Identification of protein expression signatures in gastric carcinomas using clustering analysis

Background and Aim: The identification of gastric carcinomas (GC) has traditionally been based on histomorphology. Recently, DNA microarrays have successfully been used to identify tumors through clustering of the expression profiles. Random forest clustering is widely used for tissue microarrays and other immunohistochemical data, because it handles highly-skewed tumor marker expressions well, and weighs the contribution of each marker according to its relatedness with other tumor markers. In the present study, we e identified biologically- and clinically-meaningful groups of GC by hierarchical clustering analysis of immunohistochemical protein expression. Methods: We selected 28 proteins (p16, p27, p21, cyclin D1, cyclin A, cyclin B1, pRb, p53, c-met, c-erbB-2, vascular endothelial growth factor, transforming growth factor [TGF]-beta I, TGF-beta II, MutS homolog-2, bcl-2, bax, bak, bcl-x, adenomatous polyposis coli, clathrin, E-cadherin, beta-catenin, mucin (MUC) 1, MUC2, MUC5AC, MUC6, matrix metalloproteinase [ MMP]-2, and MMP-9) to be investigated by immunohistochemistry in 482 GC. The analyses of the data were done using a random forest-clustering method. Results: Proteins related to cell cycle, growth factor, cell motility, cell adhesion, apoptosis, and matrix remodeling were highly expressed in GC. We identified protein expressions associated with poor survival in diffuse-type GC. Conclusions: Based on the expression analysis of 28 proteins, we identified two groups of GC that could not be explained by any clinicopathological variables, and a subgroup of long-surviving diffuse-type GC patients with a distinct molecular profile. These results provide not only a new molecular basis for understanding the biological properties of GC, but also better prediction of survival than the classic pathological grouping.

Preliminary study of Porcine circovirus type 2 and Torque teno sus virus coinfection frequencies in Brazilian pig herds

Torque teno sus virus (TTSuV) is emergent in swine herds. Recent studies have shown an increased frequency of TTSuV2 in Porcine circovirus type 2 (PCV2)-associated diseases (PCVAD), which are endemic in many swine-producing countries, including Brazil. Coinfection with several other viral and bacterial agents results in an increased incidence of more severe PCVAD. Given the limited information on TTSuV and PCV2 coinfection, especially in Brazilian swine herds, this study made a preliminary estimation of the occurrence of coinfection in swine herds by testing samples from different categories. Between 2008 and 2009, 111 samples of feces and 23 serum samples from 5 swine herds were tested for PCV2 and TTSuVs and the results analyzed for associations between these agents. No significant differences in coinfection frequency were observed for PCV2 1 + TTSuV1 or for PCV2 1 TTSuV2 between nursery piglets (P = 0.730), growing pigs (P = 0.331), or sows (P = 0.472). However, a significant difference was observed for PCV2 1 TTSuV1 1 TTSuV2 between nursery piglets and growing pigs (P = 0.004; Fisher's exact test). Phylogenetic studies agreed with the grouping of TTSuV1 and TTSuV2 into 2 different clades, with no distinct pattern of clustering of these isolates with the animal categories.

PXRF and multivariate statistics analysis of pre-colonial pottery from northeast of Brazil

Portable system of energy dispersive X-ray fluorescence was used to determine the elemental composition of 68 pottery fragments from Sambaqui do Bacanga, an archeological site in Sao Luis, Maranhao, Brazil. This site was occupied from 6600 BP until 900 BP. By determining the element chemical composition of those fragments, it was possible to verify the existence of engobe in 43 pottery fragments. Obtained from two-dimensional graphs and hierarchical cluster analysis performed in fragments of stratigraphies from surface and 113-cm level, and 10 to 20, 132 and 144-cm level, it was possible to group these fragments in five distinct groups, according to their stratigraphies. The results of data grouping (two-dimensional graphics) are in agreement with hierarchical cluster analysis by Ward method. Copyright (C) 2011 John Wiley & Sons, Ltd.

