Furthermore, phyllosphere and rhizosphere microbiomes were shown to have distinct functional gene profiles and presence of potential PSM metabolism genes that also varied across milkweed species. Rhizosphere microbiomes had a greater overall capacity for PSM metabolism compared to the phyllosphere, having more genes, and associated metabolic pathways involved in degradation or detoxification of known classes of PSMs. However, plant associated microbiomes were not generally affected by monarch feeding, evidenced by few changes in taxonomic composition or abundance of genes predicted to be involved in PSM metabolism. Interestingly, monarch microbiomes shared >90% of their taxa with their host plants, but there was little evidence of PSM metabolism genes present in functional gene profiles. Overall, this dissertation lays the foundation for understanding how PSMs shape all the microbial communities associated with monarchs and their milkweed hosts. Findings suggest plant defensive responses affect the assembly, functional potential and ultimately the evolution of plant and insect microbiomes.</p>

S. aureus est un pathogène majeur de l’Homme capable de produire une grande variété de facteurs de virulence tels que les phénol-solubles modulines alpha (PSM) et l’hémolysine delta (Hld). La transmission de S. aureus est essentiellement manu-portée mais les éléments favorisant sa dissémination dans la population restent inconnus. Les mastocytes étant connus pour libérer des médiateurs pruritogènes, nous avons suspecté leur implication dans la physiopathologie et la transmission des infections cutanées staphylococciques. Sur une lignée de mastocytes humains, l’Hld et les PSM1, montrés pour être produits in vivo, déclenchaient la libération de tels médiateurs. Chez S. aureus, la production des toxines est sous la dépendance du système de régulation globale Agr. Les souches de S. aureus appartenant au type Agr1, produisant significativement plus d’Hld et de PSM que les autres souches, ont été les plus fréquemment retrouvées au cours de l’année 2017 dans les infections cutanées staphylococciques. Ceci corrobore l’hypothèse selon laquelle une souche de S. aureus produisant des toxines capables d’interagir avec les mastocytes et induisant un prurit, diffuse plus facilement dans la population. Nous avons ensuite étudié la modulation de l’expression des PSM et d’Hld par des concentrations sub-inhibitrices d’antibiotiques. L’oxacilline induisait une inhibition de l’expression des PSM et d’Hld alors que la clindamycine entraînait plus fréquemment une induction de leur expression. Ces observations nous ont interrogé sur l’utilisation de la clindamycine considérée habituellement comme anti-toxinique et sur l’effet bénéfique ou délétère de l’effet inhibiteur de l’oxacilline / S. aureus is a major human pathogen able to produce several virulence factors such as phenol-solublemodulins alpha (PSMalpha) and delta hemolysin (Hld). S. aureus is essentially spread through hand butthe elements promoting its spreading stay unsolved. Mast cells release several soluble mediatorstriggering itching behavior. We suspect the mast cell involvement in spreading of S. aureus strains andin physiopathology of staphylococcal skin infections. Upon human mast cell line, we showed thatPSMalpha1 and Hld induced the release of mediators triggering itching behavior. Moreover, these toxinswere produced in vivo during staphylococcal skin infections. Expression of staphylococcal virulencefactors is regulated by global regulatory system Agr. Interestingly, we observed that S. aureus strainsbelonging in Agr1 produced higher quantity of PSMalpha and Hld than those belonging to Agr2 and Agr3,and were more frequently responsible to skin infections during the last year. This observation supportsour hypothesis whereby a strain producing toxins able to trigger mast cell mediator inducingscratching behavior, spreads electively in the community. Thereafter, we studied modulation of PSMalphaand Hld expression by sub-inhibitory concentration of antibiotics. We reported that oxacillin inducedan inhibitory effect on PSMalpha and Hld expression, while clindamycin resulted in more frequently aninducer effect. These results are discordant with these observed with Panton-Valentine leucocidin andalpha hemolysin and interrogate on clindamycin use for its anti-toxin activity and on benefic ordeleterious effect of oxacillin inhibitory effect

