Integrating data from heterogeneous DNA microarray platforms

DNA microarrays are one of the most used technologies for gene expression measurement. However, there are several distinct microarray platforms, from different manufacturers, each with its own measurement protocol, resulting in data that can hardly be compared or directly integrated. Data integration from multiple sources aims to improve the assertiveness of statistical tests, reducing the data dimensionality problem. The integration of heterogeneous DNA microarray platforms comprehends a set of tasks that range from the re-annotation of the features used on gene expression, to data normalization and batch effect elimination. In this work, a complete methodology for gene expression data integration and application is proposed, which comprehends a transcript-based re-annotation process and several methods for batch effect attenuation. The integrated data will be used to select the best feature set and learning algorithm for a brain tumor classification case study. The integration will consider data from heterogeneous Agilent and Affymetrix platforms, collected from public gene expression databases, such as The Cancer Genome Atlas and Gene Expression Omnibus.

DNA barcodes de peixes marinhos da Europa: compilação de uma biblioteca de referência validada e investigação de padrões de divergência genética

Dissertação de mestrado em Ecologia

Inter-informant agreement and prevalence estimates for substance use disorders: direct interview versus family history method.

OBJECTIVES: Family studies typically use multiple sources of information on each individual including direct interviews and family history information. The aims of the present study were to: (1) assess agreement for diagnoses of specific substance use disorders between direct interviews and the family history method; (2) compare prevalence estimates according to the two methods; (3) test strategies to approximate prevalence estimates according to family history reports to those based on direct interviews; (4) determine covariates of inter-informant agreement; and (5) identify covariates that affect the likelihood of reporting disorders by informants. METHODS: Analyses were based on family study data which included 1621 distinct informant (first-degree relatives and spouses) - index subject pairs. RESULTS: Our main findings were: (1) inter-informant agreement was fair to good for all substance disorders, except for alcohol abuse; (2) the family history method underestimated the prevalence of drug but not alcohol use disorders; (3) lowering diagnostic thresholds for drug disorders and combining multiple family histories increased the accuracy of prevalence estimates for these disorders according to the family history method; (4) female sex of index subjects was associated with higher agreement for nearly all disorders; and (5) informants who themselves had a history of the same substance use disorder were more likely to report this disorder in their relatives, which entails the risk of overestimation of the size of familial aggregation. CONCLUSION: Our findings have important implications for the best-estimate procedure applied in family studies.

The Rio de Janeiro HIV Vaccine Site: I. Recruitment Strategies and Socio-demographic Data of a HIV Negative Homosexual and Bisexual Male Cohort in Rio de Janeiro, Brazil

The initial effort of the Brazilian Ministry of Health to be an active partner in the world effort in the preparation of future accurate human immune deficiency virus (HIV) efficacy trials was the establishment of a multi-centered cohort of homosexual and bisexual men. An open cohort was established to determine the HIV incidence and the socio-behavioral aspects involved in Rio de Janeiro. A total of 318 potential participants, originated from multiple sources (health units, public information, snowball recruitment), were screened and recruitment became effective through the direct involvement of target communities (with the support of Non Governmental Organizations) and the population. Among this group, seropositivity for sexually transmitted diseases was high with 23, 32 and 46% for HIV, syphilis and hepatitis B, respectively. The socio-demographic data from the first 200 participants of this HIV negative cohort suggests that the cohort volunteers are an appropriate sample of the general male population of the State of Rio de Janeiro

Congenital hydrocephalus--prevalence, prenatal diagnosis and outcome of pregnancy in four European regions.

