Differentiation of Metabolically Distinct Areas within Head and Neck Region using Dynamic 18F-FDG Positron Emission Tomography Imaging

Positron Emission Tomography (PET) using ¹⁸F-FDG is playing a vital role in the diagnosis and treatment planning of cancer. However, the most widely used radiotracer, ¹⁸F-FDG, is not specific for tumours and can also accumulate in inflammatory lesions as well as normal physiologically active tissues making diagnosis and treatment planning complicated for the physicians. Malignant, inflammatory and normal tissues are known to have different pathways for glucose metabolism which could possibly be evident from different characteristics of the time activity curves from a dynamic PET acquisition protocol. Therefore, we aimed to develop new image analysis methods, for PET scans of the head and neck region, which could differentiate between inflammation, tumour and normal tissues using this functional information within these radiotracer uptake areas. We developed different dynamic features from the time activity curves of voxels in these areas and compared them with the widely used static parameter, SUV, using Gaussian Mixture Model algorithm as well as K-means algorithm in order to assess their effectiveness in discriminating metabolically different areas. Moreover, we also correlated dynamic features with other clinical metrics obtained independently of PET imaging. The results show that some of the developed features can prove to be useful in differentiating tumour tissues from inflammatory regions and some dynamic features also provide positive correlations with clinical metrics. If these proposed methods are further explored then they can prove to be useful in reducing false positive tumour detections and developing real world applications for tumour diagnosis and contouring.

Chemical composition, acetylcholinesterase inhibitory and antifungal activities of Pera glabrata (Schott) Baill. (Euphorbiaceae)

Pera glabrata (Schott) Baill. was selected for this study after showing a preliminary positive result in a screening of Atlantic Forest plant species in the search for acetylcholinesterase inhibitors and antifungal compounds. The bioassays were conducted with crude ethanol extract of the leaves using direct bioautography method for acetylcholinesterase and antifungal activities. This extract was partitioned with hexane, chloroform and ethyl acetate solvents. The active chloroform fraction was submitted to silica gel chromatography column affording 12 groups. Caffeine, an alkaloid, which showed detection limits of 0.1 and 1.0 µg for anticholinesterasic and antifungal activities, respectively, was isolated from group nine. After microplate analyses, only groups four, nine, 10, 11 and 12 showed acetylcholinesterase inhibitory activity of 40% or higher. The group 12 was purified by preparative layer chromatography affording four sub-fractions. Two sub-fractions from this group were analyzed by gas chromatography-mass spectrometry and gas chromatography-flame ionization detector. The first sub-fraction showed anticholinesterasic activity and contained two major compounds: 9-hydroxy-4-megastigmen-3-one (84%) and caffeine (6%). The second sub-fraction presented five major compounds identified as 9-hydroxy-4-megastigmen-3-one, isololiolide, (-) loliolide, palmitic acid and lupeol and did not show activity.

Serodiagnosis of Helicobacter pylori infection by Cobas Core ELISA in adults from Minas Gerais, Brazil

We evaluated the accuracy of a 2nd generation ELISA to detect Helicobacter pylori infection in adults from a developing country in view of variations in sensitivity and specificity reported for different populations. We studied 97 non-consecutive patients who underwent endoscopy for evaluation of dispeptic symptoms. The presence of H. pylori was determined in antral biopsy specimens by culture, by the preformed urease test and in carbolfuchsin-stained smears. Patients were considered to be H. pylori positive if at least two of the three tests presented a positive result or if the culture was positive, and negative if the three tests were negative. Sixty-five adults (31 with peptic ulcer) were H. pylori positive and 32 adults were H. pylori negative. Antibodies were detected by Cobas Core anti-H. pylori EIA in 62 of 65 H. pylori-positive adults and in none of the negative adults. The sensitivity, specificity and positive and negative predictive values of the test were 95.4, 100, 100 and 91.4%, respectively. The Cobas Core anti-H. pylori EIA presented high sensitivity and specificity when employed for a population in Brazil, permitting the use of the test both to confirm the clinical diagnosis and to perform epidemiologic surveys.

