To a person with an upper limb amputation or congenital defect, a well-functioning prosthesis can open the door to many work and life opportunities. A fundamental component of many modern prostheses is the myoelectric control system, which uses the myoelectric signals from an individual's muscles to control prosthetic movements. Though much research has been done involving the myoelectric control of arm and gross hand movements, more dexterous finger control has not received the same attention. Consequently, the goal of this study was to determine an optimal approach to the myoelectric signal classification of a set of typing motions. Two different movement sets involving the fingers of the right hand were tested: one involving digits two through five (4F - "four finger"), and the other involving digits one and two (FT - "finger/thumb"). Myoelectric data were collected from the forearm muscles of twelve normally-limbed subjects as they performed a set of typing tasks. These data were then used to test a series of classification systems, each comprising a different combination of system element choices. The best classification system over all subjects and the best classification system for each subject were determined for both movement sets. The optimal subject-specific classification systems yielded classification accuracies of 92.8 ± 2.7% for the 4F movement set and 93.6 ± 6.1% for the FT movement set, whereas the optimal overall classification systems yielded significantly lower performance (p<0.05): 89.6 ± 3.4% for the 4F movement set and 89.8 ± 8.5% for the FT movement set. No significant difference in classification accuracy was found between movement sets (p=0.802). A two-way repeated measures ANOVA (α=0.05) was used to determine both significance results. / Thesis (Master, Electrical & Computer Engineering) -- Queen's University, 2008-10-31 14:59:43.151

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Answer typing is an important aspect of the question answering process. Most commonly addressed with the use of a fixed set of possible answer classes via question classification, answer typing influences which answers will ultimately be selected as correct. Answer typing introduces the concept of type-appropriate responses. Such responses are plausible in the context of question answering when they are believable as answers to a given question. This notion of type-appropriateness is distinct from correctness, as there may exist many type-appropriate responses that are not correct answers. Type-appropriate responses can even exist for other kinds of queries that are not strictly questions. This work introduces class-free models of answer type for certain kinds of questions as well as models of type-appropriateness useful to the domain of information retrieval. Models built for both open-ended noun phrase questions and how-adjective questions are designed to evaluate the type-appropriateness of a candidate answer directly rather than via the use of an intermediary question class (as is done with question classification). Experiments show a meaningful improvement over alternative typing strategies for these kinds of questions. Ideas from these models are then applied outside of the domain of question answering in an effort to improve traditional information retrieval results. Experiments comparing reranked results with those of the Google search engine show improvements are made in those rare situations for which Google provides less than ideal results.

This thesis proposes that there are two kinds of clauses: indexical clauses, which are evaluated with respect to the speech situation; and anaphoric clauses, which are evaluated with respect to a contextually-given (anaphoric) situation. Empirical motivation for this claim comes from the clause-typing system of Plains Cree, an Algonquian language spoken on the Canadian plains, which morpho-syntactically distinguishes between two types of clauses traditionally called INDEPENDENT and CONJUNCT orders. In the current analysis, the INDEPENDENT order instantiates indexical clauses, and the CONJUNCT order instantiates anaphoric clauses. After laying out the proposal (chapter 1) and establishing the morphosyntax of Plains Cree CPs (chapter 2), the remaining chapters discuss the proposal in detail. Chapter 3 focusses on the syntax and semantics of indexical clauses (Plains Cree’s INDEPENDENT order). Syntactically, I show that there is an anti-c-command and an anti-precedence condition on indexical clauses. Semantically, I show that indexical clauses are always and only evaluated with respect to the speech situation, including the speech time (temporal anchoring), speech place (spatial anchoring), and speaker (referential anchoring). Chapter 4 focusses on the syntax and semantics of anaphoric clauses (Plains Cree’s CONJUNCT order). Syntactically, I show that anaphoric clauses must always be either preceded or dominated by some other antecedent clause. Semantically, I show that the value of temporal/spatial/referential dependent elements within an anaphoric clause is determined by an antecedent. Chapter 5 turns to the syntactic subclassification of Plains Cree’s CONJUNCT (i.e., anaphoric) clauses. I propose that there are three classes: chained clauses, adjunct clauses, and mediated argument clauses. I provide two kinds of diagnostics that distinguish these classes, and explore the consequences of this classification for argument clauses and complementation. Finally, Chapter 6 proposes a semantic subclassification of Plains Cree’s CONJUNCT (i.e., anaphoric) clauses. I propose that there is a direct mapping between the morphology and the semantics: one complementizer encodes presupposition of the proposition, the lack of a complementizer encodes a-veridicality of the proposition, and one complementizer is semantically unspecified (the elsewhere case). This means that Plains Cree’s clause-typing is fundamentally concerned with how the truth of the proposition is represented.

