The conjugate gradient partitioned block frequency-domain for multichannel adaptive filtering

The conjugate gradient is the most popular optimization method for solving large systems of linear equations. In a system identification problem, for example, where very large impulse response is involved, it is necessary to apply a particular strategy which diminishes the delay, while improving the convergence time. In this paper we propose a new scheme which combines frequency-domain adaptive filtering with a conjugate gradient technique in order to solve a high order multichannel adaptive filter, while being delayless and guaranteeing a very short convergence time.

Sparse hierarchical Bayesian models for detecting relevant antigenic sites in virus evolution

Understanding how virus strains offer protection against closely related emerging strains is vital for creating effective vaccines. For many viruses, including Foot-and-Mouth Disease Virus (FMDV) and the Influenza virus where multiple serotypes often co-circulate, in vitro testing of large numbers of vaccines can be infeasible. Therefore the development of an in silico predictor of cross-protection between strains is important to help optimise vaccine choice. Vaccines will offer cross-protection against closely related strains, but not against those that are antigenically distinct. To be able to predict cross-protection we must understand the antigenic variability within a virus serotype, distinct lineages of a virus, and identify the antigenic residues and evolutionary changes that cause the variability. In this thesis we present a family of sparse hierarchical Bayesian models for detecting relevant antigenic sites in virus evolution (SABRE), as well as an extended version of the method, the extended SABRE (eSABRE) method, which better takes into account the data collection process. The SABRE methods are a family of sparse Bayesian hierarchical models that use spike and slab priors to identify sites in the viral protein which are important for the neutralisation of the virus. In this thesis we demonstrate how the SABRE methods can be used to identify antigenic residues within different serotypes and show how the SABRE method outperforms established methods, mixed-effects models based on forward variable selection or l1 regularisation, on both synthetic and viral datasets. In addition we also test a number of different versions of the SABRE method, compare conjugate and semi-conjugate prior specifications and an alternative to the spike and slab prior; the binary mask model. We also propose novel proposal mechanisms for the Markov chain Monte Carlo (MCMC) simulations, which improve mixing and convergence over that of the established component-wise Gibbs sampler. The SABRE method is then applied to datasets from FMDV and the Influenza virus in order to identify a number of known antigenic residue and to provide hypotheses of other potentially antigenic residues. We also demonstrate how the SABRE methods can be used to create accurate predictions of the important evolutionary changes of the FMDV serotypes. In this thesis we provide an extended version of the SABRE method, the eSABRE method, based on a latent variable model. The eSABRE method takes further into account the structure of the datasets for FMDV and the Influenza virus through the latent variable model and gives an improvement in the modelling of the error. We show how the eSABRE method outperforms the SABRE methods in simulation studies and propose a new information criterion for selecting the random effects factors that should be included in the eSABRE method; block integrated Widely Applicable Information Criterion (biWAIC). We demonstrate how biWAIC performs equally to two other methods for selecting the random effects factors and combine it with the eSABRE method to apply it to two large Influenza datasets. Inference in these large datasets is computationally infeasible with the SABRE methods, but as a result of the improved structure of the likelihood, we are able to show how the eSABRE method offers a computational improvement, leading it to be used on these datasets. The results of the eSABRE method show that we can use the method in a fully automatic manner to identify a large number of antigenic residues on a variety of the antigenic sites of two Influenza serotypes, as well as making predictions of a number of nearby sites that may also be antigenic and are worthy of further experiment investigation.

Towards in silico IBV vaccine design: defining the role of polymorphism in viral attenuation