OBJECTIVE: To describe prevalence, prenatal diagnosis and outcome for fetuses and infants with congenital hydrocephalus. METHODS: Data were taken from four European registries of congenital malformations (EUROCAT). The registries included are based on multiple sources of information and include information about livebirths, fetal deaths with GA > or = 20 weeks and terminations of pregnancy for fetal anomaly (TOPFA). All cases from the four registries diagnosed with congenital hydrocephalus and born in the period 1996-2003 were included in the study. Cases with hydrocephalus associated with neural tube defects were not included in the study. RESULTS: Eighty-seven cases with congenital hydrocephalus were identified during the study period giving an overall prevalence of 4.65 per 10,000 births. There were 41 livebirths (47%), four fetal deaths (5%) and 42 TOPFA (48%). Nine percent of all cases were from a multiple pregnancy. Additional non-cerebral major malformations were diagnosed in 38 cases (44%) and karyotype anomalies in eight cases (9%). Median GA at TOPFA was 21 weeks. Among livebirths 61% were diagnosed prenatally at a median GA of 31 weeks (range 17-40 weeks) and median GA at birth was 37 weeks. Fourteen liveborn infants (34%) died within the first year of life with the majority of deaths during the first week after birth. CONCLUSION: Congenital hydrocephalus is a severe congenital malformation often associated with other congenital anomalies. CH is often diagnosed prenatally, although sometimes late in pregnancy. A high proportion of affected pregnancies result in termination for severe fetal anomaly and there is a high mortality in livebirths.

Oesophageal atresia: prevalence, prenatal diagnosis and associated anomalies in 23 European regions.

OBJECTIVE: To describe prevalence, prenatal diagnosis and epidemiological data on oesophageal atresia from 23 well-defined European regions and compare the prevalence between these regions. DESIGN: Population-based study using data from a large European database for surveillance of congenital anomalies (EUROCAT) for two decades (1987-2006). SETTINGS: Twenty-three participating registries based on multiple sources of information including information about live births, fetal deaths with gestational age ≥20 weeks and terminations of pregnancy. PATIENTS: 1222 cases of oesophageal atresia in a population of 5 019 804 births. RESULTS: The overall prevalence was 2.43 cases per 10 000 births (95% CI 2.30 to 2.57). There were regional differences in prevalence ranging from 1.27 to 4.55. Prenatal detection rates varied by registry from >50% of cases to <10% of cases. A total of 546 cases (44.7%) had an isolated oesophageal anomaly, 386 (31.6%) were multiple malformed and 290 (23.7%) had an association or a syndrome. There were 1084 live born cases (88.7%), 43 cases were fetal deaths and 95 cases were terminations of pregnancy. One-week survival for live births was 86.9% and 99.2% if the gestational age was ≥38 weeks and isolated oesophageal atresia was present. Males accounted for 57.3% of all cases and 38.5% of live born cases were born with gestational age <37 weeks. CONCLUSION: There were regional differences in prevalence of oesophageal atresia in Europe. Half of all cases had associated anomalies. Prenatal detection rate increased from 26% to 36.5% over the two decades. Survival in infants with isolated oesophageal atresia born at term is high.

Predicting cancer involvement of genes from heterogeneous data

Background: Systematic approaches for identifying proteins involved in different types of cancer are needed. Experimental techniques such as microarrays are being used to characterize cancer, but validating their results can be a laborious task. Computational approaches are used to prioritize between genes putatively involved in cancer, usually based on further analyzing experimental data. Results: We implemented a systematic method using the PIANA software that predicts cancer involvement of genes by integrating heterogeneous datasets. Specifically, we produced lists of genes likely to be involved in cancer by relying on: (i) protein-protein interactions; (ii) differential expression data; and (iii) structural and functional properties of cancer genes. The integrative approach that combines multiple sources of data obtained positive predictive values ranging from 23% (on a list of 811 genes) to 73% (on a list of 22 genes), outperforming the use of any of the data sources alone. We analyze a list of 20 cancer gene predictions, finding that most of them have been recently linked to cancer in literature. Conclusion: Our approach to identifying and prioritizing candidate cancer genes can be used to produce lists of genes likely to be involved in cancer. Our results suggest that differential expression studies yielding high numbers of candidate cancer genes can be filtered using protein interaction networks.

