Supporting content-based image retrieval and computer-aided diagnosis systems with association rule-based techniques

In this work, we take advantage of association rule mining to support two types of medical systems: the Content-based Image Retrieval (CBIR) systems and the Computer-Aided Diagnosis (CAD) systems. For content-based retrieval, association rules are employed to reduce the dimensionality of the feature vectors that represent the images and to improve the precision of the similarity queries. We refer to the association rule-based method to improve CBIR systems proposed here as Feature selection through Association Rules (FAR). To improve CAD systems, we propose the Image Diagnosis Enhancement through Association rules (IDEA) method. Association rules are employed to suggest a second opinion to the radiologist or a preliminary diagnosis of a new image. A second opinion automatically obtained can either accelerate the process of diagnosing or to strengthen a hypothesis, increasing the probability of a prescribed treatment be successful. Two new algorithms are proposed to support the IDEA method: to pre-process low-level features and to propose a preliminary diagnosis based on association rules. We performed several experiments to validate the proposed methods. The results indicate that association rules can be successfully applied to improve CBIR and CAD systems, empowering the arsenal of techniques to support medical image analysis in medical systems. (C) 2009 Elsevier B.V. All rights reserved.

Relationship between serum and saliva antibodies to Candida and isolation of Candida species from the mucosa of HIV-infected individuals

Colonisation and infection by Candida species occur frequently in acquired immunodeficiency syndrome (AIDS), but their relationship to the humoral immunity against candidiasis is controversial. To evaluate the levels of antibodies to Candida in the serum and in the saliva of HIV-1-infected patients in relation to the presence of immunodeficiency, oral candidiasis and Candida colonisation, Candida was investigated in the urine and in the oral and anal mucosae of HIV-1-infected patients, AIDS patients and healthy controls. The levels of IgG, IgM and IgA antibodies to Candida were determined in the serum and in the saliva by immunoassay. Candida species were detected in 76% of the patients. Mucosal yeast colonisation and the levels of serum and saliva antibodies to Candida were similar between asymptomatic HIV-infected and non-infected patients. Mucosal colonisation was highest in AIDS patients, who also had higher serum IgA and saliva IgG antibodies. Antibody levels were similar in patients with and without candidiasis oral lesions. Asymptomatic HIV-infected individuals are similar to non-infected individuals with respect to mucosal colonisation as well as serum and saliva levels of antibodies to Candida. The higher mucosal colonisation and clinical candidiasis observed in the AIDS patients apparently stimulated a more intense humoral response to the yeast.

Isolation and characterization of microsatellite markers from the stingless bee Nannotrigona testaceicornis

Conservation of natural populations and handling of breeding programs would benefit from the availability of molecular markers. Stingless bees are one of the most important pollinators in several ecosystems. Thus, seventeen microsatellite markers were developed from an enriched genomic library of Nannotrigona testaceicornis. They were characterized using 50 samples. The expected and observed heterozygosities ranged from 0.59 to 0.89 and from 0.39 to 0.79, respectively. These markers will contribute to advance researches on the genetic conservation, characterization and preservation of the Brazilian native bees.

Inhibition of Snake Venoms and Phospholipases A(2) by Extracts from Native and Genetically Modified Eclipta alba: Isolation of Active Coumestans

We genetically modified Eclipta alba using Agrobacterium rhizogenes LBA 9402, with the aim of producing secondary metabolites with pharmacological properties against phospholipase A(2) and the myotoxic activities of snake venom. Extracts from in natura aerial parts and roots, both native and genetically modified (in vitro), were prepared and analysed by high-performance liquid chromatography. In natura materials showed the coumestan wedelolactone at higher concentration in the aerial parts, while demethylwedelolactone appeared at higher concentration in roots. Among the modified roots, clone 19 showed higher concentrations of these coumestans. Our results show that the in natura extracts of plants collected from Botucatu and Ribeirao Preto were efficient in inhibiting snake venom phospholipase A(2) activity. Regarding in vitro material, the best effect against Crotalus durissus terrificus venom was that of clone 19. Clone 19 and isolated coumestans (wedelolactone and demethylwedelolactone) inhibited the myotoxic activity induced by basic phospholipases A(2) isolated from the venoms of Crotalus durissus terrificus (CB) and Bothrops jararacussu (BthTX-I and II). The search for antivenom is justified by the need of finding active principles that are more efficient in neutralizing snake venoms and also as an attempt to complement serum therapy.

