Leishmania sp identification by PCR associated with sequencing of target SSU rDNA in paraffin-embedded skin samples stored for more than 30 years

Paraffin-embedded samples commonly stored at educational and research institutions constitute tissues banks for follow-up or epidemiological studies; however, the paraffin inclusion process involves the use of substances that can cause DNA degradation. In this study, a PCR protocol was applied to identify Leishmania strains in 33 paraffin-embedded skin samples of patients with American cutaneous leishmaniasis. DNA was obtained by the phenol-chloroform protocol following paraffin removal and then used in PCR or nested PCR based on the nucleotide sequence of the small subunit ribosomal RNA (SSU rDNA). The amplicons obtained were cloned and sequenced to determine the single nucleotide polymorphism that distinguishes between different Leishmania species or groups. This assay allowed to distinguish organisms belonging to the subgenus Viannia and identify L. (Leishmania) amazonensis and L. (L.) chagasi of the Leishmania subgenus. Of the 33 samples, PCR and nested PCR identified 91% of samples. After sequencing the PCR product of 26 samples, 16 were identified as L. (L.) amazonensis, the other 10 contain organisms belonging to the L. (Viannia) sub-genus. These results open a huge opportunity to study stored samples and promote relevant contributions to epidemiological studies.

miRNA analysis of prostate cancer by quantitative real time PCR: Comparison between formalin-fixed paraffin embedded and fresh-frozen tissue

Objective: Micro RNA (miRNA) is a class of small noncoding RNA that plays a major role in the regulation of gene expression, which has been related to cancer behavior. The possibility of analyzing miRNA from the archives of pathology laboratories is exciting, as it allows for large retrospective studies. Formalin is the most common fixative used in the surgical pathology routine, and its promotion of nucleic acid degradation is well known. Our aim is to compare miRNA profiles from formalin-fixed paraffin embedded (FFPE) tissues with fresh-frozen prostate cancer tissues. Methods: The expression of 14 miRNAs was determined by quantitative real time polymerase chain reaction (qRT-PCR) in 5 paired fresh-frozen and FFPE tissues, which were representative of prostate carcinoma. Results: There was a very good correlation of the miRNA expression of miR-let7c and miR-32 between the fresh-frozen and FFPE tissues, with Pearson`s correlation coefficients of 0.927 (P = 0.023) and 0.960 (P = 0.010), respectively. For the remaining miRNAs, the correlation was good with Spearman correlation coefficient of 0.638 (P < 0.001). Conclusion: Analysis of miRNAs from routinely processed and stored FFPE prostate tissue is feasible for some miRNAs using qRT-PCR. Further studies should be conducted to confirm the reliability of using stock tissues for miRNA expression determination. (C) 2011 Elsevier Inc. All rights reserved.

The embedded cluster DBSB 48 in the nebula Hoffleit 18: Comparison with Trumpler 14

We derive fundamental parameters of the embedded cluster DBSB 48 in the southern nebula Hoffleit 18 and the very young open cluster Trumpler 14, by means of deep JHK(s) infrared photometry. We build colour-magnitude and colour-colour diagrams to derive reddening and age, based on main sequence and pre-main sequence distributions. Radial stellar density profiles are used to study cluster structure and guide photometric diagram extractions. Field-star decontamination is applied to uncover the intrinsic cluster sequences in the diagrams. Ages are inferred from K-excess fractions. A prominent pre-main sequence population is present in DBSB 48, and the K-excess fraction f(K) = 55 +/- 6% gives an age of 1.1 +/- 0.5 Myr. A mean reddening of A(Ks) = 0.9 +/- 0.03 was found, corresponding to A(v) = 8.2 +/- 0.3. The cluster CMD is consistent with the far kinematic distance of 5 kpc for Hoffleit 18. For Trumpler 14 we derived similar parameters as in previous studies in the optical, in particular an age of 1.7 +/- 0.7 Myr. The fraction of stars with infrared excess in Trumpler 14 is f(K) = 28 +/- 4%. Despite the young ages, both clusters are described by a King profile with core radii R-core = 0.46 +/- 0.05 pc and R-core = 0.35 +/- 0.04 pc, respectively, for DBSB 48 and Trumpler 14. Such cores are smaller than those of typical open clusters. Small cores are probably related to the cluster formation and/or parent molecular cloud fragmentation. In DBSB 48, the magnitude extent of the upper main sequence is Delta K-s approximate to 2 mag, while in Trumpler 14 it is Delta K-s approximate to 5 mag, consistent with the estimated ages. (c) 2008 Elsevier B.V. All rights reserved.