Phylogenetic relationship of dengue virus type 3 isolated in Brazil and Paraguay and global evolutionary divergence dynamics

Background: Dengue is the most important mosquito-borne viral disease worldwide. Dengue virus comprises four antigenically related viruses named dengue virus type 1 to 4 (DENV1-4). DENV-3 was re-introduced into the Americas in 1994 causing outbreaks in Nicaragua and Panama. DENV-3 was introduced in Brazil in 2000 and then spread to most of the Brazilian States, reaching the neighboring country, Paraguay in 2002. In this study, we have analyzed the phylogenetic relationship of DENV-3 isolated in Brazil and Paraguay with viruses isolated worldwide. We have also analyzed the evolutionary divergence dynamics of DENV-3 viruses. Results: The entire open reading frame (ORF) of thirteen DENV-3 isolated in Brazil (n = 9) and Paraguay (n = 4) were sequenced for phylogenetic analysis. DENV-3 grouped into three main genotypes (I, II and III). Several internal clades were found within each genotype that we called lineage and sub-lineage. Viruses included in this study belong to genotype III and grouped together with viruses isolated in the Americas within the lineage III. The Brazilian viruses were further segregated into two different sub-lineage, A and B, and the Paraguayan into the sub-lineage B. All three genotypes showed internal grouping. The nucleotide divergence was in average 6.7% for genotypes, 2.7% for lineages and 1.5% for sub-lineages. Phylogenetic trees constructed with any of the protein gene sequences showed the same segregation of the DENV-3 in three genotypes. Conclusion: Our results showed that two groups of DENV-3 genotypes III circulated in Brazil during 2002-2009, suggesting different events of introduction of the virus through different regions of the country. In Paraguay, only one group DENV-3 genotype III is circulating that is very closely related to the Brazilian viruses of sub-lineage B. Different degree of grouping can be observed for DENV-3 and each group showed a characteristic evolutionary divergence. Finally, we have observed that any protein gene sequence can be used to identify the virus genotype.

Signal transduction-related responses to phytohormones and environmental challenges in sugarcane

Abstract Background Sugarcane is an increasingly economically and environmentally important C4 grass, used for the production of sugar and bioethanol, a low-carbon emission fuel. Sugarcane originated from crosses of Saccharum species and is noted for its unique capacity to accumulate high amounts of sucrose in its stems. Environmental stresses limit enormously sugarcane productivity worldwide. To investigate transcriptome changes in response to environmental inputs that alter yield we used cDNA microarrays to profile expression of 1,545 genes in plants submitted to drought, phosphate starvation, herbivory and N2-fixing endophytic bacteria. We also investigated the response to phytohormones (abscisic acid and methyl jasmonate). The arrayed elements correspond mostly to genes involved in signal transduction, hormone biosynthesis, transcription factors, novel genes and genes corresponding to unknown proteins. Results Adopting an outliers searching method 179 genes with strikingly different expression levels were identified as differentially expressed in at least one of the treatments analysed. Self Organizing Maps were used to cluster the expression profiles of 695 genes that showed a highly correlated expression pattern among replicates. The expression data for 22 genes was evaluated for 36 experimental data points by quantitative RT-PCR indicating a validation rate of 80.5% using three biological experimental replicates. The SUCAST Database was created that provides public access to the data described in this work, linked to tissue expression profiling and the SUCAST gene category and sequence analysis. The SUCAST database also includes a categorization of the sugarcane kinome based on a phylogenetic grouping that included 182 undefined kinases. Conclusion An extensive study on the sugarcane transcriptome was performed. Sugarcane genes responsive to phytohormones and to challenges sugarcane commonly deals with in the field were identified. Additionally, the protein kinases were annotated based on a phylogenetic approach. The experimental design and statistical analysis applied proved robust to unravel genes associated with a diverse array of conditions attributing novel functions to previously unknown or undefined genes. The data consolidated in the SUCAST database resource can guide further studies and be useful for the development of improved sugarcane varieties.

Using Mitrofanoff's principle and Monti's technique as a surgical option for bladder augmentation with a continent stoma: a case report

Abstract Introduction Hydronephrosis, reflux and renal failure are serious complications that occur in patients with neurogenic bladder associated with myelomeningocele. When the bladder compliance is lost, it is imperative to carry out surgery aimed at reducing bladder storage pressure. An ileocystoplasty, and for patients not suitable for intermittent catheterization, using the Mitrofanoff principle to form a continent stoma and the subsequent closure of the bladder neck, can be used. We report here, for the first time to the best of our knowledge, an association between two previously described techniques (the Mitrofanoff principle and the technique of Monti), that can solve the problem of a short appendix in obese patients. Case presentation A 33-year-old male Caucasian patient with myelomeningocele and neurogenic bladder developed low bladder compliance (4.0 mL/cm H2O) while still maintaining normal renal function. A bladder augmentation (ileocystoplasty) with continent derivation principle (Mitrofanoff) was performed. During surgery, we found that the patient's appendix was too short and was insufficient to reach the skin. We decided to make an association between the Mitrofanoff conduit and the ileal technique of Monti, through which we performed an anastomosis of the distal stump of the appendix to the bladder (with an antireflux valve). Later, the proximal stump of the appendix was anastomosed to an ileal segment of 2.0 cm that was open longitudinally and reconfigured transversally (Monti technique), modeled by a 12-Fr urethral catheter, and finally, the distal stump was sutured at the patient's navel. After the procedure, a suprapubic cystostomy (22 Fr) and a Foley catheter (10 Fr) through the continent conduit were left in place. The patient had recovered well and was discharged on the tenth day after surgery. He remained with the Foley catheter (through the conduit) for 21 days and cystostomy for 30 days. Six months after surgery he was continent with good bladder compliance without reflux and fully adapted to catheterization through the navel. Conclusion The unpublished association between the Mitrofanoff and Monti techniques is feasible and a very useful alternative in urologic cases of derivation continent in which the ileocecal appendix is too short to reach the skin (i.e., in obese patients).