The gammacoronavirus, Infectious Bronchitis Virus (IBV), is a respiratory pathogen of chickens. IBV is a constant threat to poultry production as established vaccines are often ineffective against emerging strains. This requires constant and rapid vaccine production by a process of viral attenuation by egg passage, but the essential forces leading to attenuation in the virus have not yet been characterised. Knowledge of these factors will lead to the development of more effective, rationally attenuated, live vaccines and reduction of the mortality and morbidity caused by this pathogen. M41 CK strain was egg passaged four times many years ago at Houghton Poultry Research Station and stored as M41-CK EP4 (stock virus at The Pirbright Institute since 1992). It was the first egg passage to have its genome pyrosequenced and was therefore used as the baseline reference. The overall aim of this project was to analyse deep sequence data obtained from four IBV isolates (called A, A1, C and D) each originating from the common M41-CK EP4 (ep4) and independently passaged multiple times in embryonated chicken eggs (figure 1.1). Highly polymorphic encoding regions of the IBV genome were then identified which are likely involved in the attenuation process through the formation of independent SNPs and/or SNP clusters. This was then used to direct targeted investigation of SNPs during the attenuation process of the four IBV passages. A previously generated deep sequence dataset was used as a preliminary map of attenuation for one virulent strain of IBV. This investigation showed the nucleocapsid and spike as two highly polymorphic encoding regions within the IBV genome with the highest proportion of SNPs compared to encoding region size. This analysis then led to more focussed studies of the nucleocapsid and spike encoding region with the ultimate aim of mapping key attenuating regions and nucleotide positions. The 454 pyrosequencing data and further investigation of nucleocapsid and spike encoding regions have identified the SNPs present at the same nucleotide positions within analysed A, A1, C and D isolates. These SNPs probably play a crucial role in viral attenuation and universal vaccine production but it is not clear if independent SNPs are also involved in loss of virulence. The majority of SNPs accumulated at different nucleotide positions without further continuation in Sanger sequenced egg passages presenting S2 subunit (spike) and nucleocapsid as polymorphic encoding regions which in nature remain highly conserved.

Design of the ATAQ peptide and its evaluation as an immunogen to develop a Rhipicephalus vaccine

2016

Dissection of the protective response elicited by the DOMV component of the 4CMenB vaccine

Neisseria meningitidis serogroup B is the major etiological agent of meningitis and life-threatening sepsis, against which two vaccines are licensed. The 4CMenB vaccine is composed of three major protein antigens (fHbp, NHBA and NadA) and detergent-extracted outer membrane vesicles (DOMV) from the NZ98/254 strain. DOMV are safe, immunogenic and able to raise bactericidal antibodies, mainly attributed to the immunodominant PorA protein. Nevertheless, DOMV offer a complex reservoir of potentially immunogenic proteins, whose relative contribution in protection is still poorly characterized. By testing antisera from vaccinated infants in serum bactericidal assay, we observed that the addition of DOMV in the vaccine formulation enhanced breadth of coverage compared to recombinant proteins alone against a panel of 11 meningococcal strains mismatched for the vaccine antigens. To unravel the DOMV components involved in such protection, 30 DOMV antigens were cloned and expressed in Escherichia coli as recombinant proteins and/or in vesicles to maintain their native conformation. Samples obtained were both included in tailor-made protein-microarrays to immunoprofile the antibody repertoire raised by DOMV-containing formulations and were individually used for mouse immunization studies to assess their ability to induce bactericidal antibodies. The protein-array immunosignature of mouse DOMV/4CMenB antisera unveiled a subset of 8 DOMV-reactive proteins potentially responsible for the additional protective responses. The antisera derived from mouse immunizations showed high levels of antibodies and recognized the corresponding antigen across different meningococcal strains. Among the protein-array reactive antigens, OpcA, NspA and PorB induced antibodies able to kill 10 of the 11 genetically diverse meningococcal strains and the specificity of the protective role of OpcA and PorB was also confirmed in 4CMenB infant vaccinee sera. In conclusion, we identified additional PorA-independent antigens within DOMV involved in broadening the coverage of 4CMenB, thus supporting the key role played by vesicles in this multivalent formulation.

Research of predictive biomarkers to anti-CD22 antibody-drug conjugate treatment in B-cell acute lymphoblastic leukemia