GEMINI near-infrared spectroscopic observations of young massive stars embedded in molecular clouds

K-band spectra of young stellar candidates in four Southern hemisphere clusters have been obtained with the Gemini Near-Infrared Spectrograph in Gemini South. The clusters are associated with IRAS sources that have colours characteristic of ultracompact H II regions. Spectral types were obtained by comparison of the observed spectra with those of a near-infrared (NIR) library; the results include the spectral classification of nine massive stars and seven objects confirmed as background late-type stars. Two of the studied sources have K-band spectra compatible with those characteristic of very hot stars, as inferred from the presence of C IV, N III and N V emission lines at 2.078, 2.116 and 2.100 mu m, respectively. One of them, I16177_IRS1, has a K-band spectrum similar to that of Cyg OB2 7, an O3If* supergiant star. The nebular K-band spectrum of the associated Ultra-Compact (UC) H II region shows the s-process [Kr III] and [Se IV] high excitation emission lines, previously identified only in planetary nebula. One young stellar object was found in each cluster, associated with either the main IRAS source or a nearby resolved Midecourse Space eXperiment (MSX) component, confirming the results obtained from previous NIR photometric surveys. The distances to the stars were derived from their spectral types and previously determined JHK magnitudes; they agree well with the values obtained from the kinematic method, except in the case of IRAS 15408-5356, for which the spectroscopic distance is about a factor of 2 smaller than the kinematic value.

Hyperfine and magnetic properties of Fe-Cu clusters and Fe precipitates embedded in a Cu matrix

Using the first-principles real-space linear muffin-tin orbital method within the atomic sphere approximation (RS-LMTO-ASA) we study hyperfine and local magnetic properties of substituted pure Fe and Fe-Cu clusters in an fcc Cu matrix. Spin and orbital contributions to magnetic moments, hyperfine fields and the Mossbauer isomer shifts at the Fe sites in Fe precipitates and Fe-Cu alloy clusters of sizes up to 60 Fe atoms embedded in the Cu matrix are calculated and the influence of the local environment on these properties is discussed.

Tori embedded in R(3) with dense principal lines

In this paper are given examples of tori T(2) embedded in R(3) with all their principal lines dense. These examples are obtained by stereographic projection of deformations of the Clifford torus in S(3). (C) 2008 Elsevier Masson SAS. All rights reserved.

Correlation between metal-ceramic bond strength and coefficient of linear thermal expansion difference

The purpose of this study was to evaluate the metal-ceramic bond strength (MCBS) of 6 metal-ceramic pairs (2 Ni-Cr alloys and 1 Pd-Ag alloy with 2 dental ceramics) and correlate the MCBS values with the differences between the coefficients of linear thermal expansion (CTEs) of the metals and ceramics. Verabond (VB) Ni-Cr-Be alloy, Verabond II (VB2), Ni-Cr alloy, Pors-on 4 (P), Pd-Ag alloy, and IPS (I) and Duceram (D) ceramics were used for the MCBS test and dilatometric test. Forty-eight ceramic rings were built around metallic rods (3.0 mm in diameter and 70.0 mm in length) made from the evaluated alloys. The rods were subsequently embedded in gypsum cast in order to perform a tensile load test, which enabled calculating the CMBS. Five specimens (2.0 mm in diameter and 12.0 mm in length) of each material were made for the dilatometric test. The chromel-alumel thermocouple required for the test was welded into the metal test specimens and inserted into the ceramics. ANOVA and Tukey's test revealed significant differences (p=0.01) for the MCBS test results (MPa), with PI showing higher MCBS (67.72) than the other pairs, which did not present any significant differences. The CTE (10-6 oC-1) differences were: VBI (0.54), VBD (1.33), VB2I (-0.14), VB2D (0.63), PI (1.84) and PD (2.62). Pearson's correlation test (r=0.17) was performed to evaluate of correlation between MCBS and CTE differences. Within the limitations of this study and based on the obtained results, there was no correlation between MCBS and CTE differences for the evaluated metal-ceramic pairs.

