Avaliação da atividade antiviral dos compostos do esmalte de unha (acetato de etila e acetato de butila) no herpesvírus bovino tipo 5

Pós-graduação em Enfermagem - FMB

Intensidade do estresse hídrico modula a expressão de aquaporinas durante a reidratação em Sorghum bicolor

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Fatores ergonômicos críticos de mochos odontológicos e sua relação com a produtividade e satisfação de cirurgiões dentistas

The purpose of the ergonomics is to generate adequate working conditions, by the correct use of equipment and appropriate anatomic positions. Ergonomics has become essential in the dentist's life while in the dental practice. The misuse of equipment in performing tasks or the wrong choice of equipment can initiate various problems like back pain, bursitis, repetitive strain injury (RSI), limitation of movement, and stress. Using a survey that was implemented with professional dentists linked to Paulista Association of Dental Surgeons (APCD) and graduate students at the Universidade Estadual Paulista (UNESP) in the São José dos Campos (SP) region, this study intends to propose an adequate research instrument to identify ergonomic critical factors of dental stools and their relation to productivity and satisfaction of dentists. The survey was developed with Google Docs Forms tool and was designed by analysis of other studies, existing surveys and other papers in this area. Relevant content were discussed and developed questions about the stool used by dentists in their activities, the occurrence of any problems arising from the exercise of their profession and the views of respondents about the influence of using the dental stool in these cited problems as well as their productivity. Due to obstacles encountered during the project, particularly bureaucratic issues, the survey cannot be implemented as needed, resulting in a test with reduced number of answers. The users' opinion varies according to the stool used, bringing some difficulty to generalizing the answers, but if treated properly, it is possible to obtain relevant conclusions about the main aspects perceived by users in relation to the stool and the needs pointed as most important

Importância da resposta auditiva de estado estável no diagnóstico da surdez em lactentes com risco para a deficiência auditiva: correlações com os achados do potencial evocado auditivo de tronco encefálico

Pós-graduação em Bases Gerais da Cirurgia - FMB

Fatores ergonômicos críticos de mochos odontológicos e sua relação com a produtividade e satisfação de cirurgiões dentistas

The purpose of the ergonomics is to generate adequate working conditions, by the correct use of equipment and appropriate anatomic positions. Ergonomics has become essential in the dentist's life while in the dental practice. The misuse of equipment in performing tasks or the wrong choice of equipment can initiate various problems like back pain, bursitis, repetitive strain injury (RSI), limitation of movement, and stress. Using a survey that was implemented with professional dentists linked to Paulista Association of Dental Surgeons (APCD) and graduate students at the Universidade Estadual Paulista (UNESP) in the São José dos Campos (SP) region, this study intends to propose an adequate research instrument to identify ergonomic critical factors of dental stools and their relation to productivity and satisfaction of dentists. The survey was developed with Google Docs Forms tool and was designed by analysis of other studies, existing surveys and other papers in this area. Relevant content were discussed and developed questions about the stool used by dentists in their activities, the occurrence of any problems arising from the exercise of their profession and the views of respondents about the influence of using the dental stool in these cited problems as well as their productivity. Due to obstacles encountered during the project, particularly bureaucratic issues, the survey cannot be implemented as needed, resulting in a test with reduced number of answers. The users' opinion varies according to the stool used, bringing some difficulty to generalizing the answers, but if treated properly, it is possible to obtain relevant conclusions about the main aspects perceived by users in relation to the stool and the needs pointed as most important

Importância da resposta auditiva de estado estável no diagnóstico da surdez em lactentes com risco para a deficiência auditiva: correlações com os achados do potencial evocado auditivo de tronco encefálico

Pós-graduação em Bases Gerais da Cirurgia - FMB

Complete denture wear during sleep in elderly sleep apnea patients-a preliminary study