Background: The treatment of B-cell acute lymphoblastic leukemia (B-ALL) has been enriched by novel agents targeting surface markers CD19 and CD22. Inotuzumab ozogamicin (INO) is a CD22-calicheamicin conjugated monoclonal antibody approved in the setting of relapse/refractory (R/R) B-ALL able to induce a high rate of deep responses, not durable over time. Aims: This study aims to identify predictive biomarkers to INO treatment in B- ALL by flow cytometric analysis of CD22 expression and gene expression profile. Materials and methods: Firstly, the impact on patient outcome in 30 R/R B-ALL patients of baseline CD22 expression in terms of CD22 blast percentage and CD22 fluorescent intensity (CD22-FI) was explored. Secondly, baseline gene expression profile of 18 R/R B-ALL patient samples was analyzed. For statistical analysis of differentially expressed genes (DEGs) patients were divided in non-responders (NR), defined as either INO-refractory or with duration of response (DoR) < 3 months, and responders (R). Gene expression results were analyzed with Ingenuity pathway analysis (IPA). Results: In our patient set higher CD22-FI, defined as higher quartiles (Q2-Q4), correlated with better patient outcome in terms of CR rate, OS and DoR, compared to lower CD22-FI (Q1). CD22 blast percentage was less able to discriminate patients’ outcome, although a trend for better outcome in patients with CD22 ≥ 90% could be appreciated. Concerning gene expression profile, 32 genes with corrected p value <0.05 and absolute FC ≥2 were differentially expressed in NR as compared to R. IPA upstream regulator and regulator effect analysis individuated the inhibition of tumor suppressor HIPK2 as causal upstream condition of the downregulation of 6 DEGs. Conclusions: CD22-FI integrates CD22-percentage on leukemic blasts for a more comprehensive target pre-treatment evaluation. Moreover, a unique pattern of gene expression signature based on HIPK2 downregulation was identified, providing important insights in mechanisms of resistance to INO.

Intravesical Bacillus Calmette-guérin Efficiently Reduces P70s6k1 But Not 4e-bp1 Phosphorylation In Nonmuscle Invasive Bladder Cancer.

We characterized the functional consequences of intravesical bacillus Calmette-Guérin on the molecular mechanism of the AKT/mTOR signaling pathway in nonmuscle invasive bladder cancer. To our knowledge this has not been reported previously. At age 7 weeks female Fischer 344 rats received 1.5 mg/kg MNU intravesically every other week for 6 weeks. They were randomized at 10 per group to MNU (0.2 ml vehicle), bacillus Calmette-Guérin (10(6) cfu Connaught strain), rapamycin (15 μg/ml) and bacillus Calmette-Guérin plus simultaneous rapamycin, each intravesically for 6 weeks. At week 15 the bladders were collected for histopathology, immunohistochemistry and immunoblot to determine p-AKT, Rictor, Raptor, p-4E-BP1, p-p70S6K1, p-AMPK-α, p-mTOR and p-p53. Papillary carcinoma (pTa) and high grade intraepithelial neoplasia (pTis) predominated in the MNU group while normal urothelium, papillary and flat hyperplasia were more common in treated groups. Nonmuscle invasive bladder cancer treated with bacillus Calmette-Guérin showed suppression of p70S6K1 but not 4E-BP1 phosphorylation. This suggests that 4E-BP1 is regulated differently than p70S6K1, escaping the bacillus Calmette-Guérin action that occurs in a mTOR independent manner. The association of bacillus Calmette-Guérin with rapamycin but not rapamycin monotherapy affected p70S6K1 and 4E-BP1 phosphorylation with no features of in situ carcinoma (pTis). The activation status of p70S6K1 and 4E-BP1 might be used to stratify patients who could benefit from targeting such molecular elements with multitarget/multidrug intravesical therapy. In the future 4E-BP1 might be a worthwhile new target for bacillus Calmette-Guérin refractory nonmuscle invasive bladder cancer.

Produção de micropartículas de alginato contendo Flavobacterium columnare inativada pelo método de emulsão para vacinação de peixes por via oral

Alginate microparticles were prepared by an emulsion method aiming oral controlled release of antigens to fish. The effects of emulsification temperature and impeller type on particle morphology, average diameter, and size distribution were evaluated. Microparticles contaning formalin-killed Flavobacterium columnare cells (a model antigen) were prepared and characterized regarding bacterial release and particle stability when exposed to Nile tilapia (Oreochromis niloticus) typical gastrointestinal conditions. This methodology allowed the production of microparticles containing up to 14.3 g/L of bacterin, stable at a pH range from 2.0 to 9.0 for 12 h and smaller than 35 μm.

Perspectives of vaccination in Chagas disease revisited

The perspectives for a Chagas Disease vaccine 30 years ago and today are compared. Antigens and adjuvants have improved, but logistic problems remain the same. Sterilizing vaccines have not been produced and animal models for chronic Chagas have not been developed. Vector control has been successful and Chagas incidence has come to a halt. We do not have a population candidate to vaccination now in Brazil. And if we had, we would not know how to evaluate the success of vaccination in a short time period. A vaccine may not seem important at the moment. However, scientific reasons and incertitudes about the future recommend that a search for a vaccine be continued.

