A conceptual approach to gene expression analysis enhanced by visual analytics

The analysis of gene expression data is a complex task for biologists wishing to understand the role of genes in the formation of diseases such as cancer. Biologists need greater support when trying to discover, and comprehend, new relationships within their data. In this paper, we describe an approach to the analysis of gene expression data where overlapping groupings are generated by Formal Concept Analysis and interactively analyzed in a tool called CUBIST. The CUBIST workflow involves querying a semantic database and converting the result into a formal context, which can be simplified to make it manageable, before it is visualized as a concept lattice and associated charts

Solução para computador do método analítico de Chomard

O método analítico de Chomard é operacionalmente simples, mas envolve uma marcha de cálculo longa e demorada. Apresenta-se o programa para computador que permite, a partir de três operações de extinção (φ, Θ, ψ), determinar 2V, o sinal ótico do mineral e localizar 2V mediante os ângulos diretores dos eixos óticos. Inclui-se um exemplo da aplicação do método em um grupamento de plagioclásio, comparando-se os valores de 2V obtidos por diferentes métodos.Chomard's analytical method is operationally simple but rather involved in calculation procedure. A computer programe is presented to determine the angle 2V, the optical sign of the mineral and the direction cosines of the optical axes. An example of the application of the method for a plagioclase twinning is presented and the values of 2 V compared with other methods

Formas de administração de concentrados para vacas em lactação

Twelve crossbred cows were used in a “switch -back” design, 2 x 2 factorial arrangement with four treatments concerning feeding concentrate meals: A) once a day, by individual milk production; B) once a day, by average production of all cows; C) twice a day, by individual milk production; and D) twice a day, by average production of all cows. Milk production, 4% FCM production and fat production were not statistically differents.Doze vacas mestiças foram utilizadas em um delineamento “switch -back” comparando , em um arranjo fatorial 2x2, os seguintes tratamentos, concernentes a administração de concentrados: A) uma vez por dia, quantificada pela produção individual; B) uma vez por dia, quantificada pela produção média geral; C) duas vezes por dia, quantificada pela produção individual, e D) duas vezes por dia, quantificada pela produção média geral. As produções de leite não corrigidas, as produções de leite corrigidas para 4% de gordura e as quantidades de gordura produz idas pelos diferentes tratamentos não diferiram estatisticamente

Glutamine/Glutamate Metabolism Studied with Magnetic Resonance Spectroscopic Imaging for the Characterization of Adrenal Nodules and Masses

Purpose. To assess glutamine/glutamate (Glx) and lactate (Lac) metabolism using proton magnetic resonance spectroscopic imaging (1H-MRS) in order to differentiate between adrenal gland nodules and masses (adenomas, pheochromocytomas, carcinomas, and metastases). Materials and Methods. Institutional review board approval and informed consent were obtained. A total of 130 patients (47 men) with 132 adrenal nodules/masses were prospectively assessed (54 +/- 14.8 years). A multivoxel system was used with a two-dimensional point-resolved spectroscopy/chemical-shift imaging sequence. Spectroscopic data were interpreted by visual inspection and peak amplitudes of lipids (Lip), choline (Cho), creatine (Cr), Lac, and Glx. Lac/Cr and Glx/Cr were calculated. Glx/Cr was assessed in relation to lesion size. Results. Statistically significant differences were observed in Glx/Cr results between adenomas and pheochromocytomas (P < 0.05), however, with a low positive predictive value (PPV). Glx levels were directly proportional to lesion size in carcinomas. A cutoff point of 1.44 was established for the differentiation between carcinomas larger versus smaller than 4 cm, with 75% sensitivity, 100% specificity, 100% PPV, and 80% accuracy. Lac/Cr results showed no differences across lesions. A cutoff point of -6.5 for Lac/Cr was established for carcinoma diagnosis. Conclusion. Glx levels are directly proportional to lesion size in carcinomas. A cutoff point of -6.5 Lac/Cr differentiates carcinomas from noncarcinomas.Universidade Federal de São Paulo, Dept Diagnost Imaging, BR-04024002 São Paulo, BrazilUniversidade Federal de São Paulo, Dept Endocrinol, BR-04024002 São Paulo, BrazilUniversidade Federal de São Paulo, Dept Urol, BR-04024002 São Paulo, BrazilUniversidade Federal de São Paulo, Dept Diagnost Imaging, BR-04024002 São Paulo, BrazilUniversidade Federal de São Paulo, Dept Endocrinol, BR-04024002 São Paulo, BrazilUniversidade Federal de São Paulo, Dept Urol, BR-04024002 São Paulo, BrazilWeb of Scienc