There is no consensus in the literature about the impact of complete denture wear on obstructive sleep apnea (OSA). The goal of this randomized clinical study was to assess if complete denture wear during sleep interferes with the quality of sleep. Elderly edentulous OSA patients from a complete denture clinic were enrolled and received new complete dentures. An objective sleep analysis was determined with polysomnography performed at the sleep laboratory for all patients who slept either with or without their dentures. Twenty-three patients (74% females) completed the study with a mean age of 69.6 years and a mean body mass index of 26.7 kg/m(2). The apnea and hypopnea index (AHI) was significantly higher when patients slept with dentures compared to without (25.9 +/- 14.8/h vs. 19.9 +/- 10.2/h; p > 0.005). In the mild OSA group, the AHI was significantly higher when patients slept with the dentures (16.6 +/- 6.9 vs. 8.9 +/- 2.4; p < 0.05), while in moderate to severe OSA patients, the AHI was not significantly different when sleeping with dentures (.30.8 +/- 15.6 vs. 25.7 +/- 7.5; p = 0.2). The supine AHI in mild patients was related to a higher increase in AHI while wearing dentures (12.7 +/- 8.4/h vs. 51.9 +/- 28.6/h; p < 0.001). A limitation of the study is that the mild OSA patients had a higher BMI when compared to the moderate to severe OSA patients. Ten out of 14 patients who preferred to sleep with their upper and lower dentures showed an increase in their AHI while wearing dentures to sleep. Contrary to previous studies, we found that OSA patients may experience more apneic events if they sleep with their dentures in place. Specifically, in mild OSAS patients, the use of dentures substantially increases the AHI especially when in the supine position.

Motion-based wave estimation: Small-scale tests with a crane-barge model

This paper provides additional validation to the problem of estimating wave spectra based on the first-order motions of a moored vessel. Prior investigations conducted by the authors have attested that even a large-volume ship, such as an FPSO unit, could be adopted for on-board estimation of the wave field. The obvious limitation of the methodology concerns filtering of high-frequency wave components, for which the vessel has no significant response. As a result, the estimation range is directly dependent on the characteristics of the vessel response. In order to extend this analysis, further small-scale tests were performed with a model of a pipe-laying crane-barge. When compared to the FPSO case, the results attest that a broader range of typical sea states can be accurately estimated, including crossed-sea states with low peak periods. (C) 2012 Elsevier Ltd. All rights reserved.

Do changes in carbon allocation account for the growth response to potassium and sodium applications in tropical Eucalyptus plantations?

Understanding the underlying mechanisms that account for the impact of potassium (K) fertilization and its replacement by sodium (Na) on tree growth is key to improving the management of forest plantations that are expanding over weathered tropical soils with low amounts of exchangeable bases. A complete randomized block design was planted with Eucalyptus grandis (W. Hill ex Maiden) to quantify growth, carbon uptake and carbon partitioning using a carbon budget approach. A combination of approaches including the establishment of allometric relationships over the whole rotation and measurements of soil CO2 efflux and aboveground litterfall at the end of the rotation were used to estimate aboveground net production (ANPP), total belowground carbon flux and gross primary production (GPP). The stable carbon isotope (delta C-13) of stem wood alpha-cellulose produced every year was used as a proxy for stomatal limitation of photosynthesis. Potassium fertilization increased GPP and decreased the fraction of carbon allocated belowground. Aboveground net production was strongly enhanced, and because leaf lifespan increased, leaf biomass was enhanced without any change in leaf production, and wood production (P-W) was dramatically increased. Sodium application decreased the fraction of carbon allocated belowground in a similar way, and enhanced GPP, ANPP and P-W, but to a lesser extent compared with K fertilization. Neither K nor Na affected delta C-13 of stem wood alpha-cellulose, suggesting that water-use efficiency was the same among the treatments and that the inferred increase in leaf photosynthesis was not only related to a higher stomatal conductance. We concluded that the response to K fertilization and Na addition on P-W resulted from drastic changes in carbon allocation.