Perfil sociodemográfico e padrão de utilização dos serviços de saúde do Sistema Único de Saúde (SUS), 2003- 2008

O objetivo foi analisar a evolução do perfil de utilização de serviços de saúde, entre 2003 e 2008, no Brasil e nas suas macrorregiões. Foram utilizados dados da PNAD. A utilização de serviços de saúde foi medida pela proporção de pessoas que procuraram e foram atendidas nas 2 semanas anteriores e pelos que relataram internação nos últimos 12 meses, segundo SUS e não SUS. Foram analisadas as características socioeconômicas dos usuários, o tipo de atendimento e de serviço e os motivos da procura. A proporção de indivíduos que procuraram serviços de saúde não se alterou, assim como a parcela dos que conseguiram atendimento (96%), entre 2003 e 2008. O SUS respondeu por 56,7% dos atendimentos, realizando a maior parte das internações, vacinação e consultas e somente 1/3 das consultas odontológicas. Em 2008, manteve-se o gradiente de redução de utilização de serviços de saúde SUS conforme o aumento de renda e escolaridade. Houve decréscimo da proporção dos que procuraram serviços de saúde para ações de prevenção e aumento de procura para problemas odontológicos, acidentes e lesões e reabilitação. O padrão de utilização do SUS por região esteve inversamente relacionado à proporção de indivíduos com posse de planos privados de saúde.

Vigilância de eventos adversos pós-vacinação e segurança de programas de imunização

O objetivo da revisão foi analisar aspectos conceituais e operacionais de sistemas de vigilância de eventos adversos pós-vacina. Foram incluídos artigos disponíveis em formato eletrônico, publicados entre 1985 e 2009, selecionados nas bases Medline/PubMed, com as palavras-chave: "adverse events following vaccine", "adverse events following vaccine surveillance", "post-marketing surveillance" e "safety vaccine" e "Phase IV clinical trials", e excluídos aqueles com foco em tipos específicos desses eventos. Foram apontados os principais aspectos que justificam a importância dos eventos adversos pós-vacina em saúde pública, os instrumentos que garantem a segurança das vacinas e as finalidades, atributos, tipos, interpretações de dados, limitações e novos desafios da vigilância de eventos adversos pós-vacina, bem como estratégias para aumentar sua sensibilidade. A revisão é concluída com desafios para os próximos anos, visando à segurança e confiabilidade dos programas de vacinação.

Cobertura vacinal em menores de dois anos a partir de registro informatizado de imunização em Curitiba, PR

OBJETIVO: Avaliar o programa de imunização de crianças de 12 e de 24 meses de idade, com base no registro informatizado de imunização. MÉTODOS: Estudo descritivo em amostra probabilística de 2.637 crianças nascidas em 2002 e residentes em Curitiba, PR. As fontes de dados foram: registro informatizado de imunização do município, Sistema de Informação de Nascidos Vivos e inquérito domiciliar para casos com registro incompleto. As coberturas foram estimadas aos 12 e aos 24 meses de vida e analisadas segundo características socioeconômicas de cada distrito sanitário e o vínculo das crianças aos serviços de saúde. Foram analisadas a abrangência, completude e duplicidades do registro informatizado de imunização. RESULTADOS: A cobertura do esquema de imunização foi de 95,3% aos 12 meses sem diferenças entre os distritos e de 90,3% aos 24 meses, tendo sido mais elevada em um distrito com piores indicadores socioeconômicos (p = 0,01). A proporção de vacinas, segundo o tipo, aplicadas antes e após a idade recomendada foi de até 0,9% e até 32,2%, respectivamente. A cobertura do registro informatizado de imunização foi de 98% na amostra estudada, o sub-registro de doses de vacinas foi de 11% e a duplicidade de registro foi de 20,6%. Os grupos que apresentaram maiores coberturas foram: crianças com cadastro definitivo, aquelas com três ou mais consultas pelo Sistema Único de Saúde e as atendidas em Unidades Básicas de Saúde que adotam plenamente a Estratégia de Saúde da Família. CONCLUSÕES: A cobertura vacinal em Curitiba mostrou-se elevada e homogênea entre os distritos, e o vínculo com os serviços de saúde foi fator importante para tais resultados. O registro informatizado de imunização mostrou-se útil no monitoramento da cobertura vacinal; no entanto, é importante a prévia avaliação do seu custo-efetividade para que seja amplamente utilizado pelo Programa Nacional de Imunização.