Detection of cytomegalovirus infections by PCR in renal transplant patients

Cytomegalovirus (CMV) is the single most important infectious agent affecting recipients of organ transplants. To evaluate the incidence and the clinical importance of CMV infection in renal transplants in Brazil, 37 patients submitted to renal allograft transplants were tested periodically for the presence of cytomegalovirus DNA in urine using the polymerase chain reaction (PCR), and for the presence of IgM and IgG antibodies against CMV by enzyme-linked immunosorbent assay (ELISA) and indirect immunofluorescence (IIF). The PCR-amplified products were detected by gel electrophoresis and confirmed by dot-blot hybridization with oligonucleotide probes. Thirty-two of the 37 patients (86.4%) were positive by at least one of the three methods. In six patients, PCR was the only test which detected the probable CMV infection. Ten patients had a positive result by PCR before transplantation. In general, the diagnosis was achieved earlier by PCR than by serologic tests. Active infection occurred more frequently during the first four months after transplantation. Sixteen of the 32 patients (50%) with active CMV infection presented clinical symptoms consistent with CMV infection. Five patients without evidence of active CMV infection by the three tests had only minor clinical manifestations during follow-up. Our results indicate that PCR is a highly sensitive procedure for the early detection of CMV infection and that CMV infection in renal transplant patients is a frequent problem in Brazil.

Presence of the RHD pseudogene and the hybrid RHD-CE-Ds gene in Brazilians with the D-negative phenotype

The molecular basis for RHD pseudogene or RHDpsi is a 37-bp insertion in exon 4 of RHD. This insertion, found in two-thirds of D-negative Africans, appears to introduce a stop codon at position 210. The hybrid RHD-CE-Ds, where the 3' end of exon 3 and exons 4 to 8 are derived from RHCE, is associated with the VS+V- phenotype, and leads to a D-negative phenotype in people of African origin. We determined whether Brazilian blood donors of heterogeneous ethnic origin had RHDpsi and RHD-CE-Ds. DNA from 206 blood donors were tested for RHDpsi by a multiplex PCR that detects RHD, RHDpsi and the C and c alleles of RHCE. The RHD genotype was determined by comparison of size of amplified products associated with the RHD gene in both intron 4 and exon 10/3'-UTR. VS was determined by amplification of exon 5 of RHCE, and sequencing of PCR products was used to analyze C733G (Leu245Val). Twenty-two (11%) of the 206 D-negative Brazilians studied had the RHDpsi, 5 (2%) had the RHD-CE-Ds hybrid gene associated with the VS+V- phenotype, and 179 (87%) entirely lacked RHD. As expected, RHD was deleted in all the 50 individuals of Caucasian descent. Among the 156 individuals of African descent, 22 (14%) had inactive RHD and 3% had the RHD-CE-Ds hybrid gene. These data confirm that the inclusion of two different multiplex PCR for RHD is essential to test the D-negative Brazilian population in order to avoid false-positive typing of polytransfused patients and fetuses.

Newborn screening for biotinidase deficiency in Brazil: biochemical and molecular characterizations

Biotinidase deficiency is an inherited metabolic disorder characterized by neurological and cutaneous symptoms. Fortunately, it can be treated and the symptoms prevented by oral administration of the vitamin biotin. Using dried blood-soaked filter paper cards, biotinidase activity was determined in the sera of 225,136 newborns in Brazil. Mutation analysis performed on DNA from 21 babies with low serum biotinidase activity confirmed that 3 had profound biotinidase deficiency (less than 10% of mean normal sera biotinidase activity), 10 had partial biotinidase deficiency (10 to 30% of mean normal serum activity), 1 was homozygous for partial biotinidase deficiency, 4 were heterozygous for either profound or partial deficiency, and 3 were normal. Variability in serum enzyme activities and discrepancies with mutation analyses were probably due to inappropriate handling and storage of samples sent to the laboratory. Obtaining an appropriate control serum at the same time as that of the suspected child will undoubtedly decrease the false-positive rate (0.09%). Mutation analysis can be used to confirm the genotype of these children. The estimated incidence of biotinidase deficiency in Brazil is about 1 in 9,000, higher than in most other countries. Screening and treatment of biotinidase deficiency are effective and warranted. These results strongly suggest that biotinidase deficiency should be included in the newborn mass screening program of Brazil.