Isolation of transcripts overexpressed in the human pathogen Trichophyton rubrum grown in lipid as carbon source

Trichophyton rubrum is the most common etiological agent of human dermatophytosis. Despite the incidence and medical importance of this dermatophyte, little is known about the mechanisms of host invasion and pathogenicity. Host invasion depends on the adaptive cellular responses of the pathogen that allow it to penetrate the skin layers, which are mainly composed of proteins and lipids. In this study, we used suppression subtractive hybridization to identify transcripts over-expressed in T rubrum cultured in lipid as carbon source. Among the subtractive cDNA clones isolated, 85 clones were positively screened by cDNA array dot blotting and were sequenced. The putative proteins encoded by the isolated transcripts showed similarities to fungal proteins involved in metabolism, signaling, defense, and virulence, such as the MDR/ABC transporter, glucan 1,3-beta-glucosidase, chitin synthase B, copper-sulfate-regulated protein, and serine/threonine phosphatase (calcineurin A). These results provide the first molecular insight into the genes differentially expressed during the adaptation of T. rubrum to a lipidic carbon source.

Performance of a chromogenic medium for the isolation of Listeria monocytogenes in food

According to the producers, CHROMagar (TM) Listeria medium comes to facilitate the detection, differentiating Listeria monocytogenes from the other species, directly on the isolation process, allowing final results in 72 h, while the traditional method takes up to 10 days. A total of 120 food samples of sliced cooked ham, ground beef and frankfurters was analyzed. From 151 colonies presenting typical L. monocytogenes characteristics on CHROMagar (TM) Listeria (bluish, surrounded by a white halo), only 95 (62.9%) were confirmed as L. monocytogenes. The medium was highly sensitive to detect L. monocytogenes in ground beef and frankfurter, but not in sliced ham. (c) 2007 Elsevier Ltd. All rights reserved.

Impact of implementing an exclusively dedicated respiratory isolation room in a Brazilian tertiary emergency department

Background Occupational risk due to airborne disease challenges healthcare institutions. Environmental measures are effective but their cost-effectiveness is still debatable and most of the capacity planning is based on occupational rates. Better indices to plan and evaluate capacity are needed. Goal To evaluate the impact of installing an exclusively dedicated respiratory isolation room (EDRIR) in a tertiary emergency department (ED) determined by a time-to-reach-facility method. Methods A group of patients in need of respiratory isolation were first identified-group I (2004; 29 patients; 44.1 +/- 3.4 years) and the occupational rate and time intervals (arrival to diagnosis, diagnosis to respiratory isolation indication and indication to effective isolation) were determined and it was estimated that adding an EDRIR would have a significant impact over the time to isolation. After implementing the EDRIR, a second group of patients was gathered in the same period of the year-group II (2007; 50 patients; 43.4 +/- 1.8 years) and demographic and functional parameters were recorded to evaluate time to isolation. Cox proportional hazard models adjusted for age, gender and inhospital respiratory isolation room availability were obtained. Results Implementing an EDRIR decreased the time from arrival to indication of respiratory isolation (27.5 +/- 9.3 X 3.7 +/- 2.0; p = 0.0180) and from indication to effective respiratory isolation (13.3 +/- 3.0 X 2.94 +/- 1.06; p = 0.003) but not the respiratory isolation duration and total hospital stay. The impact on crude isolation rates was very significant (8.9 X 75.4/100.000 patients; p < 0.001). The HR for effective respiratory isolation was 26.8 (95% CI 7.42 to 96.9) p < 0.001 greater for 2007. Conclusion Implementing an EDRIR in a tertiary ED significantly reduced the time to respiratory isolation.