Cardiovascular autonomic dysfunction in sickle cell anemia

Sickle cell anemia (SCA) is associated to increased cardiac output, normal heart rate (HR), abnormal QT dispersion and lower diastolic blood pressure (DBP). The mechanisms are still unknown. The objective of this study was to test the hypothesis that there is cardiovascular autonomic dysfunction (CAD) in SCA. The secondary objectives were to distinguish the roles of chronic anemia and hemoglobinopathy and to evaluate the predominance of the sympathetic or parasympathetic systems in the pathogenesis of CAD. Sixteen subjects with SCA, 13 with sickle cell trait (SCT), 13 with iron deficiency anemia (IDA), and 13 healthy volunteers (HV) were evaluated. All subjects were submitted to 24 h-electrocardiogram (24 h-ECG), plasma norepinephrine (NE) measurement before and after isometric exercise (IE), and also Valsalva maneuver (VM), diving maneuver (DV), and tilt test (TT). Baroreflex sensitivity (BRS) was also evaluated. The minimum, average and maximum HR as well as the percentage of bradycardia and tachycardia at 24-h ECG were similar in all groups. NE at baseline and after IE did not differ between groups. The SCA group showed less bradycardia at phase IV of VM, less bradycardia during DV, and also less tachycardia and lower DBP during TT. BRS for bradycardia and tachycardia reflex was decreased in the SCA and SCT groups. In conclusion, 1) there is CAD in SCA, and it is characterized by the reduction of BRS and the limitation of HR modulation mediated by the parasympathetic system; 2) cardiovascular sympathetic activity is preserved in SCA; and 3) hemoglobinopathy is the preponderant ethiopathogenic factor. (C) 2011 Elsevier B.V. All rights reserved.

Prevalência de infecção pelo T. cruzi em doadores de sangue nos hemocentros coordenadores do Brasil em 2007

Objetivo: conhecer a prevalência de Trypanosoma cruzi entre os doadores de sangue, analisar a organização da rede de hemoterapia e as normas de segurança do sangue para transfusão no Brasil no ano de 2007. Métodos: estudo descritivo utilizando-se os Regulamentos Técnicos para hemoterapia definidos pela Agência Nacional de Vigilância Sanitária (Anvisa) e o questionário aplicado aos Hemocentros Coordenadores (HC) do Brasil. Resultados: responderam 84% dos hemocentros, onde doaram sangue 3.251.361 indivíduos, sendo 1.192 (0,04%) excluídos na triagem clínica por risco presumido para doença de Chagas; foram realizadas 2.726.668 sorologias; 5.432 (0,20%) foram reagentes para Trypanosoma cruzi e 3.065 (0,11%) inconclusivas. Conclusão: a falta de resposta dos Estados de Pernambuco, Bahia, Paraíba, Goiás e Rondônia constituiu limitação ao estudo; entretanto, os resultados obtidos sugerem baixa prevalência de Trypanosoma cruzi entre os doadores de sangue e indicam o cumprimento dos procedimentos para a segurança do sangue definidos pela Anvisa.

Air to muscle O2 delivery during exercise at altitude

[EN] Hypoxia-induced hyperventilation is critical to improve blood oxygenation, particularly when the arterial Po2 lies in the steep region of the O2 dissociation curve of the hemoglobin (ODC). Hyperventilation increases alveolar Po2 and, by increasing pH, left shifts the ODC, increasing arterial saturation (Sao2) 6 to 12 percentage units. Pulmonary gas exchange (PGE) is efficient at rest and, hence, the alveolar-arterial Po2 difference (Pao2-Pao2) remains close to 0 to 5mm Hg. The (Pao2-Pao2) increases with exercise duration and intensity and the level of hypoxia. During exercise in hypoxia, diffusion limitation explains most of the additional Pao2-Pao2. With altitude, acclimatization exercise (Pao2-Pao2) is reduced, but does not reach the low values observed in high altitude natives, who possess an exceptionally high DLo2. Convective O2 transport depends on arterial O2 content (Cao2), cardiac output (Q), and muscle blood flow (LBF). During whole-body exercise in severe acute hypoxia and in chronic hypoxia, peak Q and LBF are blunted, contributing to the limitation of maximal oxygen uptake (Vo2max). During small-muscle exercise in hypoxia, PGE is less perturbed, Cao2 is higher, and peak Q and LBF achieve values similar to normoxia. Although the Po2 gradient driving O2 diffusion into the muscles is reduced in hypoxia, similar levels of muscle O2 diffusion are observed during small-mass exercise in chronic hypoxia and in normoxia, indicating that humans have a functional reserve in muscle O2 diffusing capacity, which is likely utilized during exercise in hypoxia. In summary, hypoxia reduces Vo2max because it limits O2 diffusion in the lung.