Leishmania infantum heat shock protein 83 for the serodiagnosis of tegumentary leishmaniasis

The serologic assay is an important tool in the diagnosis of leishmaniasis. One of the most commonly used tests is enzyme-linked immunosorbent assay (ELISA). Since total Leishmania promastigotes are used as antigen in the routine assay, false-positive reactions are frequent due to cross-reaction with sera from other diseases, mainly Chagas' disease. Therefore, an antigen that determines less cross-reactivity has been pursued for the serodiagnosis of leishmaniasis. In the present study we analyzed the use of recombinant Leishmania infantum heat shock protein (Hsp) 83 in ELISA for the serodiagnosis of cutaneous (N = 12) and mucocutaneous leishmaniasis (N = 14) and we observed the presence of anti-L. infantum Hsp 83 antibodies in all samples as well as anti-Leishmania total antigen antibodies. When cross-reactivity was tested, chronic Chagas' disease patients (N = 10) did not show any reactivity. Therefore, we consider this L. infantum Hsp 83 to be a good antigen for routine use for serodiagnosis of tegumentary leishmaniasis.

Neonatal screening for cystic fibrosis in São Paulo State, Brazil: a pilot study

Cystic fibrosis is one of the most common autosomal recessive hereditary diseases in the Caucasian population, with an incidence of 1:2000 to 1:3500 liveborns. More than 1000 mutations have been described with the most common being F508del. It has a prevalence of 23-55% within the Brazilian population. The lack of population-based studies evaluating the incidence of cystic fibrosis in São Paulo State, Brazil, and an analysis concerning the costs of implantation of a screening program motivated the present study. A total of 60,000 dried blood samples from Guthrie cards obtained from April 2005 to January 2006 for neonatal screening at 4 reference centers in São Paulo State were analyzed. The immunoreactive trypsinogen (IRT)/IRT protocol was used with the cut-off value being 70 ng/mL. A total of 532 children (0.9%) showed IRT >70 ng/mL and a 2nd sample was collected from 418 (80.3%) of these patients. Four affected children were detected at two centers, corresponding to an incidence of 1:8403. The average age at diagnosis was 69 days, and 3 of the children already showed severe symptoms of the disease. The rate of false-positive results was 95.2% and the positive predictive value for the test was 8%. The cost of detecting an affected subject was approximately US$8,000.00 when this cystic fibrosis program was added to an existing neonatal screening program. The present study clearly shows the difficulties involved in cystic fibrosis screening using the IRT/IRT protocol, particularly in a population with no long-term tradition of neonatal screening.

Generative Part-Based Gabor Object Detector

Object detection is a fundamental task of computer vision that is utilized as a core part in a number of industrial and scientific applications, for example, in robotics, where objects need to be correctly detected and localized prior to being grasped and manipulated. Existing object detectors vary in (i) the amount of supervision they need for training, (ii) the type of a learning method adopted (generative or discriminative) and (iii) the amount of spatial information used in the object model (model-free, using no spatial information in the object model, or model-based, with the explicit spatial model of an object). Although some existing methods report good performance in the detection of certain objects, the results tend to be application specific and no universal method has been found that clearly outperforms all others in all areas. This work proposes a novel generative part-based object detector. The generative learning procedure of the developed method allows learning from positive examples only. The detector is based on finding semantically meaningful parts of the object (i.e. a part detector) that can provide additional information to object location, for example, pose. The object class model, i.e. the appearance of the object parts and their spatial variance, constellation, is explicitly modelled in a fully probabilistic manner. The appearance is based on bio-inspired complex-valued Gabor features that are transformed to part probabilities by an unsupervised Gaussian Mixture Model (GMM). The proposed novel randomized GMM enables learning from only a few training examples. The probabilistic spatial model of the part configurations is constructed with a mixture of 2D Gaussians. The appearance of the parts of the object is learned in an object canonical space that removes geometric variations from the part appearance model. Robustness to pose variations is achieved by object pose quantization, which is more efficient than previously used scale and orientation shifts in the Gabor feature space. Performance of the resulting generative object detector is characterized by high recall with low precision, i.e. the generative detector produces large number of false positive detections. Thus a discriminative classifier is used to prune false positive candidate detections produced by the generative detector improving its precision while keeping high recall. Using only a small number of positive examples, the developed object detector performs comparably to state-of-the-art discriminative methods.

