964 resultados para alignment-free methods


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Free-living adult Amblyomma incisum ticks were collected in an Atlantic rainforest area at Intervales State Park, State of Sao Paulo, Brazil. From an A. incisum specimen, rickettsiae were successfully isolated in Vero cell culture by the shell vial technique. Rickettsial isolation was confirmed by optical microscopy, transmission electron microscopy, and PCRs targeting portions of the rickettsial genes gltA, htrA, rrs, and sca1 on infected cells. Fragments of 1,089, 457, 1,362, and 443 nucleotides of the gltA, htrA, rrs, and sca1 genes, respectively, were sequenced. By BLAST analysis, the partial sequence of rrs of the A. incisum rickettsial isolate was closest to the corresponding sequence of Rickettsia bellii (99.1% similarity). The gltA partial sequence was closest to the corresponding sequences of ""Candidatus Rickettsia tarasevichiae"" (96.1% similarity) and Rickettsia canadensis (95.8% similarity). The htrA partial sequence was closest to the corresponding sequence of R. canadensis (89.8% similarity). The sca1 partial sequence was closest to the corresponding sequence of R. canadensis (95.2% similarity). Since our rickettsial isolate was genetically distinct from other Rickettsia species, we propose a new species designated Rickettsia monteiroi sp. nov. Phylogenetic analyses indicated that R. monteiroi belongs to the canadensis group within the genus Rickettsia, together with the species R. canadensis and ""Candidatus R. tarasevichiae"". Little or no antibody cross-reaction was observed between sera of R. monteiroi-inoculated guinea pigs and R. bellii-, Rickettsia rickettsii-, or R. canadensis-inoculated guinea pigs.

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A standardised nested-PCR method that amplifies a region of the glycoprotein E gene of avian infectious laryngotracheitis virus (ILTV) has been developed for the diagnosis of infection by Gallid herpesvirus 1. The two sets of primers employed produced the expected ampIification products of 524bp(externa I primers) and 219bp (internal primers) in the presence of ILTV DNA, whereas no Such amplicons were obtained with other avian respiratory pathogens or with DNA extracted from the cells of uninfected chickens. The identity of the 219bp amplified product was con firmed by DNA sequencing. The standardised nested-PCR method detected ILTV DNA from trachea, lung, conjunctiva and trigeminal ganglia samples from flocks of birds with and without clinical signs. and showed hi.-h sensitivity (95.4%) and specificity (93.1%) when compared with the reference test involving virus isolation in specific-pathogen-free chicken embryos. The standardised nested-PCR method described may be used to detect clinical and latent ILTV infections, and will be of significant value for both diagnostic and epidemiological Studies. (c) 2008 Elsevier B.V. All rights reserved.

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Simple, rapid and stable sperm evaluation methods which have been optimized for common marmoset (Callithrix jacchus) are critical for studies involving collection and evaluation of sperm in the field. This is particularly important for new species groups such as Callitrichidae where the sperm have been little studied. Of this family, C jacchus is the best known, and has been chosen as a model species for other members of the genus Callithrix. The fundamental evaluation parameters for sperm of any species are viability and acrosomal status. Semen samples were collected by penile vibratory stimulation. To evaluate sperm plasma membrane integrity, Eosin-Nigrosin was tested here for the common marmoset sperm to be used under field conditions. Further, a non-fluorescent stain for acrosome, the ""Simple"" stain, developed for domestic and wild cats, was tested on common marmoset sperm. This was compared with a fluorescent staining, Fluorescein isothiocyanate-Pisum sativum agglutinin (FITC-PSA), routinely used and validated for common marmoset at the German Primate Centre to evaluate acrosomal integrity. Results obtained with the ""Simple"" stain showed a marked differentiation between sperm with intact and non-intact acrosome both with and without ionophore treatment and closely correlated with results obtained with FITC-PSA. Temperature had no effect on the results with the ""Simple"" stain and the complete processing is simple enough to be carried out under field conditions. These findings indicated that the ""Simple"" stain and Eosin-Nigrosin provide rapid and accurate results for C. jacchus sperm and that those methods can be reliably used as field tools for sperm evaluation for this species. (c) 2008 Elsevier Inc. All rights reserved.

