Multicentric validation of proteomic biomarkers in urine specific for diabetic nephropathy

Background: Urine proteome analysis is rapidly emerging as a tool for diagnosis and prognosis in disease states. For diagnosis of diabetic nephropathy (DN), urinary proteome analysis was successfully applied in a pilot study. The validity of the previously established proteomic biomarkers with respect to the diagnostic and prognostic potential was assessed on a separate set of patients recruited at three different European centers. In this case-control study of 148 Caucasian patients with diabetes mellitus type 2 and duration >= 5 years, cases of DN were defined as albuminuria >300 mg/d and diabetic retinopathy (n = 66). Controls were matched for gender and diabetes duration (n = 82). Methodology/Principal Findings: Proteome analysis was performed blinded using high-resolution capillary electrophoresis coupled with mass spectrometry (CE-MS). Data were evaluated employing the previously developed model for DN. Upon unblinding, the model for DN showed 93.8% sensitivity and 91.4% specificity, with an AUC of 0.948 (95% CI 0.898-0.978). Of 65 previously identified peptides, 60 were significantly different between cases and controls of this study. In <10% of cases and controls classification by proteome analysis not entirely resulted in the expected clinical outcome. Analysis of patient's subsequent clinical course revealed later progression to DN in some of the false positive classified DN control patients. Conclusions: These data provide the first independent confirmation that profiling of the urinary proteome by CE-MS can adequately identify subjects with DN, supporting the generalizability of this approach. The data further establish urinary collagen fragments as biomarkers for diabetes-induced renal damage that may serve as earlier and more specific biomarkers than the currently used urinary albumin

LinkedScales : bases de dados em multiescala

Orientador: André SantanchèTese (doutorado) - Universidade Estadual de Campinas, Instituto de ComputaçãoResumo: As ciências biológicas e médicas precisam cada vez mais de abordagens unificadas para a análise de dados, permitindo a exploração da rede de relacionamentos e interações entre elementos. No entanto, dados essenciais estão frequentemente espalhados por um conjunto cada vez maior de fontes com múltiplos níveis de heterogeneidade entre si, tornando a integração cada vez mais complexa. Abordagens de integração existentes geralmente adotam estratégias especializadas e custosas, exigindo a produção de soluções monolíticas para lidar com formatos e esquemas específicos. Para resolver questões de complexidade, essas abordagens adotam soluções pontuais que combinam ferramentas e algoritmos, exigindo adaptações manuais. Abordagens não sistemáticas dificultam a reutilização de tarefas comuns e resultados intermediários, mesmo que esses possam ser úteis em análises futuras. Além disso, é difícil o rastreamento de transformações e demais informações de proveniência, que costumam ser negligenciadas. Este trabalho propõe LinkedScales, um dataspace baseado em múltiplos níveis, projetado para suportar a construção progressiva de visões unificadas de fontes heterogêneas. LinkedScales sistematiza as múltiplas etapas de integração em escalas, partindo de representações brutas (escalas mais baixas), indo gradualmente para estruturas semelhantes a ontologias (escalas mais altas). LinkedScales define um modelo de dados e um processo de integração sistemático e sob demanda, através de transformações em um banco de dados de grafos. Resultados intermediários são encapsulados em escalas reutilizáveis e transformações entre escalas são rastreadas em um grafo de proveniência ortogonal, que conecta objetos entre escalas. Posteriormente, consultas ao dataspace podem considerar objetos nas escalas e o grafo de proveniência ortogonal. Aplicações práticas de LinkedScales são tratadas através de dois estudos de caso, um no domínio da biologia -- abordando um cenário de análise centrada em organismos -- e outro no domínio médico -- com foco em dados de medicina baseada em evidênciasAbstract: Biological and medical sciences increasingly need a unified, network-driven approach for exploring relationships and interactions among data elements. Nevertheless, essential data is frequently scattered across sources with multiple levels of heterogeneity. Existing data integration approaches usually adopt specialized, heavyweight strategies, requiring a costly upfront effort to produce monolithic solutions for handling specific formats and schemas. Furthermore, such ad-hoc strategies hamper the reuse of intermediary integration tasks and outcomes. This work proposes LinkedScales, a multiscale-based dataspace designed to support the progressive construction of a unified view of heterogeneous sources. It departs from raw representations (lower scales) and goes towards ontology-like structures (higher scales). LinkedScales defines a data model and a systematic, gradual integration process via operations over a graph database. Intermediary outcomes are encapsulated as reusable scales, tracking the provenance of inter-scale operations. Later, queries can combine both scale data and orthogonal provenance information. Practical applications of LinkedScales are discussed through two case studies on the biology domain -- addressing an organism-centric analysis scenario -- and the medical domain -- focusing on evidence-based medicine dataDoutoradoCiência da ComputaçãoDoutor em Ciência da Computação141353/2015-5CAPESCNP