Diversity of Apolipoprotein E genetic polymorphism significance on cardiovascular risk is determined by the presence of Metabolic Syndrome among hypertensive patients

Background: Hypertension has a significant relevance as a cardiovascular risk factor. A consistent increase on world's Metabolic Syndrome (MetS) incidence has been associated with an epidemic cardiovascular risk in different populations. Dislipidemia plays a major role determining the epidemic CV burden attributed to MetS. Apolipoprotein E (ApoE) is involved on cholesterol and triglycerides metabolism regulation. Once ApoE polymorphism may influence lipid metabolism, it is possible that it brings on individual susceptibility consequences for the development of MetS and cardiovascular risk. the objective of the study is to measure the discriminatory power of ApoE polymorphism in determining cardiovascular risk stratification based on the presence MetS in a cohort of hypertensive patients.Methods: It was enrolled 383 patients, divided in two groups, classified by MetS presence (IDF criteria): Group 1: 266 patients with MetS (MetS +) and Group 2: 117 patients without Mets (MetS -). Patient's data were collected by clinical evaluation, physical exam, file reviews and laboratory testing. Polymorphic ApoE analysis was performed by PCR amplification. Groups were compared on clinical and laboratory characteristics as well as allele and genotype distribution towards ApoE polymorphism. Mets CVD prevalence was analysed according to E4 allele prevalence.Results: the results evidenced 184 men (48%), 63,7% whites, 45,1% diabetics and 11,7% of patients were smokers. Mean age was 64,0 +/- 12,0 years. When genotypic distribution was analyzed, E3/3 genotype and E3 allele frequencies were more prevalent. Among patients with MetS, we observed an independent association between CVD prevalence and E4 allele frequency (OR 2.42 (1.17-5.0, p < 0,05)). On the opposite direction, in those without MetS, there was lesser CVD burden in E4 allele carriers (OR 0,14 (0,02-0,75)). These associations remained significant even after confounding factor corrections.Conclusions: the results presented demonstrate that the association between ApoE gene and CVD may be modulated by the presence of MetS, with an increased CV burden observed among E4 allele carriers with the syndrome. On the opposite way, E4 allele carriers without visceral obesity had lesser prevalence of CVD.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Universidade Federal de São Paulo, Div Nephrol, BR-04039032 São Paulo, BrazilTufts Univ, New England Med Ctr, Div Nephrol, Boston, MA 02111 USAHosp Israelita Albert Einstein, Res & Educ Inst, São Paulo, BrazilUniversidade Federal de São Paulo, Div Nephrol, BR-04039032 São Paulo, BrazilWeb of Scienc

Citrus: A Perspective for Developing Phytomedicines for Neurodegenerative Diseases

The antioxidant and anti-inflammatory properties of Citrus flavonoids can play a key role in their activity against several degenerative diseases and particularly brain diseases. In Brazil promising studies deposited in the patents “pharmaceutical formulation” form was obtained from the inclusion of Citrus sinensis L. (orange) essential oil with β-cyclodextrin and Citrus limon (lemon) compounds and their applications in therapy of Alzheimer’s disease. In this chapter, we report activities of active compounds present in the genus Citrus, which include antioxidant, anti-inflammatory, anxiolytic, insecticidal, and anticholinesterase activities. These activities are associated with some neurodegenerative diseases such as Alzheimer’s disease (AD). Pharmaceutical formulations containing such compounds (for example, inhibitors such as acetylcholinesterase (AChE) of C. limon (5,8-dimethoxy-psoralen and 5,7-dimethoxycumarin) and essential oil from C. sinensis oils are reported in this chapter. These results indicate that the effects of the essential oil and substances of Citrus species are very interesting for further isolation of AChE inhibitors that can be used in the formulation of natural products for neurodegenerative diseases