Impatto di rifaximina sul microbiota intestinale: selezione di bifidobatteri antibiotico resistenti

The ideal approach for the long term treatment of intestinal disorders, such as inflammatory bowel disease (IBD), is represented by a safe and well tolerated therapy able to reduce mucosal inflammation and maintain homeostasis of the intestinal microbiota. A combined therapy with antimicrobial agents, to reduce antigenic load, and immunomodulators, to ameliorate the dysregulated responses, followed by probiotic supplementation has been proposed. Because of the complementary mechanisms of action of antibiotics and probiotics, a combined therapeutic approach would give advantages in terms of enlargement of the antimicrobial spectrum, due to the barrier effect of probiotic bacteria, and limitation of some side effects of traditional chemiotherapy (i.e. indiscriminate decrease of aggressive and protective intestinal bacteria, altered absorption of nutrient elements, allergic and inflammatory reactions). Rifaximin (4-deoxy-4’-methylpyrido[1’,2’-1,2]imidazo[5,4-c]rifamycin SV) is a product of synthesis experiments designed to modify the parent compound, rifamycin, in order to achieve low gastrointestinal absorption while retaining good antibacterial activity. Both experimental and clinical pharmacology clearly show that this compound is a non systemic antibiotic with a broad spectrum of antibacterial action, covering Gram-positive and Gram-negative organisms, both aerobes and anaerobes. Being virtually non absorbed, its bioavailability within the gastrointestinal tract is rather high with intraluminal and faecal drug concentrations that largely exceed the MIC values observed in vitro against a wide range of pathogenic microorganisms. The gastrointestinal tract represents therefore the primary therapeutic target and gastrointestinal infections the main indication. The little value of rifaximin outside the enteric area minimizes both antimicrobial resistance and systemic adverse events. Fermented dairy products enriched with probiotic bacteria have developed into one of the most successful categories of functional foods. Probiotics are defined as “live microorganisms which, when administered in adequate amounts, confer a health benefit on the host” (FAO/WHO, 2002), and mainly include Lactobacillus and Bifidobacterium species. Probiotic bacteria exert a direct effect on the intestinal microbiota of the host and contribute to organoleptic, rheological and nutritional properties of food. Administration of pharmaceutical probiotic formula has been associated with therapeutic effects in treatment of diarrhoea, constipation, flatulence, enteropathogens colonization, gastroenteritis, hypercholesterolemia, IBD, such as ulcerative colitis (UC), Crohn’s disease, pouchitis and irritable bowel syndrome. Prerequisites for probiotics are to be effective and safe. The characteristics of an effective probiotic for gastrointestinal tract disorders are tolerance to upper gastrointestinal environment (resistance to digestion by enteric or pancreatic enzymes, gastric acid and bile), adhesion on intestinal surface to lengthen the retention time, ability to prevent the adherence, establishment and/or replication of pathogens, production of antimicrobial substances, degradation of toxic catabolites by bacterial detoxifying enzymatic activities, and modulation of the host immune responses. This study was carried out using a validated three-stage fermentative continuous system and it is aimed to investigate the effect of rifaximin on the colonic microbial flora of a healthy individual, in terms of bacterial composition and production of fermentative metabolic end products. Moreover, this is the first study that investigates in vitro the impact of the simultaneous administration of the antibiotic rifaximin and the probiotic B. lactis BI07 on the intestinal microbiota. Bacterial groups of interest were evaluated using culture-based methods and molecular culture-independent techniques (FISH, PCR-DGGE). Metabolic outputs in terms of SCFA profiles were determined by HPLC analysis. Collected data demonstrated that rifaximin as well as antibiotic and probiotic treatment did not change drastically the intestinal microflora, whereas bacteria belonging to Bifidobacterium and Lactobacillus significantly increase over the course of the treatment, suggesting a spontaneous upsurge of rifaximin resistance. These results are in agreement with a previous study, in which it has been demonstrated that rifaximin administration in patients with UC, affects the host with minor variations of the intestinal microflora, and that the microbiota is restored over a wash-out period. In particular, several Bifidobacterium rifaximin resistant mutants could be isolated during the