First isolation and molecular characterization of Ehrlichia canis in Costa Rica, Central America

The present study investigated Ehrlichia species in blood samples from dogs suspected of clinical ehrlichiosis, using molecular and isolation techniques in cell culture. From a total of 310 canine blood samples analyzed by 16S rRNA nested PCR, 148 (47.7%) were positive for Ehrlichia canis. DNA from Ehrlichia chaffeensis or Ehrlichia ewingii was not detected in any sample using species-specific primers in separated reactions. Leukocytes from five PCR-positive dogs were inoculated into DH82 cells; successful isolation of E. canis was obtained in four samples. Partial sequence of the dsb gene of eight canine blood samples (including the five samples for in vitro isolation) was obtained by PCR and their analyses through BLAST showed 100% of identity with the corresponding sequence of E. canis in GenBank. This study represents the first molecular diagnosis, isolation, and molecular characterization of E. canis in dogs from Costa Rica. (C) 2010 Elsevier Ltd. All rights reserved.

Ticks (Acari : ixodidae) infesting wild birds in an Atlantic forest area in the state of Sao Paulo, Brazil, with isolation of Rickettsia from the tick Amblyomma longirostre

During field work in Nazare Paulista, state of Sao Paulo, Brazil, we found 13 (56.5%) of 23 birds (mostly Passeriformes) to be infested by 28 larvae and I nymph of Amblyomma spp. Two larvae were reared to the adult stage, being taxonomically identified as Amblyomma parkeri Fonseca and Aragao, whereas five larvae and one nymph were identified as Amblyomma longirostre Koch. All six A. longirostre specimens were shown to be infected by rickettsia, as demonstrated by polymerase chain reaction (PCR) targeting two rickettsial genes (gltA and ompA) or isolation of rickettsia in cell culture from one of the ticks. This isolate was designated as strain AL, which was established in Vero cell culture and was molecularly characterized by DNA sequencing fragments of the rickettsial genes gltA, htrA, ompA, and ompB. Phylogenetic analyses inferred from ompA and ompB partial sequences showed a high degree of similarity of strain AL with Rickettsia sp. strain ARANHA, previously detected by PCR in A. longirostre ticks from Rondonia, northern Brazil. We conclude that strain AL is a new rickettsia genotype belonging to the same species of strain ARANHA, which are closely related to Candidatus `R. amblyomniii`. Further studies should elucidate if strains AL and ARANHA are different strains of Candidatus `R. amblyommii` or are a new species.

Rickettsial infections of dogs, horses and ticks in Juiz de Fora, southeastern Brazil, and isolation of Rickettsia rickettsii from Rhipicephalus sanguineus ticks

The present study was performed in an area endemic for Brazilian spotted fever (BSF) in Juiz de Fora, state of Minas Gerais, Brazil, during the years 2007 and 2008, when fatal cases of BSF (caused by Rickettsia rickettsii) were reported. Adult ticks (Acari: Ixodidae) identified as Rhipicephalus sanguineus (Latreille) and Amblyomma cajennense (Fabricius) were collected from dogs and horses, respectively, and tested by polymerase chain reaction (PCR). Overall, 13.1% of the Rh. sanguineus ticks and none of the A. cajennense were found to be infected with R. rickettsii. Two isolates of R. rickettsii were successfully established in Vero cell culture from two Rh. sanguineus ticks. An indirect immunofluorescence assay (IFA) using R. rickettsii antigens detected blood serological reaction to R. rickettsii in 67.9% (53/78) of dogs and 41.0% (16/39) of horses living in the study area. Larval offspring from two Rh. sanguineus engorged females, naturally infected by R. rickettsii, were reared to adult stage in the laboratory. All active stages (larvae, nymphs, adults) remained 100% infected by R. rickettsii, which was efficiently transmitted to naive rabbits. Overall, the results of the present study indicate a potential risk for transmission of R. rickettsii to humans by Rh. sanguineus, an occurrence yet to be documented in Brazil.