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Non-invasive techniques such as the measurement of fecal steroids are now widely used to monitor reproductive hormones in captive and free-ranging wild-life. These methods offer great advantages and deserve to be used in domestic animals. The aim of the present study was to determine the endocrine profile of dairy goats throughout pregnancy by the quantification of fecal progestins and estrogens and assess its con-elation with serum concentrations. Blood and fecal samples were collected weekly from I I adult, multiparous goats, from mating through pregnancy and 2 weeks post-partum. The extraction of estradiol and progesterone fecal metabolites was performed by dilution in ethanol. The radioimmunoassay (RIA) in solid phase was used to quantify serum 17 beta-estradiol (estradiol) and progesterone, as well as their fecal metabolites. The mean concentrations of both fecal and serum estradiol started to increase between weeks 7 and 11, reached peak values near parturition and then decreased sharply (range: 19.8 +/- 5.8 ng/g of feces to 608.6 +/- 472.4 ng/g of feces and 0.007 +/- 0.005 ng/ml to 0.066 +/- 0.024 ng/ml). An increase in both fecal and blood progestagens occurred in the second week, mean concentrations remained greater until week 20, and then decreased in the last week of gestation and 2 weeks post-partum (range: 108.8 +/- 43.6 ng/g of feces to 3119.5 +/- 2076.9 ng/g of feces and 0. 12 +/- 0.04 ng/ml to 13.10 +/- 4.29 ng/ml). The changes in blood and fecal hormone concentrations were analyzed and compared throughout gestation for each single goat, for each breed and for the whole group. Results indicated that matched values of serum and fecal hormone concentrations were correlated (r = 0.79; p < 0.001 for progesterone and r = 0.84;p < 0.001 for estradiol mean concentrations in the whole group). Regression analysis showed that logarithmic model allows significant prediction of serum from fecal concentrations with an R-2 = 0.729 (y = 0.013 1n x - 0.021) for estradiol and R-2 = 0.788 (y = 3.835 1n x - 18.543) for progesterone. Neither fecal nor serum concentrations were affected by the breed but a significant effect of the number of fetuses on progestin concentrations was found. Therefore, the profiles of progesterone and estradiol fecal metabolites reflect the serum concentrations of the same hormones in pregnant goats. (C) 2006 Elsevier B.V. All rights reserved.

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In wild and domestic birds, cryptosporidiosis is often associated with infections by Cryptosporidium galli, Cryptosporidium baileyi and Cryptosporidium meleagridis. In addition to these species, a number of avian Cryptosporidium species yet to be fully characterized are commonly found among exotic and wild avian isolates. The present study aimed to detect and identify samples of Cryptosporidium spp. from free-living wild birds, in order to contribute to the knowledge of the variability of this parasite in the free-living population of Brazil. Stool samples were collected from 242 birds, with the following proportions of individuals: 50 Emberizidae (20.7%), 112 Psittacidae (46.3%), 44 Cardinalidae (18.2%), 12 Turdidae (5.0%), eight Ramphastidae (3.3%), seven Icteridae (2.9%), three Estrilididae (1.2%), two Contigidae (0.8%), two Thraupidae (0.8%) and two Fringilidae (0.8%). Among the 242 fecal samples from wild birds, 16(6.6%) were positive for the presence of oocysts of Cryptosporidium. Molecular characterization of the 16 samples of Cryptosporidium, were performed with phylogenetic reconstructions employing 292 positions of 18S rDNA. None of the samples of birds was characterized as C meleagridis. C gall was identified in one rufous-bellied thrush (Turdus rufiventris), five green-winged saltators (Saltator similis), one slate-coloured seedeater (Sporophila schistacea), one goldfinch (Carduelis carduelis) and three saffron finches (Sicalis flaveola). One goldfinch isolate, one buff-fronted seedeater (Sporophila frontalis), one red-cowled cardinal (Paroaria dominicana) and one other saffron finch (S. flaveola) were identified as C. baileyi. Avian genotype II was found in an isolate from a white-eyed parakeet (Aratinga leucophthalma). Clinical symptoms of cryptosporidiosis in birds have already been described and the number of wild birds which were shedding parasites was high. Therefore, further epidemiological research and disease surveillance of birds in the wild is warranted. (C) 2010 Elsevier B.V. All rights reserved.