Toxigenic potential of Aspergillus flavus tested in different culture conditions

The objective of the present work was to evaluate the capacity of three isolates of Aspergillus flavus to produce aflatoxin under different culture conditions. This experiment was based on a 2³ factorial design, in which the independent variables were temperature (20-40 °C), incubation time (7-21 days), and the pH (2.0-6.0) in two different synthetic media. The optimal conditions were applied to non-aflatoxigenic isolates previously tested in coconut agar. Aflatoxin B1 was extracted directly from the synthetic cultures with chloroform. Thin Layer Chromatography (TLC) and Photographic Photometry were utilized to identify and quantify the compounds. Preliminary results showed that YES agar was an alternative medium for detecting the toxigenic potential of Aspergillus flavus in the following conditions: pH of 5.2, temperature of 25 °C, and incubation time of 11 days producing 206.05 ng.CFU-1 of aflatoxin B1. Of the 30 non-aflatoxigenic isolates, 12 presented a positive result in the optimal media and conditions tested.

Epstein-Barr-viruksen antigeeniosoitustestin kehittäminen

Epstein-Barr-virus (EBV) aiheuttaa mononukleoosia eli pusutautia, joka ilmenee yleensä murrosiällä tai nuorella aikuisiällä. Mononukleoosissa on tyypilliset nielutulehduksen oireet, minkä takia sitä on vaikea erottaa muiden taudinaiheuttajien aiheuttamista nielutulehduksista. Erotusdiagnostiikan käyttö nielutulehduksessa on oleellista, koska vain Streptokokki-bakteerien aiheuttamat nielutulehdukset vaativat antibioottihoitoa. Akuutin EBV-infektion pikadiagnostiikka perustuu nykyisellään infektion seurauksena muodostuvien heterofiilisten vasta-aineiden mittaamiseen verestä. Niiden mittaamisessa on useita ongelmia, koska useilla lapsilla niitä ei muodostu lainkaan ja vanhemmillakin niitä muodostuu yleensä vasta viikon päästä mononukleoosin oireiden alkamisesta. Mittaamalla EBV:n antigeeneja saataisiin positiivinen testitulos vasta-ainetestiä nopeammin. EBV:lle ei ole kuitenkaan kehitetty antigeeniosoitustestiä todennäköisesti siksi, että EBV:n erittymisen terveiden viruksen kantajien limakalvoille uskotaan olevan ongelma antigeenitestauksessa. Diplomityön tavoitteena oli kehittää akuutin EBV-infektion pikadiagnostiikkaan soveltuva limakalvonäytteestä tehtävä immunometrinen antigeeniosoitustesti. Työssä kehitettiin uusia polyklonaalisia vasta-aineita sekä testattiin kaupallisia vasta-aineita. Vasta-aineiden toimintaa tutkittiin immunomäärityksissä kokonaista EBV:ta ja puhdistettuja proteiiniantigeeneja vastaan. Monoklonaalisten vasta-aineiden kehitys lopetettiin ennen varsinaista tuottoa, koska ensin kehitetyt polyklonaaliset vasta-aineet eivät tunnistaneet natiivia virusta vaan pelkästään immunisointeihin käytetyt rekombinanttiset kohdeproteiinit. Kaupallisista vasta-aineista yhdellä onnistuttiin kehittämään tiettävästi maailman ensimmäinen immunometrinen EBV-antigeeniosoitustesti, jossa saatiin tunnistus sekä natiivilla EBV:lla että puhdistetulla proteiiniantigeenilla. Testin herkkyys proteiiniantigeenilla oli hyvä (4 pM) ja puhdistetulla EBV-virusvalmisteellakin todennäköisesti riittävä (6,2×106 viruspartikkelia/ml) kliiniseen diagnostiikkaan. Testillä ei kuitenkaan saatu suppeasta mononukleoosipotilaiden nielunäyteaineistosta yhtään EBV-positiivista tulosta. Referenssiksi tilatut PCR-testit osoittivat näytteiden EBV-pitoisuuksien olevan liian alhaisia osoitettavaksi kehitetyllä EBV-antigeeniosoitustestillä. PCR-testauksessa mononukleoosipotilaiden nielunäytteistä osoitettujen alhaisten EBV-määrien perusteella spekuloitiin, että olisiko edustavin näytteenottopaikka akuutissa EBV-infektiossa sittenkin nielun sijaan nenänielu. Myös kirjallisuudesta löytyi tälle tukea. EBV-antigeeniosoitustestin osoitettiin toimivan hyvin standardinäyte-materiaalilla. Testikehitysprojektin jatkon kannalta oleellista on kuitenkin vielä selvittää laajemmalla kliinisellä näyteaineistolla, mistä EBV:n antigeeneja pitäisi osoittaa akuutissa EBV-infektiossa ja ovatko niiden pitoisuudet riittävän korkeita.

