Structural matching of 2D electrophoresis gels using deformed graphs

2D electrophoresis is a well-known method for protein separation which is extremely useful in the field of proteomics. Each spot in the image represents a protein accumulation and the goal is to perform a differential analysis between pairs of images to study changes in protein content. It is thus necessary to register two images by finding spot correspondences. Although it may seem a simple task, generally, the manual processing of this kind of images is very cumbersome, especially when strong variations between corresponding sets of spots are expected (e.g. strong non-linear deformations and outliers). In order to solve this problem, this paper proposes a new quadratic assignment formulation together with a correspondence estimation algorithm based on graph matching which takes into account the structural information between the detected spots. Each image is represented by a graph and the task is to find a maximum common subgraph. Successful experimental results using real data are presented, including an extensive comparative performance evaluation with ground-truth data. (C) 2010 Elsevier B.V. All rights reserved.

Formulação e caracterização de matérias-primas para revestimento cerâmico Semi-Poroso com adição de chamote de telhas

The ceramics industry in Piauí is nowadays with 55 industries where 11 are in Teresina which is the mainstream of the state, producing 55 million shingles; in which 10 % is of this production is wasted being sometimes thrown on the margins of rivers, roads and highways provoking an environmental degradation. The main goal of this work is to verify the potential of producing semi porous ceramic using grog of shingles, on the first part of this work bodies-of-proof were produced from a basic formula of an industry, doping it with 5 %, 10 %, 15 % and 20 % in mass and in the second part of this work some bodies-of-proof were produced from a formula where one raw material was substituted by 50 % of grog and another substituting it all by grog, bodies-of-proof made of a basic formula previously announced was used for experiment control.The grog and the raw materials were characterized by: particle size analysis , thermal differential analysis, X ray diffraction , X ray fluorescence, an thermal gravimetric analysis and rational analyses. The bodies-of-proof were sintetisized in an industrial oven obeying the normal cycle adopted by an industry, with peak temperatures of 1135 oC and a fast burning cycle of 25 minutes having as energetic fuel liquefied petroleum gas . The pieces that were obtained by this were submersed in rehearsed physics of: water absorption of, apparent specific mass, apparent porosity, lineal retraction, rupture tension to the flexural and dilatometry; mineralogical analysis for X ray diffraction; and microstructural for electronic microscope of sweeping. For all the formulas with addition of grog, superior priorities to the requested by the requirements for semi porous and for the formula to F2-2,5 superior priorities to standard formulas which justifies the incorporation of the shingles in mass for the semi porous ceramic

Produção de grês porcelanato a partir de matérias-primas do Rio Grande do Norte e queima a gás natural

The State of Rio Grande do Norte, Brazil, possess major deposits of feldspar, clay, kaolin and talc, all raw materials used in the production of porcelainized stoneware tiles. Conversely, state industries manufacture only low added value red ceramics. Porcelainized stoneware tiles is one of the noblest ceramics, depicting low water absorption (typically below of 0,5%), in addition to excellent staining resistance and mechanical strength. The present work aims at investigating the potential of local raw materials for the production of porcelainized stoneware tiles. To that end, these materials were characterized by X-ray fluorescence, X-ray diffraction, particle size analysis, thermal gravimetric analysis and thermal differential analysis. Admixtures containing different compositions were prepared and fired at three temperatures, 1150, 1200 and 1250°C for 30 min. After firing, tests samples were characterized by water absorption tests, linear retraction, dilatometric analysis, apparent porosity, apparent specific mass, flexural strength, and microstructural analysis by XRD and SEM. The results revealed that ceramics with porcelainized stoneware tiles characteristics could be produced from raw materials originated in the State of Rio Grande do Norte