Alterações de parâmetros relacionados ao metabolismo ósseo em mulheres submetidas à derivação gástrica em Y de Roux

OBJETIVO: Avaliar o metabolismo ósseo e a densidade mineral óssea (DMO) em mulheres adultas pós-derivação gástrica em Y de Roux (DGYR). SUJEITOS E MÉTODOS: Estudo transversal com 48 mulheres submetidas a DGYR há três anos e 41 saudáveis. Dados obtidos: índice de massa corporal (IMC), atividade física, consumo alimentar e DMO da coluna lombar, colo e fêmur total. Dosagem de cálcio, fósforo, magnésio, albumina, fosfatase alcalina, telopeptídeo-C (CTX), paratormônio (PTH), 25-hidroxivitamina D (25OHD), osteocalcina e cálcio urinário. RESULTADOS: Maiores alterações no grupo DGYR observadas nos níveis de osteocalcina (p < 0,001), CTX (p < 0,001) e PTH (p < 0,001). Deficiência de 25OHD foi a mais frequente no grupo DGYR (p = 0,010). Deficiência/insuficiência de 25OHD associou-se com hiperparatiroidismo secundário (p = 0,025). Não houve diferença entre os grupos em relação à DMO. A ingestão de energia (p = 0,036) e proteína (p = 0,004) foi maior no grupo controle. CONCLUSÃO: Em mulheres pós-DGYR, encontraram-se alta frequência de deficiência de vitamina D, hiperparatireoidismo secundário e elevação nos marcadores de remodelação óssea, sem alteração na DMO quando comparado com o grupo controle não obeso.

Assessing the extent of colon lengthening due to splenic flexure mobilization techniques: a cadaver study

CONTEXT: Failure of a colorectal anastomosis represents a life-threatening complication of colorectal surgery. Splenic flexure mobilization may contribute to reduce the occurrence of anastomotic complications due to technical flaws. There are no published reports measuring the impact of splenic flexure mobilization on the length of mobilized colon viable to construct a safe colorectal anastomosis. OBJECTIVE: The aim of the present study was to determine the effect of two techniques for splenic flexure mobilization on colon lengthening during open left-sided colon surgery using a cadaver model. DESIGN: Anatomical dissections for left colectomy and colorectal anastomosis at the sacral promontory level were conducted in 20 fresh cadavers by the same team of four surgeons. The effect of partial and full splenic flexure mobilization on the extent of mobilized left colon segment was determined. SETTING: University of Sao Paulo Medical School, Sao Paulo, SP, Brazil. Tertiary medical institution and university hospital. PARTICIPANTS: A team of four surgeons operated on 20 fresh cadavers. RESULTS: The length of resected left colon enabling a tension-free colorectal anastomosis at the level of sacral promontory achieved without mobilizing the splenic flexure was 46.3 (35-81) cm. After partial mobilization of the splenic flexure, an additionally mobilized colon segment measuring 10.7 (2-30) cm was obtained. After full mobilization of the distal transverse colon, a mean 28.3 (10-65) cm segment was achieved. CONCLUSION: Splenic flexure mobilization techniques are associated to effective left colon lengthening for colorectal anastomosis. This result may contribute to decision-making during rectal surgery and low colorectal and coloanal anastomosis.