Material and Construction Optimization for Prevention of Premature Pavement Distress in PCC Pavements, September 2004

The chemistry of today’s concrete mixture designs is complicated by many variables, including multiple sources of aggregate and cements and a plethora of sometimes incompatible mineral and chemical admixtures. Concrete paving has undergone significant changes in recent years as new materials have been introduced into concrete mixtures. Supplementary cementitious materials such as fly ash and ground granulated blast furnace slag are now regularly used. In addition, many new admixtures that were not even available a few years ago now have widespread usage. Adding to the complexity are construction variables such as weather, mix delivery times, finishing practices, and pavement opening schedules. Mixture materials, mix design, and pavement construction are not isolated steps in the concrete paving process. Each affects and is affected by the other in ways that determine overall pavement quality and long-term performance. Equipment and procedures commonly used to test concrete materials and concrete pavements have not changed in decades, leaving serious gaps in our ability to understand and control the factors that determine concrete durability. The concrete paving community needs tests that will adequately characterize the materials, predict interactions, and monitor the properties of the concrete.

Biana: a software framework for compiling biological interactions and analyzing networks

Background: The analysis and usage of biological data is hindered by the spread of information across multiple repositories and the difficulties posed by different nomenclature systems and storage formats. In particular, there is an important need for data unification in the study and use of protein-protein interactions. Without good integration strategies, it is difficult to analyze the whole set of available data and its properties.Results: We introduce BIANA (Biologic Interactions and Network Analysis), a tool for biological information integration and network management. BIANA is a Python framework designed to achieve two major goals: i) the integration of multiple sources of biological information, including biological entities and their relationships, and ii) the management of biological information as a network where entities are nodes and relationships are edges. Moreover, BIANA uses properties of proteins and genes to infer latent biomolecular relationships by transferring edges to entities sharing similar properties. BIANA is also provided as a plugin for Cytoscape, which allows users to visualize and interactively manage the data. A web interface to BIANA providing basic functionalities is also available. The software can be downloaded under GNU GPL license from http://sbi.imim.es/web/BIANA.php.Conclusions: BIANA's approach to data unification solves many of the nomenclature issues common to systems dealing with biological data. BIANA can easily be extended to handle new specific data repositories and new specific data types. The unification protocol allows BIANA to be a flexible tool suitable for different user requirements: non-expert users can use a suggested unification protocol while expert users can define their own specific unification rules.

Ignoring information in binary choice with continuous variables: When is less 'more'?

When can a single variable be more accurate in binary choice than multiple sources of information? We derive analytically the probability that a single variable (SV) will correctly predict one of two choices when both criterion and predictor are continuous variables. We further provide analogous derivations for multiple regression (MR) and equal weighting (EW) and specify the conditions under which the models differ in expected predictive ability. Key factors include variability in cue validities, intercorrelation between predictors, and the ratio of predictors to observations in MR. Theory and simulations are used to illustrate the differential effects of these factors. Results directly address why and when one-reason decision making can be more effective than analyses that use more information. We thus provide analytical backing to intriguing empirical results that, to date, have lacked theoretical justification. There are predictable conditions for which one should expect less to be more.

Holt Oram syndrome: a registry-based study in Europe.