Effect of eugenol-based endodontic sealer on the adhesion of intraradicular posts cemented after different periods

OBJECTIVE: This study evaluated in vitro the influence of an eugenol-based sealer (EndoFill) on the retention of stainless steel prefabricated posts cemented with zinc phosphate and resin-based (Panavia F) cements after different periods of root canal obturation, using the pull-out test. MATERIAL AND METHODS: Sixty upper canines were decoronated and the roots were embedded in resin blocks. The specimens were distributed into 3 groups, according to the period elapsed between canal obturation and post cementation: Group I - immediately; Group II - 72 h and Group III - 4 months. The groups were subdivided according to the type of cement used for post cementation: A - zinc phosphate and B - Panavia F. Following the experimental periods, specimens were subjected to pullout test in an Instron machine with application of tensile force at a crosshead speed of 0.5 mm/min until post dislodgement. The maximum forces required for post removal were recorded (kN) and means were subjected to statistical analysis by 2-way ANOVA and Tukey-Kramer test (α=0.001) RESULTS: There were statistically significant differences (p<0.01) between the posts cemented with zinc phosphate cement (0.2112 kN) and Panavia F (0.0501 kN). However, no statistically significant differences (p>0.05) were found between the three post cementation periods, regardless of the cement. CONCLUSIONS: It was concluded that the eugenol-based sealer influenced the tensile strength of the posts cemented with the resin cement, but had no influence on the time waited between root canal obturation and post space preparation/post cementation.

Adhesion of an endodontic sealer to dentin and gutta-percha: shear and push-out bond strength measurements and SEM analysis

The use of an adequate method for evaluation of the adhesion of root canal filling materials provides more reliable results to allow comparison of the materials and substantiate their clinical choice. The aims of this study were to compare the shear bond strength (SBS) test and push-out test for evaluation of the adhesion of an epoxy-based endodontic sealer (AH Plus) to dentin and gutta-percha, and to assess the failure modes on the debonded surfaces by means of scanning electron microscopy (SEM). Three groups were established (n=7): in group 1, root cylinders obtained from human canines were embedded in acrylic resin and had their canals prepared and filled with sealer; in group 2, longitudinal sections of dentin cylinders were embedded in resin with the canal surface smoothed and turned upwards; in group 3, gutta-percha cylinders were embedded in resin. Polyethylene tubes filled with sealer were positioned on the polished surface of the specimens (groups 2 and 3). The push-out test (group 1) and the SBS test (groups 2 and 3) were performed in an Instron universal testing machine running at crosshead speed of 1 mm/min. Means (±SD) in MPa were: G1 (8.8±1.13), G2 (5.9±1.05) and G3 (3.8±0.55). Statistical analysis by ANOVA and Student's t-test (a=0.05) revealed statistically significant differences (p<0.01) among the groups. SEM analysis showed a predominance of adhesive and mixed failures of AH Plus sealer. The tested surface affected significantly the results with the sealer reaching higher bond strength to dentin than to gutta-percha with the SBS test. The comparison of the employed methodologies showed that the SBS test produced significantly lower bond strength values than the push-out test, was skilful in determining the adhesion of AH Plus sealer to dentin and gutta-percha, and required specimens that could be easily prepared for SEM, presenting as a viable alternative for further experiments.