antibiotic treatment, but they disappeared after the antibiotic suspension. Furthermore, bacteria belonging to Atopobium spp. and E. rectale/Clostridium cluster XIVa increased significantly after rifaximin and probiotic treatment. Atopobium genus and E. rectale/Clostridium cluster XIVa are saccharolytic, butyrate-producing bacteria, and for these characteristics they are widely considered health-promoting microorganisms. The absence of major variations in the intestinal microflora of a healthy individual and the significant increase in probiotic and health-promoting bacteria concentrations support the rationale of the administration of rifaximin as efficacious and non-dysbiosis promoting therapy and suggest the efficacy of an antibiotic/probiotic combined treatment in several gut pathologies, such as IBD. To assess the use of an antibiotic/probiotic combination for clinical management of intestinal disorders, genetic, proteomic and physiologic approaches were employed to elucidate molecular mechanisms determining rifaximin resistance in Bifidobacterium, and the expected interactions occurring in the gut between these bacteria and the drug. The ability of an antimicrobial agent to select resistance is a relevant factor that affects its usefulness and may diminish its useful life. Rifaximin resistance phenotype was easily acquired by all bifidobacteria analyzed [type strains of the most representative intestinal bifidobacterial species (B. infantis, B. breve, B. longum, B. adolescentis and B. bifidum) and three bifidobacteria included in a pharmaceutical probiotic preparation (B. lactis BI07, B. breve BBSF and B. longum BL04)] and persisted for more than 400 bacterial generations in the absence of selective pressure. Exclusion of any reversion phenomenon suggested two hypotheses: (i) stable and immobile genetic elements encode resistance; (ii) the drug moiety does not act as an inducer of the resistance phenotype, but enables selection of resistant mutants. Since point mutations in rpoB have been indicated as representing the principal factor determining rifampicin resistance in E. coli and M. tuberculosis, whether a similar mechanism also occurs in Bifidobacterium was verified. The analysis of a 129 bp rpoB core region of several wild-type and resistant bifidobacteria revealed five different types of miss-sense mutations in codons 513, 516, 522 and 529. Position 529 was a novel mutation site, not previously described, and position 522 appeared interesting for both the double point substitutions and the heterogeneous profile of nucleotide changes. The sequence heterogeneity of codon 522 in Bifidobacterium leads to hypothesize an indirect role of its encoded amino acid in the binding with the rifaximin moiety. These results demonstrated the chromosomal nature of rifaximin resistance in Bifidobacterium, minimizing risk factors for horizontal transmission of resistance elements between intestinal microbial species. Further proteomic and physiologic investigations were carried out using B. lactis BI07, component of a pharmaceutical probiotic preparation, as a model strain. The choice of this strain was determined based on the following elements: (i) B. lactis BI07 is able to survive and persist in the gut; (ii) a proteomic overview of this strain has been recently reported. The involvement of metabolic changes associated with rifaximin resistance was investigated by proteomic analysis performed with two-dimensional electrophoresis and mass spectrometry. Comparative proteomic mapping of BI07-wt and BI07-res revealed that most differences in protein expression patterns were genetically encoded rather than induced by antibiotic exposure. In particular, rifaximin resistance phenotype was characterized by increased expression levels of stress proteins. Overexpression of stress proteins was expected, as they represent a common non specific response by bacteria when stimulated by different shock conditions, including exposure to toxic agents like heavy metals, oxidants, acids, bile salts and antibiotics. Also, positive transcription regulators were found to be overexpressed in BI07-res, suggesting that bacteria could activate compensatory mechanisms to assist the transcription process in the presence of RNA polymerase inhibitors. Other differences in expression profiles were related to proteins involved in central metabolism; these modifications suggest metabolic disadvantages of resistant mutants in comparison with sensitive bifidobacteria in the gut environment, without selective pressure, explaining their disappearance from faeces of patients with UC after interruption of antibiotic treatment. The differences observed between BI07-wt e BI07-res proteomic patterns, as well as the high frequency of silent mutations reported for resistant