Made available in DSpace on 2014-06-11T19:32:53Z (GMT). No. of bitstreams: 0 Previous issue date: 2006-12-14Bitstream added on 2014-06-13T20:04:32Z : No. of bitstreams: 1 matsumoto_mt_dr_arafcf.pdf: 7554122 bytes, checksum: 0910afc354605fb9e82889bf3660ea86 (MD5) / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / Universidade Estadual Paulista (UNESP) / Cryptococcus neoformans é patógeno importante, principalmente em pacientes imunocomprometidos. A principal porta de entrada deste patógeno é pela via respiratória, disseminando-se posteriormente e atingindo principalmente o sistema nervoso central, provocando a meningite criptocóccica. A primeira parte deste estudo teve como objetivos determinar, nos 106 isolados clínicos de C. neoformans obtidos de dois Estados (São Paulo e Rio de Janeiro), (1) as variedades e (2) os mating-types por PCR (Polymerase Chain Reaction), (3) analisar a diversidade genética por PCR-fingerprinting com a seqüência iniciadora específica para regiões microssatélite (GACA)4, (4) por RAPD (Random Amplification of Polymorphic DNA) com o iniciador 6 e (5) por PCR-RFLP (Restriction Fragment Length Polymorphism) do gene da fosfolipase B (PLB1) digerido com a enzima de restrição AvaI e (6) determinar a sensibilidade a quatro antifúngicos (fluconazol, itraconazol, 5-fluorocitosina e anfotericina B) seguindo o método de referência (documento M27-A2) do CLSI (Clinical and Laboratory Standards Institute). A segunda parte teve como objetivo, analisar transcritos diferencialmente expressos durante a infecção pulmonar de C. neoformans, pela técnica de RDA (Representational Difference Analysis). Entre os 106 isolados, 104 foram identificados como C. neoformans e apenas dois foram C. gattii (=C. neoformans var. gattii), todos MATa. O tipo molecular VNI (C. neoformans var. grubii, sorotipo A) foi o mais prevalente entre os isolados (97/106), seguido do tipo VNII (C. neoformans var. grubii, sorotipo A) (7/106) e VGII (C. gattii, sorotipos B ou C) (2/106) quando analisados por PCR-fingerprinting e PCR-RFLP. Homogeneidade alta foi obtida com o iniciador (GACA)4, com a maioria dos isolados apresentando correlação em torno de 0,9. Os resultados do RAPD, por sua vez, revelaram maior heterogeneidade com número maior de perfis moleculares. / Cryptococcus neoformans is an important pathogen, mainly in immunocompromised patients. The pathogen penetrates mainly by respiratory way, disseminate afterward and reach specially the central nervous system causing the cryptococcal meningitis. The first part of this study had the objective to determine, in the 106 clinical isolates of C. neoformans obtained from São Paulo and Rio de Janeiro State, (1) the varieties and (2) mating-types by PCR (Polymerase Chain Reaction), (3) analyze the genetic diversity by PCR-fingerprinting with specific primer to microsatellite regions (GACA)4, (4) by RAPD (Random Amplification of Polymorphic DNA) with primer 6 and (5) by PCR-RFLP (Restriction Fragment Length Polymorphism) of the phospholipase B gene (PLB1) digested with restriction enzyme AvaI and (6) to determine the susceptibility to four antifungal (fluconazole, itraconazole, 5-flucytosine and amphotericin B) following the reference method (document M27-A2) from CLSI (Clinical and Laboratory Standard Institute). The second part had the goal to analyze differentially expressed transcription during pulmonary infection of C. neoformans, by RDA (Representational Difference Analysis) technique. Among 106 isolates, 104 were identified as C. neoformans and only two were C. gattii (=C. neoformans var. gattii), all MATa. The molecular type VNI (C. neoformans var. grubii, serotype A) was the most prevalent among the isolates (97/106), followed by VNII (C. neoformans var. grubii, serotype A) (7/106) and VGII (C. gattii, serotypes B ou C) (2/106) when analyzed by PCR-fingerprinting and PCR-RFLP. High homogeneity was obtained with the primer (GACA)4, with most of the isolates showing correlation around 0.9. By contrast, the RAPD analysis revealed more heterogeneous with more numbers of molecular profiles.