Produção de grês porcelanato a partir de matérias-primas do estado da Bahia

The State Bahia, Brazil, presents different geological sites it with a very expressive variety minerals. It is situated among the very important States which produces minerals for industries, such as pointed aggregate, ornamentals stones and ceramics raw materials. Nowadays only four companies producting ceramics tiles. Porcelainized stoneware tiles is one of the noblest ceramics, depicting low water absorption (typically below of 0,5%), in addition to excellent staining resistance and mechanical strength. The present work aims at investigating the potential of local raw materials for the production of porcelainized stoneware tiles. For this purpose, these materials were characterized by X-ray fluorescence, X-ray diffraction, particle size analysis, thermal gravimetric analysis, thermal differential analysis and dilatometric analysis. Admixtures containing different compositions were prepared and fired at four temperatures, 1100 ºC, 1150 ºC, 1200 ºC and 1250 ºC with isotherm for 60 minute and heathing rate of 5 oC/min. After firing the samples, they were characterized by water absorption tests, linear retraction, analysis, apparent porosity, apparent specific mass, flexural strength, and microstructural analysis by X-ray diffraction and scanning electron microscopy . The results revealed three ceramics with porcelainized stoneware tiles characteristics and porcelain tile will be produce from raw materials originated in the State of Bahia

Synthesis, characterization and thermal studies on solid compounds of 2-chlorobenzylidenepyruvate of heavier trivalent lanthanides and yttrium(III)

Solid-state compounds of general formula LnL(3)center dot nH(2)O, where Ln represents heavier lanthanides and yttrium and L is 2-chlorobenzylidenepyruvate, have been synthesized. Chemical analysis, simultaneous thermogravimetry-differential analysis (TG-DTA), differential scanning calorimetry (DSC), X-ray powder diffractometry, elemental analysis and infrared spectroscopy have been employed to characterize and to study the thermal behaviour of these compounds in dynamic air atmosphere.On heating these compounds decompose in four (Gd, Tb, Ho to Lu, Y) or five (Eu, Dy) steps. They lose the hydration water in the first step and the thermal decomposition of the anhydrous compounds up to 1200 degrees C occurs with the formation of the respective oxide, Tb4O7 and Ln(2)O(3) (Ln=Eu, Gd, Dy to Lu and Y) as final residue. The dehydration enthalpies found for these compounds (Eu, to Lu and Y) were: 65.77, 55.63, 86.89, 121.65, 99.80, 109.59, 131.02, 119.78, 205.46 and 83.11 kJ mol(-1), respectively.

Estudos das propriedades ópticas e térmicas dos xerogéis de sílica dopados com Rodamina B

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Perfil de alterações genômicas em angiofibromas nasofaringeos juvenis

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Síntese, caracterização e estudo do comportamento térmico dos 2-clorobenzalpiruvatos de lantânio (III), lantanídios (III) e de ítrio (III), no estado sólido

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Síntese e caracterização de complexos de cetoprofeno com lantanídeos (III) e Ítirio (III) no estado sólido com exceção do promécio

Solid-state compounds of general formula LnL3.nH2O, in wich Ln represents lanthanum, lanthanides and yttrium, L is ketoprofen, and n = 0,5 (Pr, Sm, Tb), 1 (La, Eu, Dy, Ho, Er, Tm, Lu) e 1,5 (Ce, Nd, Gd, Yb, Y) were synthesized. Simultaneous thermogravimetry-differential analysis (TG-DTA), differential scanning calorimetry (DSC), X-ray powder diffractometry, infrared spectroscopy and EDTA complexometry were employed to characterize these compounds. The TG-DTA and DSC curves provided information concerning the thermal behaviour and thermal decomposition of synthesized compounds. The experimental and theoretical infrared spectroscopic data suggested that ketoprofen acts as a bidentate ligand towards trivalent lanthanides and yttrium (III)

Caracterização de filmes de BaxSr1-xTiO3 Sintetizados pelo método hidrotermal assistido por micro-ondas e depositados por eletroforese

Pós-graduação em Ciência e Tecnologia de Materiais - FC

Mass spectrometry-based protein profiling strategies for biomarker discovery in liver and inflammatory bowel diseases