mutants of Bifidobacterium could be the consequences of an increased mutation rate, mechanism which may lead to persistence of resistant bacteria in the population. However, the in vivo disappearance of resistant mutants in absence of selective pressure, allows excluding the upsurge of compensatory mutations without loss of resistance. Furthermore, the proteomic characterization of the resistant phenotype suggests that rifaximin resistance is associated with a reduced bacterial fitness in B. lactis BI07-res, supporting the hypothesis of a biological cost of antibiotic resistance in Bifidobacterium. The hypothesis of rifaximin inactivation by bacterial enzymatic activities was verified by using liquid chromatography coupled with tandem mass spectrometry. Neither chemical modifications nor degradation derivatives of the rifaximin moiety were detected. The exclusion of a biodegradation pattern for the drug was further supported by the quantitative recovery in BI07-res culture fractions of the total rifaximin amount (100 μg/ml) added to the culture medium. To confirm the main role of the mutation on the β chain of RNA polymerase in rifaximin resistance acquisition, transcription activity of crude enzymatic extracts of BI07-res cells was evaluated. Although the inhibition effects of rifaximin on in vitro transcription were definitely higher for BI07-wt than for BI07-res, a partial resistance of the mutated RNA polymerase at rifaximin concentrations > 10 μg/ml was supposed, on the basis of the calculated differences in inhibition percentages between BI07-wt and BI07-res. By considering the resistance of entire BI07-res cells to rifaximin concentrations > 100 μg/ml, supplementary resistance mechanisms may take place in vivo. A barrier for the rifaximin uptake in BI07-res cells was suggested in this study, on the basis of the major portion of the antibiotic found to be bound to the cellular pellet respect to the portion recovered in the cellular lysate. Related to this finding, a resistance mechanism involving changes of membrane permeability was supposed. A previous study supports this hypothesis, demonstrating the involvement of surface properties and permeability in natural resistance to rifampicin in mycobacteria, isolated from cases of human infection, which possessed a rifampicin-susceptible RNA polymerase. To understand the mechanism of membrane barrier, variations in percentage of saturated and unsaturated FAs and their methylation products in BI07-wt and BI07-res membranes were investigated. While saturated FAs confer rigidity to membrane and resistance to stress agents, such as antibiotics, a high level of lipid unsaturation is associated with high fluidity and susceptibility to stresses. Thus, the higher percentage of saturated FAs during the stationary phase of BI07-res could represent a defence mechanism of mutant cells to prevent the antibiotic uptake. Furthermore, the increase of CFAs such as dihydrosterculic acid during the stationary phase of BI07-res suggests that this CFA could be more suitable than its isomer lactobacillic acid to interact with and prevent the penetration of exogenous molecules including rifaximin. Finally, the impact of rifaximin on immune regulatory functions of the gut was evaluated. It has been suggested a potential anti-inflammatory effect of rifaximin, with reduced secretion of IFN-γ in a rodent model of colitis. Analogously, it has been reported a significant decrease in IL-8, MCP-1, MCP-3 e IL-10 levels in patients affected by pouchitis, treated with a combined therapy of rifaximin and ciprofloxacin. Since rifaximin enables in vivo and in vitro selection of Bifidobacterium resistant mutants with high frequency, the immunomodulation activities of rifaximin associated with a B. lactis resistant mutant were also taken into account. Data obtained from PBMC stimulation experiments suggest the following conclusions: (i) rifaximin does not exert any effect on production of IL-1β, IL-6 and IL-10, whereas it weakly stimulates production of TNF-α; (ii) B. lactis appears as a good inducer of IL-1β, IL-6 and TNF-α; (iii) combination of BI07-res and rifaximin exhibits a lower stimulation effect than BI07-res alone, especially for IL-6. These results confirm the potential anti-inflammatory effect of rifaximin, and are in agreement with several studies that report a transient pro-inflammatory response associated with probiotic administration. The understanding of the molecular factors determining rifaximin resistance in the genus Bifidobacterium assumes an applicative significance at pharmaceutical and medical level, as it represents the scientific basis to justify the simultaneous use of the antibiotic rifaximin and probiotic bifidobacteria in the clinical treatment of intestinal disorders.