Avaliação in vitro do efeito dissolvente de bebidas carbonatadas (CocaCola® ) e soluções à base de enzimas sobre enterólitos obtidos de cavalos: estudo piloto

Enterólitos são concreções de minerais que causam obstrução parcial ou total do lume intestinal, resultando em cólica crônica e recorrente nos cavalos. Este estudo piloto teve como objetivo avaliar in vitro o efeito dissolvente sobre os enterólitos das bebidas carbonatadas (Coca-Cola® e Coca-Cola®Zero) e a solução à base das enzimas papaína e celulase (Robinson Pharma®, Santa Ana, CA, USA). Seis (6) amostras de seis (6) enterólitos de 51gramas de peso foram distribuídas em seis tratamentos de imersão: T1: Coca-Cola®; T2: Coca-Cola® Zero; T3: água destilada + papaína (90 mg) e celulase (120 mg); T4: Coca-Cola® + papaína e celulase; T5: Coca-Cola® Zero + papaína e celulase; e, CT: água destilada (controle). O volume das soluções de imersão foi de 150 mL, com pH de 7.1, usando um shaker de incubação (Heidolph®, Germany) com 37ºC e 25 rpm, durante 72 horas. A avaliação dos períodos da porcentagem de dissolução (diferenças entre o peso inicial e o peso final das amostras) foram 0, 3, 12, 24, 36, 48, 60 e 72 h. Depois de 72 h de imersão, as soluções T4, T5 e T1 apresentaram 47, 38,8 e 14,9% de dissolução, respectivamente. As outras soluções não tiveram diferenças com relação ao CT (controle). Nas condições in vitro deste estudo piloto, as enzimas papaína e celulase potenciam o efeito dissolvente das bebidas carbonatadas sobre os enterólitos obtidos de cavalos. Mais estudos são sugeridos, uma vez que só existe literatura sobre a dissolução de fitobezoares e não de enterólitos.Enteroliths are concretions of minerals that cause partial or total obstruction of the intestinal lumen, resulting in recurrent and chronic colic in horses. This pilot study aimed to evaluate the in vitro solvent effect of carbonated beverages (Coca-Cola® and Coca-Cola® Zero), and papain and cellulase enzymes (Robinson Pharma®, Santa Ana, CA, USA) on enteroliths obtained from horses. Six 51-grams samples of six enteroliths were assigned to six treatments of immersion solutions: T1, Coca-Cola®; T2: Coca-Cola® Zero; T3: distilled water + papain (90 mg) and cellulase (120 mg); T4: Coca-Cola® + papain and cellulase; T5: Coca-Cola® Zero + papain and cellulase; and, CT: distilled water (control). The volume for immersion in the assigned solution was 150 mL, at a pH of 7.1, using an incubation shaker (Heidolph® , Germany) at 37ºC and 25 rpm, for 72 h. The evaluation periods of the dissolution percentage (difference between the initial weight and final weight of the samples), were 0, 3, 12, 24, 36, 48, 60, and 72 h. After 72 h of immersion, solutions T4, T5, and T1 presented 47, 38.8, and 14.9% of dissolution, respectively. The other solutions did not have major differences with CT (control). Under the in vitro conditions of this pilot study, papain and cellulase enzymes potentiated the dissolving effect of the carbonated solutions on the enteroliths obtained from horses. Further studies are suggested since the existing literature is on the dissolution of phytobezoars and not of enteroliths.

A database of naturally occurring human urinary peptides and proteins for use in clinical applications

Owing to its availability, ease of collection and correlation with (patho-) physiology, urine is an attractive source for clinical proteomics. However, the lack of comparable datasets from large cohorts has greatly hindered development in this field. Here we report the establishment of a high resolution proteome database of naturally occurring human urinary peptides and proteins - ranging from 800-17,000 Da - from over 3,600 individual samples using capillary electrophoresis coupled to mass spectrometry, yielding an average of 1,500 peptides per sample. All processed data were deposited in an SQL database, currently containing 5,010 relevant unique urinary peptides that serve as classifiers for diagnosis and monitoring of diseases, including kidney and vascular diseases. Of these, 352 have been sequenced to date. To demonstrate the applicability of this database, two examples of disease diagnosis were provided: For renal damage diagnosis, patients with a specific renal disease were identified with high specificity and sensitivity in a blinded cohort of 131 individuals. We further show definition of biomarkers specific for immunosuppression and complications after transplantation (Kaposi's sarcoma). Due to its high information content, this database will be a powerful tool for the validation of biomarkers for both renal and non-renal diseases