The study of protein expression profiles for biomarker discovery in serum and in mammalian cell populations needs the continuous improvement and combination of proteins/peptides separation techniques, mass spectrometry, statistical and bioinformatic approaches. In this thesis work two different mass spectrometry-based protein profiling strategies have been developed and applied to liver and inflammatory bowel diseases (IBDs) for the discovery of new biomarkers. The first of them, based on bulk solid-phase extraction combined with matrix-assisted laser desorption/ionization - Time of Flight mass spectrometry (MALDI-TOF MS) and chemometric analysis of serum samples, was applied to the study of serum protein expression profiles both in IBDs (Crohn’s disease and ulcerative colitis) and in liver diseases (cirrhosis, hepatocellular carcinoma, viral hepatitis). The approach allowed the enrichment of serum proteins/peptides due to the high interaction surface between analytes and solid phase and the high recovery due to the elution step performed directly on the MALDI-target plate. Furthermore the use of chemometric algorithm for the selection of the variables with higher discriminant power permitted to evaluate patterns of 20-30 proteins involved in the differentiation and classification of serum samples from healthy donors and diseased patients. These proteins profiles permit to discriminate among the pathologies with an optimum classification and prediction abilities. In particular in the study of inflammatory bowel diseases, after the analysis using C18 of 129 serum samples from healthy donors and Crohn’s disease, ulcerative colitis and inflammatory controls patients, a 90.7% of classification ability and a 72.9% prediction ability were obtained. In the study of liver diseases (hepatocellular carcinoma, viral hepatitis and cirrhosis) a 80.6% of prediction ability was achieved using IDA-Cu(II) as extraction procedure. The identification of the selected proteins by MALDITOF/ TOF MS analysis or by their selective enrichment followed by enzymatic digestion and MS/MS analysis may give useful information in order to identify new biomarkers involved in the diseases. The second mass spectrometry-based protein profiling strategy developed was based on a label-free liquid chromatography electrospray ionization quadrupole - time of flight differential analysis approach (LC ESI-QTOF MS), combined with targeted MS/MS analysis of only identified differences. The strategy was used for biomarker discovery in IBDs, and in particular of Crohn’s disease. The enriched serum peptidome and the subcellular fractions of intestinal epithelial cells (IECs) from healthy donors and Crohn’s disease patients were analysed. The combining of the low molecular weight serum proteins enrichment step and the LCMS approach allowed to evaluate a pattern of peptides derived from specific exoprotease activity in the coagulation and complement activation pathways. Among these peptides, particularly interesting was the discovery of clusters of peptides from fibrinopeptide A, Apolipoprotein E and A4, and complement C3 and C4. Further studies need to be performed to evaluate the specificity of these clusters and validate the results, in order to develop a rapid serum diagnostic test. The analysis by label-free LC ESI-QTOF MS differential analysis of the subcellular fractions of IECs from Crohn’s disease patients and healthy donors permitted to find many proteins that could be involved in the inflammation process. Among them heat shock protein 70, tryptase alpha-1 precursor and proteins whose upregulation can be explained by the increased activity of IECs in Crohn’s disease were identified. Follow-up studies for the validation of the results and the in-depth investigation of the inflammation pathways involved in the disease will be performed. Both the developed mass spectrometry-based protein profiling strategies have been proved to be useful tools for the discovery of disease biomarkers that need to be validated in further studies.

Análisis de música grabada : baladas y scherzos de Chopin

Análisis de múltiples grabaciones de las cuatro baladas y los cuatro scherzos de Chopin realizadas por diversos intérpretes. El objetivo del proyecto será determinar las diferencias objetivas existentes entre las diferentes ejecuciones y respecto a una partitura de referencia. OBJETIVOS: Analizar las grabaciones realizadas de obras de Chopin atendiendo a criterios objetivos como el tempo y la dinámica. MÉTODO Y FASES DEL TRABAJO: Se realizará un estudio diferencial para determinar las variaciones de parámetros objetivos existentes en las diferentes grabaciones respecto a una, que será tomada como referencia, mediante herramientas informáticas. MEDIOS: Se utilizarán versiones digitalizadas de las grabaciones y la edición crítica de Jan Ekier (National Edition) de las partituras. Para la realización del análisis se recurrirá al software SonicVisualiser desarrollado por el Centre for Digital Music (Queen Mary, University of London) en conjunto con los plugins destinados al análisis temporal y espectral disponibles. Así mismo, serán utilizadas otras herramientas desarrolladas durante el Mazurka's Project realizado por el Research Centre for the History and Analysis of Recorded Music para facilitar la visualización de datos en el presente documento. OBJETIVE: To analyze several records from Chopin’s repertoire, according to objective criteria like tempi and dynamics evolution. METHODOLOGY: A differential analysis is going to be made to determine how this criterion differs from every digitalized record to another one stabilized in advance as model. In order to do so, we’ll use software tools as well as auditions to get the best detail. MEDIA: Digital editions of the recordings and the critical edition by Prof. Jan Ekier music scores have been used. We’ve chosen the software tool SonicVisualiser developed by Centre for Digital Music (Queen Mary, University of London) in conjunction with some of the temporal and spectral plugins available for this platform as our main analysis tool. We’ve also used some other tools developed by the Research Centre for the History and Analysis of Recorded Music to appropriately display some important information in the present document.