Behavioral meaningful opioidergic stimulation activates kappa receptor gene expression

The periaqueductal gray (PAG) has been reported to be a location for opioid regulation of pain and a potential site for behavioral selection in females. Opioid-mediated behavioral and physiological responses differ according to the activity of opioid receptor subtypes. The present study investigated the effects of the peripheral injection of the kappa-opioid receptor agonist U69593 into the dorsal subcutaneous region of animals on maternal behavior and on Oprk1 gene activity in the PAG of female rats. Female Wistar rats weighing 200-250 g at the beginning of the study were randomly divided into 2 groups for maternal behavior and gene expression experiments. On day 5, pups were removed at 7:00 am and placed in another home cage that was distant from their mother. Thirty minutes after removing the pups, the dams were treated with U69593 (0.15 mg/kg, sc) or 0.9% saline (up to 1 mL/kg) and after 30 min were evaluated in the maternal behavior test. Latencies in seconds for pup retrieval, grouping, crouching, and full maternal behavior were scored. The results showed that U69593 administration inhibited maternal behavior (P < 0.05) because a lower percentage of kappa group dams showed retrieval of first pup, retrieving all pups, grouping, crouching and displaying full maternal behavior compared to the saline group. Opioid gene expression was evaluated using real-time reverse-transcription polymerase chain reaction (RT-PCR). A single injection of U69593 increased Oprk1 PAG expression in both virgin (P < 0.05) and lactating female rats (P < 0.01), with no significant effect on Oprm1 or Oprd1 gene activity. Thus, the expression of kappa-opioid receptors in the PAG may be modulated by single opioid receptor stimulation and behavioral meaningful opioidergic transmission in the adult female might occur simultaneously to specific changes in gene expression of kappa-opioid receptor subtype. This is yet another alert for the complex role of the opioid system in female reproduction

Anastomose cavo-pulmonar associada ao suporte circulatório esquerdo comparada à assistência biventricular na falência cardíaca aguda

OBJETIVO: Este estudo avaliou o desempenho hemodinâmico e as alterações miocárdicas decorrentes do emprego de dispositivos de assistência ventricular esquerda (DAVE), associado ou não à descompressão do ventrículo direito por meio de derivação cavo-pulmonar, sendo esses achados comparados ao emprego de assistência circulatória biventricular. MÉTODOS: Vinte e um suínos foram submetidos à indução de insuficiência cardíaca através de fibrilação ventricular, sendo a atividade circulatória mantida por DAVE durante 180 minutos. No grupo controle, foi apenas implantado o DAVE. No grupo derivação, além do DAVE foi realizada cirurgia de derivação cavo-pulmonar. No grupo biventricular, foi instituída assistência biventricular. Foram monitoradas as pressões intracavitárias por 3 horas de assistência e amostras do endocárdio dos dois ventrículos foram coletadas e analisadas à microscopia óptica e eletrônica. RESULTADOS: O lactato sérico foi significativamente menor no grupo biventricular (P=0,014). A diferença observada entre o fluxo do DAVE nos grupos derivação e controle (+55±14 ml/kg/min, P=0,072) não foi significativa, enquanto que o fluxo no grupo biventricular foi significativamente maior (+93±17 ml/kg/min, P=0,012) e se manteve estável durante o experimento. A pressão arterial média (PAM) se manteve constante apenas no grupo biventricular (P<0,001), que também apresentou diminuição significativa das pressões em câmaras direitas. Na análise ultraestrutural, notou-se menor presença edema miocárdico no ventrículo direito no grupo biventricular (P=0,017). CONCLUSÃO: Os resultados apresentados demonstram que o desempenho hemodinâmico da assistência ventricular esquerda associada à derivação cavo-pulmonar, neste modelo experimental, não foi superior ao observado com a assistência de ventrículo esquerdo isolada e não substituiu a assistência biventricular de maneira efetiva.

Landscape and soil regionalization in southern Brazilian Amazon and contiguous areas: methodology and relevance for ecological studies

Soils of a large tropical area with differentiated landscapes cannot be treated uniformly for ecological applications. We intend to develop a framework based on physiography that can be used in regional applications. The study region occupies more than 1.1 million km² and is located at the junction of the savanna region of Central Brazil and the Amazon forest. It includes a portion of the high sedimentary Central Brazil plateau and large areas of mostly peneplained crystalline shield on the border of the wide inner-Amazon low sedimentary plain. A first broad subdivision was made into landscape regions followed by a more detailed subdivision into soil regions. Mapping information was extracted from soil survey maps at scales of 1:250000-1:500000. Soil units were integrated within a homogenized legend using a set of selected attributes such as taxonomic term, the texture of the B horizon and the associated vegetation. For each region, a detailed inventory of the soil units with their area distribution was elaborated. Ten landscape regions and twenty-four soil regions were recognized and delineated. Soil cover of a region is normally characterized by a cluster composed of many soil units. Soil diversity is comparable in the landscape and the soil regions. Composition of the soil cover is quantitatively expressed in terms of area extension of the soil units. Such geographic divisions characterized by grouping soil units and their spatial estimates must be used for regional ecological applications.