Conformational analysis of antibody binding site using EDMA methods /

Euclidean distance matrix analysis (EDMA) methods are used to distinguish whether or not significant difference exists between conformational samples of antibody complementarity determining region (CDR) loops, isolated LI loop and LI in three-loop assembly (LI, L3 and H3) obtained from Monte Carlo simulation. After the significant difference is detected, the specific inter-Ca distance which contributes to the difference is identified using EDMA.The estimated and improved mean forms of the conformational samples of isolated LI loop and LI loop in three-loop assembly, CDR loops of antibody binding site, are described using EDMA and distance geometry (DGEOM). To the best of our knowledge, it is the first time the EDMA methods are used to analyze conformational samples of molecules obtained from Monte Carlo simulations. Therefore, validations of the EDMA methods using both positive control and negative control tests for the conformational samples of isolated LI loop and LI in three-loop assembly must be done. The EDMA-I bootstrap null hypothesis tests showed false positive results for the comparison of six samples of the isolated LI loop and true positive results for comparison of conformational samples of isolated LI loop and LI in three-loop assembly. The bootstrap confidence interval tests revealed true negative results for comparisons of six samples of the isolated LI loop, and false negative results for the conformational comparisons between isolated LI loop and LI in three-loop assembly. Different conformational sample sizes are further explored by combining the samples of isolated LI loop to increase the sample size, or by clustering the sample using self-organizing map (SOM) to narrow the conformational distribution of the samples being comparedmolecular conformations. However, there is no improvement made for both bootstrap null hypothesis and confidence interval tests. These results show that more work is required before EDMA methods can be used reliably as a method for comparison of samples obtained by Monte Carlo simulations.

Dépistage de la prééclampsie au premier trimestre de la grossesse

OBJECTIF: évaluer un modèle prédictif de prééclampsie associant des marqueurs cliniques, biologiques (Inhibine A, PP-13, hCG, ADAM12, PAPP-A et PlGF) et du Doppler des artères utérines (DAU) au 1er trimestre de la grossesse. METHODE : étude prospective de cohorte de 893 nullipares chez qui DAU et prélèvement sanguin étaient réalisés à 11-14 semaines. RESULTATS : 40 grossesses se sont compliquées de prééclampsie (4,5%) dont 9 de prééclampsie précoce (1,0%) et 16 de prééclampsie sévère (1,8%). Le meilleur modèle prédictif de la prééclampsie sévère associait les marqueurs cliniques, PAPP-A et PlGF (taux de détection 87,5% pour 10% de faux positif). Le DAU étant corrélé à la concentration de PAPP-A (r=-0,117 ; p<0,001), il n’améliorait pas la modélisation. CONCLUSION : la combinaison de marqueurs cliniques et biologiques (PlGF et PAPP-A) au 1er trimestre permet un dépistage performant de la prééclampsie sévère. Le DAU n’est pas un instrument efficace de dépistage au 1er trimestre dans cette population.