Submitted by Vanessa Rafaela de Carvalho null (vanessa@fca.unesp.br) on 2016-08-17T15:38:02Z No. of bitstreams: 1 VANESSA RAFAELA DE CARVALHO.pdf: 1265274 bytes, checksum: b22dd09c9d7e691c86790c85e9d494d1 (MD5) / Approved for entry into archive by Ana Paula Grisoto (grisotoana@reitoria.unesp.br) on 2016-08-19T17:25:50Z (GMT) No. of bitstreams: 1 carvalho_vr_me_bot.pdf: 1265274 bytes, checksum: b22dd09c9d7e691c86790c85e9d494d1 (MD5) / Made available in DSpace on 2016-08-19T17:25:50Z (GMT). No. of bitstreams: 1 carvalho_vr_me_bot.pdf: 1265274 bytes, checksum: b22dd09c9d7e691c86790c85e9d494d1 (MD5) Previous issue date: 2016-08-09 / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / Desequilíbrio na composição de espécies bacterianas (disbiose) do intestino é uma característica da doença de Crohn (DC), a mais grave das doenças inflamatórias intestinais (DII). Na disbiose da DII, há um aumento de certos grupos de bactérias, tais como as Proteobacteria, em alguns pacientes. Acredita-se que o aumento destas bactérias deve contribuir para as reações inflamatórias responsáveis pelas lesões observadas no intestino de portadores de DC e retocolite ulcerativa, ao estimular a produção de citocinas por células locais do sistema imune. Proteobacteria, um dos filos predominantes da microbiota intestinal compreende bacilos gram-negativos, dos quais Escherichia coli (E. coli) é o mais conhecido. Dada a importância de Proteobacteria como patógeno ou membro da microbiota intestinal residente humana, este trabalho teve dois objetivos: 1) Investigar a ocorrência de variação numérica na população de Proteobacteria na DC e 2) Caracterizar amostras de E. coli encontradas nesta população, em relação a propriedades de virulência. Visando o primeiro objetivo, DNA de culturas em caldo MacConkey de diferentes materiais clínicos (fezes e biópsias intestinais) de 8 controles e 9 pacientes com DC foram amplificados com primers para as regiões V6-V8 do gene que codifica a fração 16S do rRNA (16S V6-V8 rDNA) e, em seguida, sequências específicas (representando táxons bacterianos particulares) contidas nos amplicons foram separadas por temperature gradient gel electrophoresis (TGGE), definindo perfis de banda que refletem a diversidade bacteriana. O segundo objetivo compreendeu a tipagem dos isolados de E. coli destas culturas através da classificação em filogrupos (A, B1, B2 e D) da coleção de referência de E. coli (EcoR), a pesquisa de sorogrupos O25 e O83, determinação das propriedades de aderência e capacidade de produzir biofilme. Análise de 32 culturas de 9 portadores de DC e 24 culturas de 8 controles mostrou uma clara diferença no número de bandas nos perfis de TGGE dos amplicons de 16S V6-V8 rDNA. Amplicons de 8 culturas de 9 portadores de DC tinham no máximo 2 bandas, ao passo que o número de bandas em amplicons de controles tinham pelo menos 3 bandas. Uma das bandas dos casos em que havia duas bandas ou a banda única dos perfis de cultura de casos teve a mesma mobilidade do amplicon de E. coli, colocado no gel como referência da corrida. PCR para detecção de genes de O25 e O83 demonstraram que estes sorogrupos foram dominantes tanto na população de E. coli de portadores de DC como de controles (apenas um paciente controle deu resultado negativo na PCR para ambos sorogrupos). Também, a maioria das cepas de E. coli, tanto de casos como de controles pertenceu ao filogrupo B2. Resultados parciais de testes de adesão em células Hep-2 revelaram que todos os pacientes (controles ou não) apresentaram E. coli aderentes, expressando o padrão agregativo. Testes para avaliar a capacidade de formação de biofilme indicaram que isolados de E. coli das regiões proximais encontrados em controles produzem biofilme de forma mais intensa do que isolados equivalentes de portadores de DC. Como conclusão, os dados apresentados sugerem que a população intestinal de Proteobacteria em portadores de CD apresenta disbiose, associada com um aumento do número de E. coli, uma propriedade que foi determinada por TGGE e confirmada com seqüenciamento de amplicons da região V6, pela técnica Ion Torrent. Por fim, com base nos resultados de tipagem e caracterização bacteriana foi possível observar que amostras tanto de caso como de