A Compact Formula for the Derivative of a 3-D Rotation in Exponential Coordinates

We present a compact formula for the derivative of a 3-D rotation matrix with respect to its exponential coordinates. A geometric interpretation of the resulting expression is provided, as well as its agreement with other less-compact but better-known formulas. To the best of our knowledge, this simpler formula does not appear anywhere in the literature. We hope by providing this more compact expression to alleviate the common pressure to reluctantly resort to alternative representations in various computational applications simply as a means to avoid the complexity of differential analysis in exponential coordinates.

Proteomic definition of normal human luminal and myoepithelial breast cells purified from reduction mammoplasties

Normal human luminal and myoepithelial breast cells separately purified from a set of 10 reduction mammoplasties by using a double antibody magnetic affinity cell sorting and Dynabead immunomagnetic technique were used in two-dimensional gel proteome studies. A total of 43,302 proteins were detected across the 20 samples, and a master image for each cell type comprising a total of 1,738 unique proteins was derived. Differential analysis identified 170 proteins that were elevated 2-fold or more between the two breast cell types, and 51 of these were annotated by tandem mass spectrometry. Muscle-specific enzyme isoforms and contractile intermediate filaments including tropomyosin and smooth muscle (SM22) alpha protein were detected in the myoepithelial cells, and a large number of cytokeratin subclasses and isoforms characteristic of luminal cells were detected in this cell type. A further 134 nondifferentially regulated proteins were also annotated from the two breast cell types, making this the most extensive study to date of the protein expression map of the normal human breast and the basis for future studies of purified breast cancer cells.

Investigação de mecanismos genéticos e epigenéticos em distúrbios do crescimento humano