Heat treatment of a direct composite resin: influence on flexural strength

The purpose of this study was to evaluate the flexural strength of a direct composite, for indirect application, that received heat treatment, with or without investment. One indirect composite was used for comparison. For determination of the heat treatment temperature, thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC) were performed, considering the initial weight loss temperature and glass transition temperature (Tg). Then, after photoactivation (600 mW/cm² - 40 s), the specimens (10 x 2 x 2 mm) were heat-treated following these conditions: 170ºC for 5, 10 or 15 min, embedded or not embedded in investment. Flexural strength was assessed as a means to evaluate the influence of different heat treatment periods and investment embedding on mechanical properties. The data were analyzed by ANOVA and Tukey's test (α = 0.05). TGA showed an initial weight loss temperature of 180ºC and DSC showed a Tg value of 157°C. Heat treatment was conducted in an oven (Flli Manfredi, Italy), after 37°C storage for 48 h. Flexural strength was evaluated after 120 h at 37°C storage. The results showed that different periods and investment embedding presented similar statistical values. Nevertheless, the direct composite resin with treatments presented higher values (178.7 MPa) compared to the indirect composite resin (146.0 MPa) and the same direct composite submitted to photoactivation only (151.7 MPa). Within the limitations of this study, it could be concluded that the heat treatment increased the flexural strength of the direct composite studied, leading to higher mechanical strength compared to the indirect composite.

Convecção linearmente organizada na área de Petrolina, semi-árido do Nordeste do Brasil: aspectos em meso e grande escala

É apresentado um estudo sobre sistemas convectivos linearmente organizados e observados por um radar meteorológico banda-C na região semi-árida do Nordeste do Brasil. São analisados três dias (27 a 29) de março de 1985, com ênfase na investigação do papel desempenhado por fatores locais e de grande escala no desenvolvimento dos sistemas. No cenário de grande escala, a área de cobertura do radar foi influenciada por um cavado de ar superior austral no dia 27 e por um vórtice ciclônico de altos níveis no dia 29. A convergência de umidade próxima à superfície favoreceu a atividade convectiva nos dias 27 e 29, enquanto que divergência de umidade próxima à superfície inibiu a atividade convectiva no dia 28. No cenário de mesoescala, foi observado que o aquecimento diurno é um fator importante para a formação de células convectivas, somando-se a ele o papel determinante da orografia na localização dos ecos. De maneira geral, as imagens de radar mostram os sistemas convectivos linearmente organizados em áreas elevadas e núcleos convectivos intensos envolvidos por uma área de precipitação estratiforme. Os resultados indicam que convergência do fluxo de umidade em grande escala e aquecimento radiativo, são fatores determinantes na evolução e desenvolvimento dos ecos na área de estudo.

O uso de sondagens dipolo-dipolo em estudos hidrogeológicos e de depósitos de resíduos

Ensaios de sondagem e caminhamento elétrico têm sido realizados globalmente na avaliação de uma grande variedade de problemas em exploração mineral e hidrogeologia, bem como na caracterização de locais com risco de contaminação. A despeito da utilidade de ensaios geoelétricos em estudos hidrogeológicos e na caracterização de depósitos de resíduos desativados, um problema na utilização de sondagens elétricas ocorre em conseqüência da falta de espaço para aquisição de dados nessas áreas. Em áreas urbanas, isto constitui uma limitação importante devido à existência de construções, o que muitas vezes interrompe o desenvolvimento de ensaios de campo com arranjos de comprimentos adequados. Embora investigações rasas tendam a ser eficazes em caracterização geoambiental, a estimativa de parâmetros-chave pode depender da investigação de porções mais profundas. Entretanto, uma profundidade de investigação ligeiramente maior é obtida pelo arranjo dipolo-dipolo em comparação aos arranjos Schlumberger e Wenner de mesmo comprimento. Essa característica do arranjo dipolo-dipolo pode ser observada em vários estudos, mas provavelmente devido à tradição e à relação sinal-ruído, a grande maioria das sondagens elétricas é feita com os arranjos Schlumberger e Wenner.O arranjo dipolo-dipolo é mais utilizado em ensaios 2D. Até onde se sabe, essa maior capacidade de investigação em profundidade do arranjo dipolo-dipolo 1D não foi explorada em estudos geoambientais e nem em estudos hidrogeológicos em áreas urbanas. Este trabalho apresenta resultados de ensaios de campo que ressaltam a utilidade de sondagens dipolo-dipolo na investigação de tais áreas.