controles, não houve uma prevalência dos sorogrupos e com base nesse resultado podemos associar que ambos os grupos de estudos freqüentam de forma rotineira o mesmo ambiente hospitalar, podendo indicar um favorecimento na aquisição desses tipos bacterianos. Resultados semelhantes ocorreram com as análises dos sorogrupos, onde apenas o filogrupo D teve prevalência significativa em indivíduos controle. Em relação à produção de biofilme, as amostras encontradas na região proximal do intestino de pacientes controles produzem mais biofilmes do que amostras de portadores de DC da mesma região intestinal, indicando que a parede da mucosa intestinal serve como substrato pode influenciar na formação do biofilme. / Imbalance in intestinal bacterial composition (dysbiosis) is a hallmark of Crohn’s disease (CD), the most severe of inflammatory bowel diseases (IBD). A characteristic of IBD dysbiosis is the elevation of certain groups of bacteria such as Proteobacteria in some patients. It is believed that the augmented bacteria may contribute for the inflammatory reactions underlying the typical lesions observed in the gut of CD and ulcerative colitis patients, by stimulating the production of cytokines by local cells of the immune system. Proteobacteria, one the most prevalent bacterial phyla of the gut microbiota are Gram negative rods of which Escherichia coli (E. coli) is the most well-known member. Given the significance of Proteobacteria as pathogens or member of resident gut microbiota, this work had two purposes: 1) to investigate the occurrence of numerical variation in the population of these bacteria in CD and 2) Characterizing E. coli isolates found in this population, in search for some virulence associated properties. For the first purpose, DNA from MacConkey broth cultures of distinct clinical materials (stools and gut mucosal biopsies) of 9 CD and 8 control patients were amplified with primers for the V6 and V8 regions of the 16S ribosomal RNA gene (16S V6-V8 rDNA) and distinct gene sequences (representing particular bacterial taxa) within the amplicons were resolved by temperature gradient gel electrophoresis (TGGE), defining band profiles, which reflect the bacterial diversity. The second objective consisted in phylotyping (determining A, B1, B2 and D phylogroups), serotyping (search for O25 and O83 genes), analyzing the E. coli isolates of the cultures for adherence properties and competence to produce biofilm. Analysis of 32 cultures from the 9 CD patients and 24 cultures from 8 control subjects showed a clear case-control difference in the number of bands in the TGGE profiles of the 16S V6-V8 rDNA amplicons. Cultures from 8 of 9 CD patients had at most 2 bands, while the number of bands in the cultures from 7 of the 8 controls subjects had at least 3 bands. One of the two bands found in the cultures from CD patients had the same mobility as E. coli, put in the gelas reference for the run. PCR screening for O25 and O83 demonstrated that these serogroups were dominant among the E. coli population from both controls and CD patients (only one control subject was negative for each of these O groups). Also, most of E. coli isolates from both control and CD patients belonged to the B2 phylogroup. Partial results of bacterial adherence to Hep-2 cells revealed that all patients (controls and CD) had aggregative adherent E. coli isolates. Tests to determine the ability to produce biofilm indicated that isolates from the proximal, but not from distal region of the gut or the stools, found in controls were stronger biofilm formers than isolates from equivalent sites of CD patients. In conclusion, the data presented here reveal that intestinal population of Proteobacteria of CD patients show dysbiosis associated with the elevation of Escherichia coli and that this variation can be assessed by TGGE and confirmed by sequencing of amplicons V6 region, the technique Ion Torrent. Finally, on the basis of the bacterial typing and characterization results, was observed that samples of both the case and controls, there was a prevalence of serogroups, based on this result we can associate both study groups frequent routinely the same hospital environment and may indicate a favoring the acquisition of these bacterial types. Similar results occurred with the analysis of serogroups, where only the filogrupo D had a significant prevalence in control subjects. For biofilm production, the samples found in the proximal region of the control patients intestine produce more biofilm than DC bearing samples of the same intestinal region, indicating that the intestinal mucosa serves as a substrate may influence the formation of biofilms. / FAPESP: 2013/04475-3