Parcela considerável de pacientes com distúrbios de crescimento não têm a causa de seus quadros clínicos estabelecida, incluindo aproximadamente 50% dos pacientes com diagnóstico clínico de síndrome de Silver−Russell (SRS) e 10-20% dos pacientes com síndrome de Beckwith-Wiedemann (BWS). O objetivo deste estudo foi investigar as causas genéticas e epigenéticas de distúrbios de crescimento, de etiologia desconhecida, numa contribuição para o entendimento de mecanismos que regulam o crescimento. O estudo compreendeu: (1) a investigação de microdesequilíbrios cromossômicos, por aCGH; (2) a análise do perfil de expressão alelo-específica de genes sujeitos a imprinting (IG), por pirossequenciamento (PSQ) ou sequenciamento de Sanger; (3) a investigação do padrão de metilação global em pacientes com restrição de crescimento, utilizando microarray de metilação. A casuística constituiu-se de 41 pacientes não aparentados, com distúrbios de crescimento, de etiologia desconhecida: (1) 25, com hipótese diagnóstica de SRS; (2) seis, com restrição de crescimento intrauterino e peso ao nascimento abaixo do 10º percentil, associados a outros sinais clínicos; (3) sete, com hipótese diagnóstica de BWS; e (4) três, com macrossomia pré-natal ou pós-natal, associada a outros sinais. A investigação de microdesequilíbrios cromossômicos foi realizada em 40 pacientes. Foram detectadas 58 variantes raras em 30/40 pacientes (75%): 40 foram consideradas provavelmente benignas (18 pacientes, 45%), 12, com efeito patogênico desconhecido (11 pacientes, 27,5%), duas, provavelmente patogênicas (um paciente, 2,5%) e quatro, patogênicas (três pacientes, 7,5%). Essas frequências são comparáveis àquelas descritas em estudos que investigaram CNV em grupos de pacientes com distúrbios de crescimento e outras alterações congênitas, incluindo SRS, e mostram a importância da investigação de microdesequilíbrios cromossômicos nesses pacientes. A diversidade dos microdesequilíbrios cromossômicos identificados é reflexo da heterogeneidade clínica das casuísticas. Neste estudo, muitos dos pacientes com hipótese diagnóstica de SRS e BWS apresentavam sinais clínicos atípicos, explicando a ausência neles das alterações (epi)genéticas que causam essas síndromes. A identificação de CNV características de outras síndromes reflete a sobreposição de sinais clínicos com BWS e SRS. A análise do perfil de expressão alelo-específica de IG foi realizada em um subgrupo de 18 pacientes com restrição de crescimento. Trinta IG com função em proliferação celular, crescimento fetal ou neurodesenvolvimento foram inicialmente selecionados. Após seleção de SNP transcritos com alta frequência na população, genotipagem de pacientes, genitores e indivíduos controle, determinação da expressão dos IG em sangue periférico e seu padrão de expressão (mono ou bialélico), 13 IG, expressos no sangue, tiveram a expressão alelo-específica avaliada, sete deles por PSQ e seis por sequenciamento de Sanger. Alterações no perfil de expressão de dois genes, de expressão normalmente paterna, foram detectadas em 4/18 pacientes (22%). Este estudo é o primeiro a utilizar pirossequenciamento e sequenciamento de Sanger na avaliação do perfil de expressão alelo-específica de IG, em pacientes com restrição de crescimento. Apesar de terem limitações, ambas as técnicas mostraram-se robustas e revelaram alterações de expressão alélica interessantes; entretanto, a relação dessas alterações com o quadro clínico dos pacientes permanece por esclarecer. A investigação da metilação global do DNA foi realizada em subgrupo de 21 pacientes com restrição de crescimento e em 24 indivíduos controle. Dois tipos de análise foram realizados: (1) análise diferencial de grupo e (2) análise diferencial individual. Na primeira análise, em que foi comparado o padrão de metilação do grupo de pacientes com quadro clínico sugestivo de SRS (n=16) com o do grupo controle (n=24), não houve indicação de hipo ou hipermetilação global no grupo SRS. Na segunda análise, foi comparado o padrão de metilação de cada um dos 21 pacientes com restrição de crescimento e dos 24 indivíduos controle, com o padrão de metilação do grupo controle. O número médio de CpG hipermetilados e de segmentos diferencialmente metilados (SDM) foi significativamente maior nos pacientes. Foram identificados 82 SDM hipermetilados, estando 57 associados a gene(s) (69,5%), em 16 pacientes, e 51 SDM hipometilados, 41 deles associados a gene(s) (80,4%), em 10 pacientes. A análise de ontologia genética dos 61 genes associados aos SDM hipo ou hipermetilados nos pacientes destacou genes que atuam no desenvolvimento e na morfogênese do sistema esquelético e de órgãos fetais, e na regulação da transcrição gênica e de processos metabólicos. Alterações de metilação em genes que atuam em processos de proliferação e diferenciação celulares e crescimento foram identificadas em 9/20 dos pacientes (45%), sugerindo implicação clínica. Não foi detectada alteração epigenética comum aos pacientes com diagnóstico clínico de SRS, explicável provavelmente pela heterogeneidade clínica. A investigação de metilação global, utilizando microarray, produziu novos dados que podem contribuir para a compreensão de mecanismos moleculares que influenciam o crescimento pré- e pós-natal. Na translocação aparentemente equilibrada - t(5;6)(q35.2;p22.3)dn, detectada em paciente com suspeita clínica de SRS, a interrupção de um gene, pela quebra no cromossomo 6, pode ser a causa do quadro clínico; alternativamente, a translocação pode ter impactado a regulação de genes de desenvolvimento localizados próximos aos pontos de quebra. A análise de expressão em sangue periférico mostrou que os níveis de cDNA do gene, interrompido pelo ponto de quebra da translocação, estavam reduzidos à metade. Além de sinais típicos da SRS, a paciente apresentava algumas características clínicas sugestivas de displasia cleidocraniana. Assim, a translocação t(5;6) pode ter alterado a interação de genes de desenvolvimento e seus elementos reguladores, levando à desregulação de sua expressão espaço-temporal, e resultando num fenótipo atípico, com características sobrepostas de mais de uma síndrome genética