In order to gain competitive advantages in markets, companies have provided a variety of customized products to satisfy customer-specific requirements, leading to not only a large amount of product data but also high cost, long lead-time and complexity of quality control. Efficient product data management throughout the product lifecycle has become increasingly crucial, of which product structure management is regarded as the most important constituent.  The study took ABB Mine Hoist system as a case to investigate how to construct a generic product structure model fit for engineer-to-order system offerings with the consideration of their sales-delivery product lifecycle. The aim of the model is to facilitate the product-related information sharing and reuse across a company, and the integration of different business operations throughout the entire product lifecycle as well. Based on the current situation analysis of product data management on ABB Mine Hoist, three major issues were identified which need to be addressed in the formulation of a generic structure model: namely the integration of requirements of multiple disciplines; the consistency of product information throughout the product lifecycle; and the constant update of product repository. Through illustrating the formulation of ABB Mine Hoist generic structure model, the method of how to construct a generic product structure model for engineer-to-order system product was presented. The model was achieved by applying the framework of the step-based product model and was regarded as a result of integrating domain-specific requirements. The adaptive generic product structure model was then employed to display the role of this generic model in the different phases of a sales-delivery lifecycle. The model could serve as a “master concept” to transfer common product information in the product lifecycle. It’s expected to benefit the business of engineer-to-order system product through improving the integration of different disciplines, enhancing information exchange and reuse. It could also provide an abstract and conceptual basis for potential product repository to reinforce data consistency and completeness.

This dissertation examines the role of public investments in inducing small firms to develop risky, early-stage technologies. It contributes to expanding our understanding of the consequences of research, innovation, and entrepreneurship policies and programs by investigating in more depth the effect of the Small Business Innovation Research (SBIR) program on the innovation effort, ability to attract external capital, and other metrics of post-entry performance of small business start-ups using a new sample and estimation approach. Unlike prior R&D subsidy studies that concentrated almost exclusively on European countries, this dissertation focused on small business start-ups in the United States using a new scientific survey of new firms. It integrated the Kauffman Firm Survey (KFS) from the Ewing Marion Kauffman Foundation with the SBIR recipient dataset from the U.S. Small Business Administration (SBA) and used advances in statistical matching to achieve better comparability between the treated and control groups of small business start-ups. The integrated KFS-SBA dataset, which contains both recipient and non-recipient small firms, and statistical matching allowed us to empirically construct the counterfactual outcomes of SBIR recipients. This dissertation balanced the pre-treatment characteristics of SBIR recipients and non-recipients through propensity score matching (PSM). It constructed the comparison sample by identifying non-recipients with nearly identical propensity scores as those of SBIR recipients. Consistent with the propensity score theorem, observations with the same distribution of propensity scores have the same distribution of observable characteristics. PSM made the comparison and treatment samples homogenous except in SBIR program exposure, making the fundamental assumption of ignorability of treatment assignment more plausible. Using the realized outcomes of observationally similar non-recipient start-ups as the counterfactual outcomes of SBIR recipients, we found empirical evidence of the input additionality effect of the SBIR program. Had they not applied for and granted SBIR R&D subsidies, recipient start-ups would have spent only $185,000 in R&D, but with SBIR their R&D effort was significantly increased to $663,000, on average. The treatment effects analyses also found a significant positive effect of SBIR on innovation propensity and employment. However, it appears that public co-financing of commercial R&D has crowded-out privately financed R&D of small business start-ups in the United States. A dollar of SBIR subsidy decreased firm-financed R&D by about $0.16. Contrary to prior SBIR studies, we did not find any significant "halo effect" or "certification effect" of receiving an SBIR award on attracting external capital. However, we discovered a different certification effect of the SBIR program: SBIR grantees are more likely to attract external patents. This finding also confirms that innovation requires a portfolio of internal and external knowledge assets as theorized by David Teece and his colleagues. This dissertation's empirical results may be relevant to the Small Business Administration, SBIR participating agencies, the U.S. Congress, other federal, state and local policymakers, small high-tech start-ups, and scholars in the field of science, technology, and innovation policy.