Isolation and partial characterization of Brazilian samples of feline immunodeficiency virus

Feline immunodeficiency virus (FIV) causes a slow progressive degeneration of the immune system which eventually leads to a disease comparable to acquired immune deficiency syndrome (AIDS) in humans. FIV has extensive sequence variation, a typical feature of lentiviruses. Sequence analysis showed that diversity was not evenly distributed throughout the genome, but was greatest in the envelope gene, env. The virus enters host cells via a sequential interaction, initiated by the envelope glycoprotein (env) binding the primary receptor molecule CD134 and followed by a subsequent interaction with chemokine co-receptor CXCR4. The purpose of this study was to isolate and characterize isolates of FIV from an open shelter in Sao Paulo, Brazil. The separated PBMC from 11 positive cats were co-cultured with MYA-1 cells. Full-length viral env glycoprotein genes were amplified and determined. Chimeric feline x human CD134 receptors were used to investigate the receptor utilization of 17 clones from Brazilian isolates of Fly. Analyses of the sequence present of molecular clones showed that all clones grouped within subtype B. In contrast to the virulent primary isolate FIV-GL8, expression of the first cysteine-rich domain (CRD1) of feline CD134 in the context of human CD134 was sufficient for optimal receptor function for all Brazilian FIV isolates tested. (C) 2011 Elsevier B.V. All rights reserved.

Isolation and genetic characterisation of Toxoplasma gondii from a red-handed howler monkey (Alouatta belzebul), a jaguarundi (Puma yagouaroundi), and a black-eared opossum (Didelphis aurita) from Brazil

Toxoplasma gondii isolates are highly diverse in domestic animals from Brazil. However, little is known about the genetics of this parasite from wild mammals in the same region. Reveal genetic similarity or difference of T. gondii among different animal populations is necessary for us to understand transmission of this parasite. Here we reported isolation and genetic characterisation of three T. gondii isolates from wild animals in Brazil. The parasite was isolated by bioassay in mice from tissues of a young male red handed howler monkey (Alouatta belzebul), an adult male jaguarundi (Puma yagouaroundi), and an adult female black-eared opossum (Didelphis aurita). The monkey and the jaguarundi had inhabited the Zoo of Parque Estadual Dois Irmaos, Pernambuco State, Northeastern Brazil, for 1 year and 8 years, respectively. The wild black-eared opossum was captured in Sao Paulo State, Southeastern Brazil, and euthanised for this study because it was seropositive for T. gondii (titre 1:100 by the modified agglutination test, MAT). Ten PCR-RFLP (Polymerase Chain Reaction-Restriction Fragment Length Polymorphism) markers, SAG1, SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1 and Apico, were used to genotype the isolates. T. gondii was isolated from the brain and heart homogenate of the monkey, the muscle homogenate of the jaguarundi, and the heart homogenate of the black-eared opossum. This was the first isolation of T. gondii from a neotropical fetid from Brazil. The isolate from the monkey (TgRhHmBr1) was not virulent in mice, whereas the isolates from the jaguarundi (TgJagBr1) and the black-eared opossum (TgOpBr1) were virulent in mice. The genotype of the isolate from the monkey has been identified in isolates from a goat and ten chickens in the same region of Brazil, suggesting that it may be a common lineage circulating in this region. The genotypes of the isolates from the jaguarundi and the black-eared opossum have not been previously reported. Although there are already 88 genotypes identified from a variety of animal hosts in Brazil, new genotypes are continuously being identified from different animal species, indicating an extremely high diversity of T. gondii in the population. (C) 2010 Elsevier B.V. All rights reserved.

Micromorphology of Resin-Dentin Interfaces Using One-Bottle Etch&Rinse and Self-Etching Adhesive Systems on Laser-Treated Dentin Surfaces: A Confocal Laser Scanning Microscope Analysis