Apolipoprotein E polymorphism modulation of asymmetric dimethylarginine in hypertensive patients is determined by renal function

Background: Endothelial dysfunction is considered an early step of atherosclerotic vascular disease. Asymmetric dimethylarginine (ADMA), the main endogenous inhibitor of nitric oxide synthase (NOS), plays a critical role in the process of atherosclerosis in a uremic environment. Increased plasma ADMA not only works as a cardiovascular morbidity biomarker but it is also involved in the genesis of atherosclerosis in renal disease. Considering the relationships of apolipoprotein E(ApoE) polymorphism with LDL cholesterol (LDL-C) levels and coronary risk, it is possible that it brings on susceptibility to endothelial dysfunction and atherogenesis seen on uremia. Methods: Six hundred twenty patients were stratified according to glomerular filtration rate (GFR) estimated by Chronic Kidney Disease Epidemiology Collaboration (CKDEPI) formula: group I > 60 mL/min, group II 15 mL/min, and group III <= 15 mL/min or in hemodialysis. Polymorphic ApoE analysis was performed by polymerase chain reaction amplification (PCR). Plasma ADMA levels were measured by high performance liquid chromatography (HPLC). Groups were compared on clinical and laboratory characteristics as well as allele and genotype distribution towards. Results: The epsilon 2 allele of ApoE was present in 62 (10.3 %) patients, epsilon 3 allele in 581 (96.2 %), and epsilon 4 allele in 114 (18.9 %). Their distribution among the 3 groups was uniform. Such uniformity was not observed when we considered endothelial function measured by asymmetric dimethylarginine. In group III, the frequency of epsilon 4 allele was significantly lower in the third tertile compared with the first tertile (14.7 versus 53.3 %, P = 0.000; Pearson chisquare). In groups I and II, there was no difference in allele frequency according to ADMA levels. This association remained significant even after confouding factors corrections (OR 0.329, 95 % CI 0.155 - 0.699, P = 0.004). Conclusions: The results of this study shows that the frequency of epsilon 4 allele of ApoE is significantly lower among hypertensive patients on hemodialysis with the highest levels of ADMA. Uremia is capable of determining lower plasma ADMA levels in hypertensive epsilon 4 allele carriers.Fundo de Amparo a Pesquisa do Estado de Sao Paulo/FAPESPUniv Fed Sao Paulo, Nephrol Div, R Pedro de Toledo 781 14 Andar, BR-04039032 Sao Paulo, BrazilTufts Univ, New England Med Ctr, Nephrol Div, Boston, MA 02111 USAHosp Israelita Albert Einstein, Res & Educ Inst, Sao Paulo, SP, BrazilUniv Fed Sao Paulo, Nephrol Div, R Pedro de Toledo 781 14 Andar, BR-04039032 Sao Paulo, BrazilWeb of Scienc

AVALIAÇÃO DOS EFEITOS DA FLUNIXINA MEGLUMINA, POR VIA SUBCONJUNTIVAL, SOBRE A CONCENTRAÇÃO E PADRÃO PROTEICO DO HUMOR AQUOSO DE CÃES SUBMETIDOS À PARACENTESE DA CÂMARA ANTERIOR