Orientador: Maria José Soares Mendes Giannini / Banca: Benedito Barraviera / Banca: Paulo Inácio da Costa / Banca: Célia Maria de Almeida Soares / Banca: Clarice Queico Fujimura Leite / Resumo: Cryptococcus neoformans é patógeno importante, principalmente em pacientes imunocomprometidos. A principal porta de entrada deste patógeno é pela via respiratória, disseminando-se posteriormente e atingindo principalmente o sistema nervoso central, provocando a meningite criptocóccica. A primeira parte deste estudo teve como objetivos determinar, nos 106 isolados clínicos de C. neoformans obtidos de dois Estados (São Paulo e Rio de Janeiro), (1) as variedades e (2) os mating-types por PCR (Polymerase Chain Reaction), (3) analisar a diversidade genética por PCR-fingerprinting com a seqüência iniciadora específica para regiões microssatélite (GACA)4, (4) por RAPD (Random Amplification of Polymorphic DNA) com o iniciador 6 e (5) por PCR-RFLP (Restriction Fragment Length Polymorphism) do gene da fosfolipase B (PLB1) digerido com a enzima de restrição AvaI e (6) determinar a sensibilidade a quatro antifúngicos (fluconazol, itraconazol, 5-fluorocitosina e anfotericina B) seguindo o método de referência (documento M27-A2) do CLSI (Clinical and Laboratory Standards Institute). A segunda parte teve como objetivo, analisar transcritos diferencialmente expressos durante a infecção pulmonar de C. neoformans, pela técnica de RDA (Representational Difference Analysis). Entre os 106 isolados, 104 foram identificados como C. neoformans e apenas dois foram C. gattii (=C. neoformans var. gattii), todos MATa. O tipo molecular VNI (C. neoformans var. grubii, sorotipo A) foi o mais prevalente entre os isolados (97/106), seguido do tipo VNII (C. neoformans var. grubii, sorotipo A) (7/106) e VGII (C. gattii, sorotipos B ou C) (2/106) quando analisados por PCR-fingerprinting e PCR-RFLP. Homogeneidade alta foi obtida com o iniciador (GACA)4, com a maioria dos isolados apresentando correlação em torno de 0,9. Os resultados do RAPD, por sua vez, revelaram maior heterogeneidade com número maior de perfis moleculares. / Abstract: Cryptococcus neoformans is an important pathogen, mainly in immunocompromised patients. The pathogen penetrates mainly by respiratory way, disseminate afterward and reach specially the central nervous system causing the cryptococcal meningitis. The first part of this study had the objective to determine, in the 106 clinical isolates of C. neoformans obtained from São Paulo and Rio de Janeiro State, (1) the varieties and (2) mating-types by PCR (Polymerase Chain Reaction), (3) analyze the genetic diversity by PCR-fingerprinting with specific primer to microsatellite regions (GACA)4, (4) by RAPD (Random Amplification of Polymorphic DNA) with primer 6 and (5) by PCR-RFLP (Restriction Fragment Length Polymorphism) of the phospholipase B gene (PLB1) digested with restriction enzyme AvaI and (6) to determine the susceptibility to four antifungal (fluconazole, itraconazole, 5-flucytosine and amphotericin B) following the reference method (document M27-A2) from CLSI (Clinical and Laboratory Standard Institute). The second part had the goal to analyze differentially expressed transcription during pulmonary infection of C. neoformans, by RDA (Representational Difference Analysis) technique. Among 106 isolates, 104 were identified as C. neoformans and only two were C. gattii (=C. neoformans var. gattii), all MATa. The molecular type VNI (C. neoformans var. grubii, serotype A) was the most prevalent among the isolates (97/106), followed by VNII (C. neoformans var. grubii, serotype A) (7/106) and VGII (C. gattii, serotypes B ou C) (2/106) when analyzed by PCR-fingerprinting and PCR-RFLP. High homogeneity was obtained with the primer (GACA)4, with most of the isolates showing correlation around 0.9. By contrast, the RAPD analysis revealed more heterogeneous with more numbers of molecular profiles. / Doutor