New approaches to open problems in gene expression microarray data

In the past decade, the advent of efficient genome sequencing tools and high-throughput experimental biotechnology has lead to enormous progress in the life science. Among the most important innovations is the microarray tecnology. It allows to quantify the expression for thousands of genes simultaneously by measurin the hybridization from a tissue of interest to probes on a small glass or plastic slide. The characteristics of these data include a fair amount of random noise, a predictor dimension in the thousand, and a sample noise in the dozens. One of the most exciting areas to which microarray technology has been applied is the challenge of deciphering complex disease such as cancer. In these studies, samples are taken from two or more groups of individuals with heterogeneous phenotypes, pathologies, or clinical outcomes. these samples are hybridized to microarrays in an effort to find a small number of genes which are strongly correlated with the group of individuals. Eventhough today methods to analyse the data are welle developed and close to reach a standard organization (through the effort of preposed International project like Microarray Gene Expression Data -MGED- Society [1]) it is not unfrequant to stumble in a clinician's question that do not have a compelling statistical method that could permit to answer it.The contribution of this dissertation in deciphering disease regards the development of new approaches aiming at handle open problems posed by clinicians in handle specific experimental designs. In Chapter 1 starting from a biological necessary introduction, we revise the microarray tecnologies and all the important steps that involve an experiment from the production of the array, to the quality controls ending with preprocessing steps that will be used into the data analysis in the rest of the dissertation. While in Chapter 2 a critical review of standard analysis methods are provided stressing most of problems that In Chapter 3 is introduced a method to adress the issue of unbalanced design of miacroarray experiments. In microarray experiments, experimental design is a crucial starting-point for obtaining reasonable results. In a two-class problem, an equal or similar number of samples it should be collected between the two classes. However in some cases, e.g. rare pathologies, the approach to be taken is less evident. We propose to address this issue by applying a modified version of SAM [2]. MultiSAM consists in a reiterated application of a SAM analysis, comparing the less populated class (LPC) with 1,000 random samplings of the same size from the more populated class (MPC) A list of the differentially expressed genes is generated for each SAM application. After 1,000 reiterations, each single probe given a "score" ranging from 0 to 1,000 based on its recurrence in the 1,000 lists as differentially expressed. The performance of MultiSAM was compared to the performance of SAM and LIMMA [3] over two simulated data sets via beta and exponential distribution. The results of all three algorithms over low- noise data sets seems acceptable However, on a real unbalanced two-channel data set reagardin Chronic Lymphocitic Leukemia, LIMMA finds no significant probe, SAM finds 23 significantly changed probes but cannot separate the two classes, while MultiSAM finds 122 probes with score >300 and separates the data into two clusters by hierarchical clustering. We also report extra-assay validation in terms of differentially expressed genes Although standard algorithms perform well over low-noise simulated data sets, multi-SAM seems to be the only one able to reveal subtle differences in gene expression profiles on real unbalanced data. In Chapter 4 a method to adress similarities evaluation in a three-class prblem by means of Relevance Vector Machine [4] is described. In fact, looking at microarray data in a prognostic and diagnostic clinical framework, not only differences could have a crucial role. In some cases similarities can give useful and, sometimes even more, important information. The goal, given three classes, could be to establish, with a certain level of confidence, if the third one is similar to the first or the second one. In this work we show that Relevance Vector Machine (RVM) [2] could be a possible solutions to the limitation of standard supervised classification. In fact, RVM offers many advantages compared, for example, with his well-known precursor (Support Vector Machine - SVM [3]). Among these advantages, the estimate of posterior probability of class membership represents a key feature to address the similarity issue. This is a highly important, but often overlooked, option of any practical pattern recognition system. We focused on Tumor-Grade-three-class problem, so we have 67 samples of grade I (G1), 54 samples of grade 3 (G3) and 100 samples of grade 2 (G2). The goal is to find a model able to separate G1 from G3, then evaluate the third class G2 as test-set to obtain the probability for samples of G2 to be member of class G1 or class G3. The analysis showed that breast cancer samples of grade II have a molecular profile more similar to breast cancer samples of grade I. Looking at the literature this result have been guessed, but no measure of significance was gived before.

Knowledge management in intelligent tutoring systems

In the last years, Intelligent Tutoring Systems have been a very successful way for improving learning experience. Many issues must be addressed until this technology can be defined mature. One of the main problems within the Intelligent Tutoring Systems is the process of contents authoring: knowledge acquisition and manipulation processes are difficult tasks because they require a specialised skills on computer programming and knowledge engineering. In this thesis we discuss a general framework for knowledge management in an Intelligent Tutoring System and propose a mechanism based on first order data mining to partially automate the process of knowledge acquisition that have to be used in the ITS during the tutoring process. Such a mechanism can be applied in Constraint Based Tutor and in the Pseudo-Cognitive Tutor. We design and implement a part of the proposed architecture, mainly the module of knowledge acquisition from examples based on first order data mining. We then show that the algorithm can be applied at least two different domains: first order algebra equation and some topics of C programming language. Finally we discuss the limitation of current approach and the possible improvements of the whole framework.