Avaliaram-se os efeitos da flunixina meglumina, pela via subconjuntival, sobre as proteínas do humor aquoso de olhos de cães submetidos à paracentese da câmara anterior. Dez animais adultos, clinicamente sadios, receberam, por aplicação subconjuntival, flunixina meglumina (1,1mg/kg) no olho direito e solução salina estéril a 0,9% no olho esquerdo, em igual volume. Mediante anestesia geral, foram submetidos a duas paracenteses de ambos os olhos para coleta de 0,2mL de aquoso primário e secundário, respectivamente. As amostras foram submetidas ao Teste de Bradford, cujas concentrações proteicas (média e desvio-padrão) obtidas foram de 15,98mg/dL ± 4,48 e 11,46mg/dL ± 2,72 para os olhos direito e esquerdo, respectivamente, na primeira paracentese, e de 119,8mg/dL ± 6,74 e 120,63mg/dL ± 22,4, para olhos direito e esquerdo, na segunda paracentese. Não houve diferença estatisticamente significativa entre os valores proteicos dos olhos tratados comparativamente aos seus controles. Quando comparadas as concentrações proteicas entre a primeira e segunda paracentese de olhos direito e esquerdo, observou-se diferença estatisticamente significativa entre esses dois momentos (

Sistemas de manejo, atributos químicos do solo e dispersão de argila em áreas de microbacias

The objective of this work was to evaluate the effect of different farm systems on clay dispersion and its relationship with soil chemical properties and the no-tillage system participatory quality index (IQP), in watershed areas in the west of the state of Paraná, Brazil. The farm systems evaluated were: no-tillage; no-tillage with crop succession; no-tillage with soil disturbance; and conventional system. In addition, the farm systems were evaluated for their IQP. Soil samples were collected at 0.0–0.20-m soil depth, in 40 agricultural areas and in 6 native forests considered as references. The degree of clay dispersion, total organic carbon, pH (CaCl2), exchangeable potassium (K+), available phosphorus (P), exchangeable calcium and magnesium (Ca2++Mg2+), and potential acidity (H+Al3+) were determined. A linear multiple regression model was fitted by the method of least squares. The averages of clay dispersion degree per watershed were compared at 5% probability. The farm systems were compared by Scott-Knott’s test. Soil chemical properties showed a higher influence on clay dispersion than the different farm systems assessed. The no-tillage system alone showed the highest content of organic carbon, which was similar to those of the native areas. The conventional system and the no-tillage system with soil disturbance showed a lower IQP and a higher degree of clay dispersion than the areas with the no-tillage system alone. The IQP allows distinguishing the conventional system from the no-tillage system.O objetivo deste trabalho foi avaliar o efeito de diferentes sistemas de manejo sobre o grau de dispersão de argila e sua relação com os atributos químicos do solo e o índice de qualidade participativo (IQP) do sistema plantio direto, em áreas de microbacias do Oeste do Paraná. Os sistemas de manejo avaliados foram: sistema plantio direto; plantio direto com sucessão de culturas; plantio direto com revolvimento do solo; e sistema convencional. Além disso, os sistemas de manejo foram avaliados quanto ao seu IQP. Amostras de solo foram coletadas a 0,0–0,20 m de profundidade do solo, em 40 áreas agrícolas e em 6 matas nativas tidas como referências. Foram avaliados grau de dispersão de argila, carbono orgânico total, pH (em CaCl2), potássio trocável (K+), fósforo disponível (P), cálcio e magnésio trocáveis (Ca2++Mg2+), e acidez potencial (H+Al3+). Ajustou-se um modelo de regressão linear múltipla pelo método dos mínimos quadrados. Realizou-se a comparação de médias do grau de dispersão de argila, por microbacia, a 5% de probabilidade. Os sistemas de manejo foram comparados pelo teste de Scott-Knott. Os atributos químicos do solo apresentaram maior influência sobre a dispersão da argila do que os diferentes sistemas de manejo avaliados. O sistema plantio direto integral apresentou o maior teor de carbono orgânico, que foi semelhante ao das áreas nativas. O sistema convencional e o plantio direto com revolvimento do solo apresentaram menor IQP e maiores taxas de dispersão de argila do que as áreas sob sistema plantio direto integral. O IQP permite diferenciar os sistemas de manejo convencional e plantio direto