Pathogenicity of different rabies virus isolates and protection test in vaccinated mice

This study was aimed to evaluate and compare the pathogenicity of rabies virus isolated from bats and dogs, and to verify the efficacy of a commercial rabies vaccine against these isolates. For evaluation of pathogenicity, mice were inoculated by the intramuscular route (IM) with 500MICLD50/0.03mL of the viruses. The cross-protection test was performed by vaccinating groups of mice by the subcutaneous route and challenged through the intracerebral (IC) route. Isolates were fully pathogenic when inoculated by the IC route. When inoculated intramuscularly, the pathogenicity observed showed different death rates: 60.0% for the Desmodus rotundus isolate; 50.0% for dog and Nyctinomops laticaudatus isolates; 40.0% for Artibeus lituratus isolate; 9.5% Molossus molossus isolate; and 5.2% for the Eptesicus furinalis isolate. Mice receiving two doses of the vaccine and challenged by the IC route with the isolates were fully protected. Mice receiving only one dose of vaccine were partially protected against the dog isolate. The isolates from bats were pathogenic by the IC route in mice. However, when inoculated through the intramuscular route, the same isolates were found with different degrees of pathogenicity. The results of this work suggest that a commercial vaccine protects mice from infection with bat rabies virus isolates, in addition to a canine rabies virus isolate.

Diversidade genotípica de rotavírus suínos no Estado de São Paulo

Rotavírus é uma das causas mais comuns de diarréia tanto em humanos quanto em diferentes espécies animais. Foi conduzido um estudo transversal a partir de 144 amostras fecais diarréicas colhidas de leitões, provenientes de 16 criações comerciais distribuídas por 10 municípios do Estado de São Paulo, Brasil, com o objetivo de se detectar a ocorrência de rotavírus e realizar sua caracterização molecular quanto seus genotipos G e P. Um total de 43 amostras (29,86%) foram positivas para rotavírus por Eletroforese em Gel de Poliacrilamida (PAGE) e ELISA, num esquema de triagem em paralelo. A caracterização mediante reações do tipo nested-multiplex RT-PCR demonstrou que, isoladamente, o genotipo P[6] foi o mais frequente, detectado em 25,58% das amostras, seguido pelo P[1] (11,63%) e P[7] (9,3%). Infecções concomitantes de genotipos P[6]+P[7] (9,3%), P[1]+P[6] (4,65%), P[1]+P[6]+P[7] (2,33%) foram também observadas. Analogamente, o genotipo G[5] foi detectado em 30,23% das amostras, seguido pelo G[10] (20,93%) e G[6] (4,65%) e G[5]+G[10] (18,6%). O genotipo G[5]P[6] foi o mais frequente (11,63%), porém outras combinações e amostras não tipificáveis também foram observadas. Considerando-se a diversidade de rotavírus suínos encontrada na população estudada, medidas profiláticas específicas devem levar em conta, para sua efetividade, o grau de proteção cruzada entre os genotipos presentes nas formulações vacinais e aqueles que realmente são circulantes numa região.

Comparison of agglutinating and neutralizing antibodies to serovar hardjo in sows immunized with two commercial whole culture polivalent anti-leptospira bacterins

It was performed the comparison of the intensity and duration of agglutinating and neutralizing antibodies to serovar Hardjo in swines vaccinated with two commercial anti-leptospira bacterins. Sows no reactive to 24 Leptospira sp serovars in the microscopic agglutination test (MAT) were divided in three groups: Group A (n=08): received two vaccine A doses with 30 days interval, Group B (n=08) two vaccine B doses with 30 days interval and Group C (n=08): control no vaccinated against leptospirosis.Blood samples were collected each 30 days during six months following the first vaccination. The sera were tested by MAT and growth inhibition test (GIT) to serovar Hardjo in order to evaluate respectively agglutinating and neutralizing antibodies. It was found that neutralizing antibodies persisted for a longer time than the agglutinating ones and that the absence of agglutinating antibodies does not means in the absence of the neutralizing. The peaks of agglutinating antibodies was obtained at least 30 days earlier than that produced by neutralizing. The duration of both kinds of antibodies measured differed between the two bacterines tested. The period for inducing neutralizing antibodies against serovar Hardjo indicated that gilts must be immunized with two doses of whole culture anti-leptospira bacterines applied 30 days each other at least 90 days before the first mating. For the maintenance of hight levels of neutralizing antibodies the revaccinations must be performed every six months after the first vaccination.