Uncovering protein interaction in abstracts and text using a novel linear model and word proximity networks

We participated in three of the protein-protein interaction subtasks of the Second BioCreative Challenge: classification of abstracts relevant for protein-protein interaction (IAS), discovery of protein pairs (IPS) and text passages characterizing protein interaction (ISS) in full text documents. We approached the abstract classification task with a novel, lightweight linear model inspired by spam-detection techniques, as well as an uncertainty-based integration scheme. We also used a Support Vector Machine and the Singular Value Decomposition on the same features for comparison purposes. Our approach to the full text subtasks (protein pair and passage identification) includes a feature expansion method based on word-proximity networks. Our approach to the abstract classification task (IAS) was among the top submissions for this task in terms of the measures of performance used in the challenge evaluation (accuracy, F-score and AUC). We also report on a web-tool we produced using our approach: the Protein Interaction Abstract Relevance Evaluator (PIARE). Our approach to the full text tasks resulted in one of the highest recall rates as well as mean reciprocal rank of correct passages. Our approach to abstract classification shows that a simple linear model, using relatively few features, is capable of generalizing and uncovering the conceptual nature of protein-protein interaction from the bibliome. Since the novel approach is based on a very lightweight linear model, it can be easily ported and applied to similar problems. In full text problems, the expansion of word features with word-proximity networks is shown to be useful, though the need for some improvements is discussed

Comparison between fresh and fixed human biopsies using spectral and lifetime measurements: Fluorescence analysis using one and two photon excitations

International audienceThe purpose of this study is to make a comparison between the fluorescence emissions of fresh extracted human biopsies and fixed human biopsies, in order to evaluate the impact of fixation on autofluoresence signal. Our group is developing an endo-microscope to image brain tissues in-vivo, however to date, in order to validate our technology the easiest type of samples we can access are fixed samples. However, the fixation is still challenging. For that, we aim through this study to determine whether we should pursue to work on fixed samples or we should shift to work on fresh biopsies. Data were collected on spectroscopic, lifetime measurement and fluorescence imaging setups with visible and two-photon excitations wavelengths. Five fresh and five fixed samples are involved in the experiment. Endogenous fluorescence of fixed biopsies were calculated. Experimental results reveal that at 405 nm and 810 nm, the fresh samples have an intensity of fluorescence two times higher than that of fixed samples. However, for each fluorophore and each excitation wavelength, the lifetime for fresh samples is shorter than that for fixed samples. Still, further studies and investigations involving the comparison between different samples are required to strengthen our findings

Experimental and analytical comparative study of optical coefficient of fresh and frozen rat tissues

International audienceOptical properties of fresh and frozen tissues of rat heart, kidney, brain, liver, and muscle were measured in the 450-to 700-nm range. The total reflectance and transmittance were measured using a well-calibrated integral sphere setup. Absorption coefficient μ a and reduced scattering coefficient μ 0 s were derived from the experimental measurements using the inverse adding doubling technique. The influence of cryogenic processing on optical properties was studied. Interindividual and intraindividual variations were assessed. These new data aim at filling the lack of validated optical properties in the visible range especially in the blue-green region of particular interest for fluorescence and optogenetics preclinical studies. Furthermore, we provide a unique comparison of the optical properties of different organs obtained using the same measurement setup for fresh and frozen tissues as well as an estimate of the intraindividual and interindividual variability

Transcriptional regulatory network discovery via multiple method integration: application to e. coli K12

Transcriptional regulatory network (TRN) discovery from one method (e.g. microarray analysis, gene ontology, phylogenic similarity) does not seem feasible due to lack of sufficient information, resulting in the construction of spurious or incomplete TRNs. We develop a methodology, TRND, that integrates a preliminary TRN, microarray data, gene ontology and phylogenic similarity to accurately discover TRNs and apply the method to E. coli K12. The approach can easily be extended to include other methodologies. Although gene ontology and phylogenic similarity have been used in the context of gene-gene networks, we show that more information can be extracted when gene-gene scores are transformed to gene-transcription factor (TF) scores using a preliminary TRN. This seems to be preferable over the construction of gene-gene interaction networks in light of the observed fact that gene expression and activity of a TF made of a component encoded by that gene is often out of phase. TRND multi-method integration is found to be facilitated by the use of a Bayesian framework for each method derived from its individual scoring measure and a training set of gene/TF regulatory interactions. The TRNs we construct are in better agreement with microarray data. The number of gene/TF interactions we discover is actually double that of existing networks