Pitfalls of artificial grouping and stratification of scientific journals based on their Impact Factor: a case study in Brazilian Zoology

The present contribution explores the impact of the QUALIS metric system for academic evaluation implemented by CAPES (Coordination for the Development of Personnel in Higher Education) upon Brazilian Zoological research. The QUALIS system is based on the grouping and ranking of scientific journals according to their Impact Factor (IF). We examined two main points implied by this system, namely: 1) its reliability as a guideline for authors; 2) if Zoology possesses the same publication profile as Botany and Oceanography, three fields of knowledge grouped by CAPES under the subarea "BOZ" for purposes of evaluation. Additionally, we tested CAPES' recent suggestion that the area of Ecology would represent a fourth field of research compatible with the former three. Our results indicate that this system of classification is inappropriate as a guideline for publication improvement, with approximately one third of the journals changing their strata between years. We also demonstrate that the citation profile of Zoology is distinct from those of Botany and Oceanography. Finally, we show that Ecology shows an IF that is significantly different from those of Botany, Oceanography, and Zoology, and that grouping these fields together would be particularly detrimental to Zoology. We conclude that the use of only one parameter of analysis for the stratification of journals, i.e., the Impact Factor calculated for a comparatively small number of journals, fails to evaluate with accuracy the pattern of publication present in Zoology, Botany, and Oceanography. While such simplified procedure might appeals to our sense of objectivity, it dismisses any real attempt to evaluate with clarity the merit embedded in at least three very distinct aspects of scientific practice, namely: productivity, quality, and specificity.

Morphology of the male agouti accessory genital glands (Dasyprocta prymnolopha Wagler, 1831)

The morphology of the accessory genital glands of the male agouti was studied in twenty-three animals that were raised in captivity. Twenty animals had their genital glands dissected in situ for macroscopic description. The samples of each gland were recovered, embedded in paraffin, sliced and stained by Hematoxylin-Eosin technique. It was founded four pairs of glands: the vesicular glands, the coagulating glands, the prostate and the bulbourethral glands. Histological characteristics of the vesicular, coagulating and prostate glands showed similar morphology, within the pseudostratified columnar epithelium. The tubulo-alveolar type of the bulbourethral glands showed a lack of connective tissue among the tubules, a small amount of red stained presented it the cytoplasm, and the presence of vacuoles in the tissue. This study concluded that the agouti showed to have similar morphological aspect described in the others species of rodents.

Etiologic diagnosis of bovine infectious abortion by PCR

Infectious abortion is a significant cause of reproductive failure and economic losses in cattle. The goal of this study was to detect nucleic acids of several infectious agents known to cause abortion including Arcanobacterium pyogenes, Bovine Herpesvirus 1, Brucella abortus, Campylobacter fetus subsp. venerealis, Chlamydophila abortus, Leptospira sp., Listeria monocytogenes, Salmonella sp., Mycoplasma bovis, Mycoplasma bovigenitalium, Neospora caninum, and Tritrichomonas foetus. Tissue homogenates from 42 fetuses and paraffin-embedded tissues from 28 fetuses and 14 placentas/endometrium were included in this study. Brucella abortus was detected in 14.2% (12/84) of the samples. Salmonella sp. DNA was amplified from 2 fetuses, and there was one positive for Neospora caninum, and another for Listeria monocytogenes. This PCR-based approach resulted in identification of the etiology in 19% of samples, or 20% if considered fetal tissues only.