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From September 2000 to January 2002, a serologic survey was conducted in a population of free-ranging Brazilian tapirs (Tapirus terrestris) inhabiting Emas National Park and surrounding areas in Goias state. central Brazil, as part of an ecologic study. Ten tapirs were immobilized with a tiletamine-zolazepam combination. and blood samples were collected. All sera were negative for Leptospira spp.. Brucella abortus, and equine infectious anemia; and one of 10 animals was positive for Toxoplasma goudii. This report represents the first serologic survey for selected infectious diseases in a free-ranging population or Brazilians tapirs in central Brazil.

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Purpose: The Gow-Gates technique is said to have several advantages over traditional techniques to achieve mandibular nerve anesthesia; however, its routine use is quite limited, mainly due to complications during visual alignment of reference landmarks. The purpose of this study was to verify the validity and accuracy of a new method to reach the injection site. Material and Methods: Fifteen magnetic resonance images were captured. Distances from the ideal injection point in the condylar neck (puncture ideal) to the injection points located in the a and 0 plane intersection (Puncture Gow-Gates and puncture modified) were measured and compared. Results: Positive and significant (P <= .003) Pearson correlations between landmarks and injection points confirmed the validity of the modified technique. Paired t test showed that the segment line puncture ideal-puncture modified, 5.17 mm, was 3 times shorter (P < .001) than the segment line puncture ideal-puncture Gow-Gates, 17.91 mm. As calculated by linear regression, establishing the injection point of the modified technique depended only on the anteroposterior and lateromedial condyle positions. Conclusions: The modified technique proved to be valid and precise and has a determined and an effective injection site. (C) 2009 American Association of Oral and Maxillofacial Surgeons J Oral Maxillofac Surg 67:2609-2616, 2009

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Introduction: There is ongoing debate regarding the ideal sequence, volume, and concentration of irrigants, length of time for irrigation, and irrigation technique to achieve debridement of the root canal system. The aim of this study was to verify the impact of the final rinse technique on smear layer removal ability of 17% ethylenediaminetetraacetic acid (EDTA). Methods: Sixteen single-rooted human teeth were instrumented and divided into 2 groups at the final rinse step according to the following final rinse techniques used: continuous rinse group, continuous rinse with EDTA during 3 minutes, and rinse and soaking group, rinse with 1 mL of EDTA, soaking of the canal for 2 minutes and 30 seconds, and rinse completion with the remaining 4 mL for 30 seconds. The specimens were split lengthwise and observed under scanning electron microscope. Results: Data were analyzed with Kruskal-Wallis and Dunn tests. The continuous rinse group presented more debris-free surfaces when compared with the rinse and soaking group (P <. 01). When the root canal areas were compared within the groups, no statistical differences were found (P > .05). Conclusions: It can be concluded that a continuous rinse with 5 mL of EDTA for 3 minutes can more efficiently remove the smear layer from root canal walls. (J Endod 2010;36:512-514)