Background and Objectives: This study evaluated the hybrid layer (HL) morphology created by three adhesive systems (AS) on dentin surfaces treated with Er:YAG laser using two irradiation parameters. Study Design: Occlusal flat dentin surfaces of 36 human third molars were assigned into nine groups (n = 4) according to the following ASs: one bottle etch&rinse Single Bond Plus (3M ESPE), two-step Clearfil Protect Bond (Kuraray), and all-in-one S3 Bond (Kuraray) self-etching, which were labeled with rhodamine B or fluorescein isothiocyanate dextran and were applied to dentin surfaces that were irradiated with Er:YAG laser at either 120 (38.7 J/cm(2)) or 200 mJ/pulse (64.5 J/cm(2)), or were applied to untreated dentin surfaces (control group). The ASs were light-activated following MI and the bonded surfaces were restored with resin composite Z250 (3M ESPE). After 24 hours of storage in vegetable oil, the restored teeth were vertically, serially sectioned into 1-mm thick slabs, which had the adhesive interfaces analyzed with confocal laser microscope (CLSM-LSM 510 Meta). CLSM images were recorded in the fluorescent mode from three different regions along each bonded interface. Results: Non-uniform HL was created on laser-irradiated dentin surfaces regardless of laser irradiation protocol for all AS, while regular and uniform HL was observed in the control groups. ""Stretch mark""-like red lines were found within the HL as a result of resin infiltration into dentin microfissures, which were predominantly observed in 200 mJ/pulse groups regardless of AS. Poor resin infiltration into peritubular dentin was observed in most regions of adhesive interfaces created by all ASs on laser-irradiated dentin, resulting in thin resin tags with neither funnel-shaped morphology nor lateral resin projections. Conclusion: Laser irradiation of dentin surfaces at 120 or 200 mJ/pulse resulted in morphological changes in HL and resin tags for all ASs evaluated in the study. Lasers Surg. Med. 42:662-670, 2010. (C) 2010 Wiley-Liss, Inc.

Evaluation of three different adhesive systems using a bacterial method to develop secondary caries in vitro

Purpose: To assess the effects of three different dental adhesive systems on the formation of secondary root caries, in vitro, with a standardized interfacial gap in a filled cavity model. Methods: 40 sound human molars were selected and randomly assigned to four experimental groups: Clearfil SE Bond (CSEB), Xeno III (X-III), Scotchbond Multi-Purpose Plus (SBMP) and negative control (NC) without an adhesive system. After the standardized Class V cavity preparations on the buccal and lingual surfaces, restorations were placed with resin composite (Filtek Z250) using a standardized interfacial gap, using a 3 x 2 mm piece of 50 mu m metal matrix. The teeth were sterilized with gamma irradiation and exposed to a cariogenic challenge using a bacterial system with Streptococcus mutans. Depth and extension of wall lesions formed and the depth of outer lesions were measured by software coupled with light microscopy. Results: For wall lesion extension the ANOVA test showed differences between groups except between X-HI and SBMP (P= 0.294). The Tukey`s test of confidence intervals indicated smaller values for the CSEB group than for the others. For wall lesion depth the CSEB group also presented the smallest mean values of wall lesion depth when compared to the others (P< 0.0001) for all comparisons using Tukey`s test. Regarding outer lesion depth, all adhesives showed statistically similar behavior. SEM evaluation of the morphologic appearance of caries lesions confirmed the statistical results showing small caries lesion development for cavities restored with CSEB adhesive system, which may suggest that this adhesive system interdiffusion zone promoted a good interaction with subjacent dentin protecting the dental tissues from recurrent caries. (Am J Dent 2010;23:93-97).

Qualitative Analysis of the Removal of the Smear Layer in the Apical Third of Curved Roots: Conventional Irrigation versus Activation Systems

Introduction: The aim of this study was to evaluate the effectiveness of different irrigant agitation techniques on smear layer removal in curved root canals. Methods: Mesiobuccal canals of 62 extracted lower molars with a curvature of 33 degrees were used and instrumented up to Pro Taper F2. The samples were divided into 3 experimental groups according to the final irrigation: conventional irrigation, ultrasonic irrigation, and sonic irrigation by using the Endo Activator system. The control group was composed of 2 specimens without any final irrigation. In all of the experimental groups, 5 mL of 17% ethylenediaminetetraacetic acid was used for 1 minute, and 5 mL of 2.5% NaOCl was used for 30 seconds. The analysis of the apical region was performed via scanning electron microscopy by 3 examiners. The data were submitted to the Kruskal-Wallis and Dunn tests (P<.05). Results: The activation systems removed significantly more smear layer than did conventional irrigation. Conclusions: Sonic and ultrasonic irrigation resulted in better removal of the smear layer in the apical third of curved root canals than did conventional irrigation. (J Endod 2011;37:1268-1271)