Caractérisation de l’infection naturelle à Cryptosporidium spp. chez le chien et le chat vus en établissement vétérinaire

Cryptosporidium spp. est un protozoaire parasite du système gastro-intestinal largement répandu chez les vertébrés et causant la cryptosporidiose, une zoonose occasionnant des troubles digestifs sévères pouvant entrainer la mort chez les individus immunodéficients. Au Canada, la déclaration de cette maladie est obligatoire depuis l’an 2000. Ainsi, il est pertinent de mieux comprendre l’infection chez les animaux de compagnie, puisqu’ils sont potentiellement un réservoir du parasite. Durant l’année 2008, des échantillons fécaux provenant de 1 202 chats (n = 371) et chiens (n = 831) de la province du Québec ont été analysés par comptage des ookystes de Cryptosporidium spp. au moyen de la technique de centrifugation en solution de sulfate de zinc. Dans cette étude,la prévalence de Cryptosporidium spp. chez les chats (28/371 : 7,55 %) et chez les chiens(88/831 : 10,59 %) de compagnie confirme leur potentiel en tant que réservoir du parasite. Au Québec, de par leur nombre, les chats sont potentiellement un réservoir zoonotique du parasite plus important que celui des chiens, bien qu’il n’existe pas de différence significative entre la prévalence du parasite chez le chat et le chien pour l’année 2008. L’âge (p = 0,0001) et l’infection concomitante par Giardia spp. (p = 0,0001) se sont avérés être des facteurs associés avec la présence de Cryptosporidium spp. chez le chien. Parmi l’ensemble des variables testées chez le chat (l’âge, le sexe, la saison et l’infection concomitante par Giardia spp.), aucune n’a été associée de manière significative à la présence du parasite chez le chat. Ceci peut être dû au nombre limité d’individus testés pour cette espèce. Un suivi de l’excrétion des ookystes de Cryptosporidium spp. chez deux chats suggère que l’excrétion des ookystes peut se faire sur une période de sept mois et que le taux d’excrétion varie dans le temps. Le diagnostic moléculaire des espèces et génotypes de Cryptosporidium spp. isolés à partir des échantillons de matières fécales devait être réalisé par la technique de PCR emboîtée des fragments des gènes ARNr 18S et HSP70 et du séquençage des produits de PCR. Aucun résultat positif n’a toutefois été obtenu. Afin d’augmenter la puissance statistique des analyses épidémiologiques sur la prévalence de Cryptosporidium spp., il serait nécessaire à l’avenir de travailler sur un nombre d’animaux beaucoup plus important.

Vulnérabilité, observance et adhésion thérapeutique : quels risques? : la prévention de la tuberculose chez les enfants immigrants à Montréal

Si le nombre de nouveaux cas de tuberculose au Québec a considérablement baissé au cours des dernières décennies, l’épidémiologie mondiale rappelle toutefois que cette maladie est responsable de plus de deux millions de morts par an. Au Canada, certains groupes seraient plus vulnérables, notamment les immigrants provenant de pays où la tuberculose est endémique. La Clinique de tuberculose du Centre hospitalier universitaire Sainte-Justine est un outil de lutte active contre cette maladie, entre autres grâce à son programme de dépistage scolaire auprès des enfants immigrants. Ce dépistage vise à identifier les porteurs de la tuberculose latente, c’est-à-dire la forme non contagieuse de la maladie. Un traitement préventif de neuf mois est offert aux enfants qui présentent un résultat positif afin de prévenir le développement de la tuberculose maladie (forme active). Dans 28 % des cas, ce traitement n’est pas adéquatement complété et dans 11 % des cas, il est refusé. La présente étude porte à la fois sur la question de l’observance thérapeutique et sur les conditions de vie post-migratoires. L’observation de consultations à la Clinique de tuberculose et les entrevues auprès des soignants et des familles ont engendré une réflexion sur la prévention de la tuberculose en contexte migratoire de même que sur le caractère multifactoriel de la non-observance thérapeutique. L’analyse des données fait ressortir l’impact du vécu migratoire et des conditions de vie (le logement, l’emploi, la maîtrise de la langue, etc.) sur la prise irrégulière du médicament, permettant une meilleure compréhension de ce comportement (chapitre 4). Il a également été possible de documenter une distinction entre les conduites (l’observance) et les attitudes (l’adhésion) nuançant la compréhension des diverses trajectoires thérapeutiques à l’aide de rationalités plurielles et diversifiées (chapitres 5 et 6). Il s’en dégage une réflexion sur le caractère normatif de la catégorisation de « groupe » et de « comportement » à risque laissant place aux différents univers référentiels et, plus globalement, aux conditions de vie des familles (chapitre 7).