Sleep disturbance prevalence in postmenopausal women

PURPOSE: to evaluate the prevalence of reported sleep disturbances through polysomnographic recording (PSG) in a sample of postmenopausal women. METHODS: thirty-three postmenopausal women with a mean age of 56 years, a mean body mass index (BMI) of 27 kg/m², with 7.7 years of recognized postmenopausal period, and a mean Kupperman index of 17, were selected. The inclusion criteria were: age range from 50 to 65 years, at least one year of amenorrhea and an FSH which equaled or exceeded 30 mU/ml; they should not be undergoing hormone therapy, and should display normal laboratory test results. The patients with severe clinical diseases and/or decompensated were excluded; also the ones with suspicion of carcinoma of endometrium and/or breast cancer, a BMI over 30 kg/m² and those who ingested hypnotic drugs. The patients followed a routine climacteric check-up, answered a questionnaire about sleep and underwent an all-night PSG recording. Frequencies in percentage of emerging sleep complaints based on the questionnaire and those pertaining to PSG diagnosis were then calculated separately. RESULTS: the subjective prevalence of insomnia was 61% against 83% in the PSG recordings. The prevalence of apnea reported was 23% against 27% in the PSG. The subjective restless legs syndrome prevalence was 45%, and the objective, 27%. CONCLUSION: there was a high prevalence of sleep disturbances in postmenopausal patients, specially insomnia, apnea and restless legs.OBJETIVO: avaliar a prevalência das queixas de distúrbios do sono pela polissonografia em amostra de mulheres na pós-menopausa. MÉTODOS: foram selecionadas 33 mulheres na pós-menopausa com média de idade de 56 anos, índice de massa corporal médio de 27, tempo de pós-menopausa de 7,7 anos e índice de Kupperman de 17. Adotaram-se os seguintes critérios de inclusão: idade entre 50 e 65anos, no mínimo um ano de amenorréia e FSH plasmático superior ou igual a 30 mU/mL, sem uso de terapia hormonal prévia e exames laboratoriais normais. Foram excluídas as pacientes com doenças clínicas graves e/ou descompensadas, suspeita de câncer de endométrio e/ou mama; índice de massa corporal maior ou igual a 30 e uso de hipnóticos. As pacientes responderam a questionário específico contendo perguntas sobre as características do sono e foram submetidas a polissonografia completa durante uma noite inteira. Foram calculadas separadamente as freqüências em porcentagens das queixas de sono e dos diagnósticos polissonográficos. RESULTADOS: a prevalência de insônia subjetiva foi 61%, sendo que na polissonografia foi de 83%. A queixa de apnéia foi registrada em 23% e, na polissonografia, em 27%. A prevalência subjetiva de movimentos periódicos de pernas foi de 45% e a objetiva foi de 27%. CONCLUSÃO: houve alta prevalência de distúrbios do sono na pós-menopausa, em especial de insônia, apnéia e de movimentos periódicos das pernas. Nesta fase da vida, ocorre piora da qualidade do sono.Universidade Federal de São Paulo (UNIFESP) Departamento de Ginecologia ambulatório de Distúrbios do SonoUniversidade Federal de São Paulo (UNIFESP) Departamento de Psicobiologia Medicina e Biologia do SonoUNIFESP, Depto. de Ginecologia ambulatório de Distúrbios do SonoUNIFESP, Depto. de Psicobiologia Medicina e Biologia do SonoSciEL

Testing extensive use of NER tools in article classification and a statistical approach for method interaction extraction in the protein-protein interaction literature

We participated (as Team 81) in the Article Classification (ACT) and Interaction Method (IMT) subtasks of the Protein-Protein Interaction task of the Biocreative III Challenge. For the ACT we pursued an extensive testing of available Named Entity Recognition (NER) tools, and used the most promising ones to extend our the Variable Trigonometric Threshold (VTT) linear classifier we successfully used in BioCreative II and II.5. Our main goal was to exploit the power of available NER tools to aid in the document classification of documents relevant for Protein-Protein Interaction. We also used a Support Vector Machine Classifier on NER features for comparison purposes. For the IMT, we experimented with a primarily statistical approach, as opposed to a deeper natural language processing strategy; in a nutshell, we exploited classifiers, simple pattern matching, and ranking of candidate matches using statistical considerations. We will also report on our efforts to integrate our IMT method sentence classifier into our ACT pipeline