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Objective: This study aimed to analyze in vitro inhibitory effects of restorative materials containing the antibacterial monomer 12-methacryloyloxydodecylpyridinium bromide (MDPB) on the formation of artificial secondary root caries lesions. Methods: Class V cavities (2 mm x 2 mm) were prepared in 75 human root fragments. Specimens were randomly divided into five groups (n = 15 fragments per group) and restored as follows: (I) MDPB-free adhesive system + MDPB-free composite (negative control); (II) resin modified glass ionomer (RM-GIC; positive control); (III) MDPB-free adhesive system + MDPB-containing composite (2.83% MDPB); (IV) MDPB-containing adhesive system + MDPB-free composite; M MDPB-containing adhesive system + MDPB-containing composite. Artificial secondary root caries lesions were produced by a biological artificial caries challenge. The restored specimens were immersed into a culture medium containing Streptococcus mutans and sucrose for 15 days. Histological slices (80 +/- 20 mu m) of the specimens were used for measuring the mean depths of the artificial lesions produced in both margins of the restorations using polarized light microscopy. Results were expressed in percentage related to the mean depth of the negative control, considered 100%. Data were compared by ANOVA followed by the Tukey`s test (p <= 0.05). Results: The depths of lesions adjacent to cavities filled with RM-GIC (GII; 85.17 +/- 15.2%) were significantly (p < 0.01) shallower than those adjacent to restorations with MDPB-free composite (GI; 100.00 +/- 10.04%), despite the presence of MDPB in the adhesive system (GIV; 101.95 +/- 21.32%). The depths of lesions adjacent to cavities restored with MDPB-containing composite (GIII; 82.68 +/- 12.81% and GV; 85.65 +/- 15.42%), despite the adhesive system used, were similar to those of RM-GIC (GII). Mean lesions depths in these groups decreased from 13% (GV) to 17% (GIII) in relation to the negative control (GI). Conclusions: MDPB-containing composite inhibits the progression of artificial secondary root caries lesions regardless of adhesive systems. (C) 2009 Elsevier Ltd. All rights reserved.

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Purpose: To evaluate the impact of adjuvant chemotherapy on the outcome of osteosarcoma of the extremities, and to identify prognostic factors using the expression of adenomatous polyposis coli (APC), cadherin and beta-catenin Wnt-signalling markers. Methods: The clinical, demographic, anatomic and pathological factors including a detailed analysis of the immunohistochemical expression of cadherin, B-catenin and APC were retrospectively examined in 97 patients with osteosarcoma of the extremities (metastatic and non-metastatic at diagnosis), treated with surgery and/or chemotherapy from 1985 to 2000. Results: APC immunoreactivity showed a statistically significant association with age and serum alkaline phosphatase levels (p = 0.025 and p = 0.038). When survival was the end-point of multivariate analysis, race segregated patients with poor survival as did lack of cadherin expression. For overall survival, cadherin immunoreactivity and the interaction between APC expression and response to adjuvant chemotherapy were significant (p = 0.012 and p < 0.001). No significant clinical association was evident with immunohistochemical expression of cadherin, beta-catenin. Conclusion: Lack of expression of cadherin was a significant variable to overall and disease-free survival. Significantly, positive APC immunoreactivity and adjuvant chemotherapy were associated with a favourable treatment response. Studies using newer immunohistochemical markers within the Wnt-signalling pathway may guide the development of more appropriate therapeutic targets for future individualised treatment. (C) 2010 Elsevier Ltd. All rights reserved.

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The possibility of obtaining transplantable oral epithelia opens new perspectives for oral treatments. Most of them are surgical, resulting in mucosal failures. As reconstructive material this in vitro epithelia would be also useful for other parts of the human body. Many researchers still use controversial methods; therefore it was evaluated and compared the efficiency of the enzymatic and direct explant methods to obtain oral keratinocytes. To this project oral epithelia fragments were used. This work compared: time needed for cell obtainment, best cell amount, life-span and epithelia forming cell capacity. The results showed the possibility to obtain keratinocytes from a small oral fragment and we could verify the advantages and peculiar restrictions. We concluded that under our conditions the enzymatic method showed the best results: in the cells obtaining time needed, cell amount and life-span. Both methods showed the same capacity to form in vitro epithelia.

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Background. Apoptosis is a genetically programmed form of cell death, of which caspases are the central components. Methods. By tissue microarray of 229 cases of oral squamous cell carcinoma (OSCC), we analyzed the immunoexpression of caspases 3, 6, 7, 8, 9, and 10. Results. All proteins that we examined were expressed in primary OSCC samples. Caspases 8 and 9 were prominently expressed, and caspases 3, 6, 7, and 10 were occasionally expressed. Disease-free survival differed significantly between caspase 7 high-expressing and low-expressing patients, and our multivariate analysis suggested that expression of caspase 7 is an independent prognostic factor for patients with OSCC. Conclusion. This study suggests that caspases regulate the tumorigenesis of OSCC and that caspase 7 expression is a predictor of locoregional recurrence of OSCC. (C) 2010 Wiley Periodicals, Inc. Head Neck 33: 1191-1198, 2011