Professional competences of nurse to work in Intensive Care Units: an integrative review

This study aimed to identify and analyze nurses' competences to work at Intensive Care Units-ICU. An integrative review method was used, and data were collected in LILACS, SciELO and BDENF, from August to October 2010. Ten articles were identified, published in the last 12 years. Data grouping permitted the construction of thematic units related to nurses' competences: nursing care management, high-complexity nursing care delivery, decision making, leadership, communication, continuing/permanent education, human resource management, material resource management. The professional competences identified can support the outline of guidelines to constitute the profile of nursing working in intensive care units and drive/mobilize the improvement of nursing care practices.

Perineal rectosigmoidectomy on treatment of rectal procidentia: analysis of 48 cases

OBJECTIVE: To evaluate results obtained in 48 cases of perineal rectosigmoidectomy in patients with rectal procidentia. METHODS: 48 medical records of patients undergoing PRS were analyzed, retrospectively. RESULTS: Before surgery, 44 patients (77.1%) reported complaints of anal mass and rectal bleeding was reported 13 times (22.8%). The period of hospitalization was 3.91 days (2 to 12 days). Women were the majority (85.4%). The mean age was 73.8 years (49 to 101 years). The average time of surgery was 72 minutes (40 to 90 minutes). Mechanical anastomosis was performed in 72.9% and manual in 27.1%. Among the 12 (25%) patients with fecal incontinence, continence was achieved in 2 cases. Postoperative complications occurred in five cases - 10.5% (two pneumonia and three anastomotic leakages). Recurrence was verified in four patients (8,3%). There were no deaths related to the procedure. CONCLUSION: Perineal rectosigmoidectomy is a good surgical option for rectal procidentia, with low morbidity and mortality, low recurrence rate and short hospitalization length.

Identification of Urban Leprosy Clusters

Overpopulation of urban areas results from constant migrations that cause disordered urban growth, constituting clusters defined as sets of people or activities concentrated in relatively small physical spaces that often involve precarious conditions. Aim. Using residential grouping, the aim was to identify possible clusters of individuals in São José do Rio Preto, Sao Paulo, Brazil, who have or have had leprosy. Methods. A population-based, descriptive, ecological study using the MapInfo and CrimeStat techniques, geoprocessing, and space-time analysis evaluated the location of 425 people treated for leprosy between 1998 and 2010. Clusters were defined as concentrations of at least 8 people with leprosy; a distance of up to 300 meters between residences was adopted. Additionally, the year of starting treatment and the clinical forms of the disease were analyzed. Results. Ninety-eight (23.1%) of 425 geocoded cases were located within one of ten clusters identified in this study, and 129 cases (30.3%) were in the region of a second-order cluster, an area considered of high risk for the disease. Conclusion.This study identified ten clusters of leprosy cases in the city and identified an area of high risk for the appearance of new cases of the disease.

Deltocyathiidae, an early-diverging family of Robust corals (Anthozoa, Scleractinia)

Over the last decade, molecular phylogenetics has called into question some fundamental aspects of coral systematics. Within the Scleractinia, most families composed exclusively by zooxanthellate species are polyphyletic on the basis of molecular data, and the second most speciose coral family, the Caryophylliidae (most members of which are azooxanthellate), is an unnatural grouping. As part of the process of resolving taxonomic affinities of caryophylliids', here a new Robust' scleractinian family (Deltocyathiidae fam. n.) is proposed on the basis of combined molecular (CO1 and 28S rDNA) and morphological data, accommodating the early-diverging clade of traditional caryophylliids (represented today by the genus Deltocyathus). Whereas this family captures the full morphological diversity of the genus Deltocyathus, one species, Deltocyathus magnificus, is an outlier in terms of molecular data, and groups with the Complex coral family Turbinoliidae. Ultrastructural data, however, place D.magnificus within Deltocyathiidae fam. nov. Unfortunately, limited ultrastructural data are as yet available for turbinoliids, but D.magnificus may represent the first documented case of morphological convergence at the microstructural level among scleractinian corals. Marcelo V.Kitahara, Centro de Biologia Marinha, Universidade de SAo Paulo, SAo SebastiAo, S.P. 11600-000, Brazil. E-mail:kitahara@usp.br