Effects of isoflavones on the skin of postmenopausal women: a pilot study

OBJECTIVE: The aim of this study was to evaluate the effects of isoflavones on the skin of postmenopausal women. DESIGN: A prospective study was performed with 30 postmenopausal women before and immediately after the end of treatment with 100 mg/day of an isoflavones-rich, concentrated soy extract for six months. A skin punch was performed in the gluteal region for sample collection before and immediately after the treatment program. Morphometric determination of epidermal thickness, the papillary index (wrinkling), and the amount of dermal elastic and collagen fibers was assessed. In addition, the number of blood vessels in the sample was also evaluated. The paired Student's t-test was used for statistical analysis (P < 0.05). RESULTS: Isoflavone treatment resulted in a 9.46% increase in the thickness of the epidermis in 23 patients. In addition, the papillary index was reduced in 21 women. The papillary index was inversely proportional to skin wrinkling, i.e., there were a large number of papillae after treatment. The amount of collagen in the dermis was increased in 25 women (86.2%). In 22 women (75.8%) we observed that the number of elastic fibers increased. The number of dermal blood vessels was significantly increased in 21 women. CONCLUSION: Our data show that the use of a concentrated, isoflavone-rich soy extract during six consecutive months caused significant increases in epithelial thickness, the number of elastic and collagen fibers, as well as the blood vessels.Federal University of São Paulo Gynecology DepartmentFederal University of São Paulo Morphology DepartmentUniversidade de São Paulo Faculdade de Medicina Laboratório de Ginecologia Estrutural e MolecularUniversidade de São Paulo Faculdade de Medicina Departamento de Obstetrícia e GinecologiaUNIFESP, Gynecology DepartmentUNIFESP, Morphology DepartmentSciEL

Efeitos da terapia de reposição hormonal estroprogestativa sobre o sistema de coagulação e de fibrinólise em mulheres na pós-menopausa

OBJECTIVE: To evaluate antithrombin III (AT), thrombin (Fragment 1+2 [F1+2] and thrombin-antithrombin [TAT]) generation markers, as well as other coagulation parameters, such as prothrombin time, partial activated thromboplastin time, thrombin time, fibrinogen, euglobulin lysis time, and platelet count, in postmenopausal women after hormonal therapy. STUDY DESIGN: Forty-five patients who received either 0.625 mg/day unopposed oral conjugated equine estrogen (CEE), 0.625 mg/day oral CEE plus medroxyprogesterone acetate (MP), or 50 &micro;g/day transdermal 17beta-estradiol plus MP, were included. Tests were performed before (T0) and after 3 (T3), 6 (T6) and 12 (T12) months of treatment. AT was determined by an amidolytic method, whereas F1+2 and TAT complex were measured by ELISA. RESULTS: There was a significant reduction in the AT level of patients who received oral CEE plus MP at T3. There was no AT reduction in patients taking either oral CEE alone or transdermal 17beta-estradiol plus MP. F1+2 increased in all patients, but it reached statistical significance only in patients receiving transdermal 17beta-estradiol MP at T3. CONCLUSIONS: The CEE associated with MP treatment may reduce AT levels, whereas unopposed CEE or transdermal 17beta-estradiol plus MP does not change AT. These changes might not be clinically relevant in the general population; however, hormonal replacement therapy may increase the risk of thrombosis in women with congenital or acquired thrombophilia.OBJETIVO: Avaliar os marcadores antitrombina III (AT), fragmento 1 + 2 da trombina (F1+2) e complexo trombina-antitrombina (TAT), bem como outros parâmetros da coagulação, como tempo de pró-trombina, tempo parcial de tromboplastina ativado, tempo de trombina, fibrinogênio e tempo de lise da euglobulina em mulheres na pós-menopausa após terapia hormonal. DESENHO DO ESTUDO: Foram incluídas 45 voluntárias que receberam estrogênios conjugados eqüinos (ECE) 0,625 mg/dia, isoladamente ou associado ao acetato de medroxiprogesterona (AMP) ou usaram o 17beta-estradiol (50 &micro;g/dia) transdérmico com AMP. Os exames foram realizados antes do tratamento (T0) e após três (T3), seis (T6) e doze (T12) meses após o início do tratamento. AT foi avaliada pelo método amidolítico, enquanto que o F1+2 e o complexo TAT por ELISA. RESULTADOS: Houve redução significante nos níveis de AT em pacientes que receberam ECE associado ao AMP no T3. Não houve redução na AT em mulheres que usaram ECE isoladamente ou aquelas com 17beta-estradiol transdérmico e AMP. O F1+2 aumentou em todos os grupos, mas apenas o grupo com 17beta-estradiol transdérmico e AMP apresentou diferença significante durante o T3. CONCLUSÕES: A associação de ECE e AMP pode reduzir os níveis de AT, enquanto ECE isoladamente ou 17beta-estradiol transdérmico com AMP não modificam-o acentuadamente. Essas alterações poderiam ser mais relevantes clinicamente na análise populacional. Todavia, a terapia de reposição hormonal aumentaria o risco de trombose em mulheres com trombofilia prévia congênita ou adquirida