Orientador: Josias Rodrigues / Resumo: Desequilíbrio na composição de espécies bacterianas (disbiose) do intestino é uma característica da doença de Crohn (DC), a mais grave das doenças inflamatórias intestinais (DII). Na disbiose da DII, há um aumento de certos grupos de bactérias, tais como as Proteobacteria, em alguns pacientes. Acredita-se que o aumento destas bactérias deve contribuir para as reações inflamatórias responsáveis pelas lesões observadas no intestino de portadores de DC e retocolite ulcerativa, ao estimular a produção de citocinas por células locais do sistema imune. Proteobacteria, um dos filos predominantes da microbiota intestinal compreende bacilos gram-negativos, dos quais Escherichia coli (E. coli) é o mais conhecido. Dada a importância de Proteobacteria como patógeno ou membro da microbiota intestinal residente humana, este trabalho teve dois objetivos: 1) Investigar a ocorrência de variação numérica na população de Proteobacteria na DC e 2) Caracterizar amostras de E. coli encontradas nesta população, em relação a propriedades de virulência. Visando o primeiro objetivo, DNA de culturas em caldo MacConkey de diferentes materiais clínicos (fezes e biópsias intestinais) de 8 controles e 9 pacientes com DC foram amplificados com primers para as regiões V6-V8 do gene que codifica a fração 16S do rRNA (16S V6-V8 rDNA) e, em seguida, sequências específicas (representando táxons bacterianos particulares) contidas nos amplicons foram separadas por temperature gradient gel electrophores... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Imbalance in intestinal bacterial composition (dysbiosis) is a hallmark of Crohn’s disease (CD), the most severe of inflammatory bowel diseases (IBD). A characteristic of IBD dysbiosis is the elevation of certain groups of bacteria such as Proteobacteria in some patients. It is believed that the augmented bacteria may contribute for the inflammatory reactions underlying the typical lesions observed in the gut of CD and ulcerative colitis patients, by stimulating the production of cytokines by local cells of the immune system. Proteobacteria, one the most prevalent bacterial phyla of the gut microbiota are Gram negative rods of which Escherichia coli (E. coli) is the most well-known member. Given the significance of Proteobacteria as pathogens or member of resident gut microbiota, this work had two purposes: 1) to investigate the occurrence of numerical variation in the population of these bacteria in CD and 2) Characterizing E. coli isolates found in this population, in search for some virulence associated properties. For the first purpose, DNA from MacConkey broth cultures of distinct clinical materials (stools and gut mucosal biopsies) of 9 CD and 8 control patients were amplified with primers for the V6 and V8 regions of the 16S ribosomal RNA gene (16S V6-V8 rDNA) and distinct gene sequences (representing particular bacterial taxa) within the amplicons were resolved by temperature gradient gel electrophoresis (TGGE), defining band profiles, which reflect the bact... (Complete abstract click electronic access below) / Mestre

There are many problems where the solution depends heavily on parametertuning and therefore on conguration. Examples include Hill Climbers andvarious Evolutionary Algorithms. The Intelligent Parameter Utilization Tool(InPUT) uses a cross-language format for describing congurations of computerexperiments, thereby aiding in documentation and communication. Itis implemented in Java, and a C++ version is being developed. This meansthat only implementations in statically typed languages currently exist. APython port would thus greatly increase the diversity of implementation languages.The goal of this project was to create an InPUT implementation inPython, and to explore the suitability of a dynamically typed language inthis context. A de facto specication was discovered by creating a suite oflearning tests, and the new implementation was developed using a test-drivenapproach. Several features of Python proved advantageous by simplifying thedevelopment process.