BACKGROUND: Holt-Oram syndrome (HOS) is an autosomal dominant disorder characterised by upper limb anomalies and congenital heart defects. We present epidemiological and clinical aspects of HOS patients using data from EUROCAT (European Surveillance of Congenital Anomalies) registries. METHODS: The study was based on data collected during 1990-2011 by 34 registries. The registries are population-based and use multiple sources of information to collect data on all types of birth using standardized definitions, methodology and coding. Diagnostic criteria for inclusion in the study were the presence of radial ray abnormalities and congenital heart disease (CHD), or the presence of either radial ray anomaly or CHD, with family history of HOS. RESULTS: A total of 73 cases of HOS were identified, including 11 (15.1%) TOPFA and 62 (84.9%) LB. Out of 73 HOS cases, 30.8% (20/65) were suspected prenatally, 55.4% (36/65) at birth, 10.7% (7/65) in the first week of life, and 3.1% (2/65) in the first year of life. The prenatal detection rate was 39.2% (20/51), with no significant change over the study period. In 55% (11/20) of prenatally detected cases, parents decided to terminate pregnancy. Thumb anomalies were reported in all cases. Agenesis/hypoplasia of radius was present in 49.2% (30/61), ulnar aplasia/hypoplasia in 24.6% (15/61) and humerus hypoplasia/phocomelia in 42.6% (26/61) of patients. Congenital heart defects (CHD) were recorded in 78.7% (48/61) of patients. Isolated septal defects were present in 54.2 (26/48), while 25% (12/48) of patients had complex/severe CHD. The mean prevalence of HOS diagnosed prenatally or in the early years of life in European registries was 0.7 per 100,000 births or 1:135,615 births. CONCLUSIONS: HOS is a rare genetic condition showing regional variation in its prevalence. It is often missed prenatally, in spite of the existence of major structural anomalies. When discovered, parents in 45% (9/20) of cases opt for the continuation of pregnancy. Although a quarter of patients have severe CHD, the overall first week survival is very good, which is important information for counselling purposes.

Iowa DOT GeoMedia Training Manual,1998.

The varying title of this manual is : Coordinated Transportation Analysis and Management System. It gives instructions on how to use GeoMedia in order to integrate data from multiple sources and formats into one environment, perform sophisticated queries and spatial analyses, and quickly produce complex maps.

Development and Implementation of an Expert System for Forecasting Fog on US Highway 30 in Cedar Rapids, Iowa, HR-357, 1996

Several accidents, some involving fatalities, have occurred on U.S. Highway 30 near the Archer Daniels Midland Company (ADM) Corn Sweeteners plant in Cedar Rapids, Iowa. A contributing factor to many of these accidents has been the large amounts of water (vapor and liquid) emitted from multiple sources at ADM's facility located along the south side of the highway. Weather and road closure data acquired from IDOT have been used to develop a database of meteorological conditions preceding and accompanying closure of Highway 30 in Cedar Rapids. An expert system and a FORTRAN program were developed as aids in decision making with regard to closure of Highway 30 near the plant. The computer programs were used for testing, evaluation, and final deployment. Reports indicate the decision tools have been successfully implemented and were judged to be helpful in forecasting road closures and in reducing costs and personnel time in monitoring the roadway.

09012-009 Little River Lake Watershed Final Report

Little River Lake watershed is a 13,305 acre subwatershed of Little River. The 788 acre lake was listed as a 303d impaired water body in 2008 due to elevated turbidity and algae levels. The Decatur SWCD has prioritized water quality protection efforts within the Little River Lake watershed because 1) portions of this watershed has been identified as the primary contributor of sediment and nutrients to Little River Lake, which provides an essential source of drinking water for Decatur County and the Southern Iowa Rural Water Association; 2) the watershed provides exemplary education and project interpretation opportunities due to its proximity to Little River Lake Recreation Area, and 3) by using targeted and proven soil conservation practices to address water quality deficiencies the probability of successfully attenuating soil erosion and ameliorating water quality impairments is enhanced. The specific goals of this proposal are to: 1. reduce annual sediment, and phosphorous delivery to the lake by 11,280 tons and 14,664 lbs., respectively, via applications of conservation practices on targeted agricultural land; 2. delist the lake as an EPA 303d impaired water body via water quality enhancement; 3. obtain a “Full Support” status for the lake’s aquatic life and recreational use; 4. reduce potable water treatment costs (minimum 50% cost reduction) associated with high suspended solid levels; and 5. restore a viable sport-fish population, thereby bolstering tourism and the economy. To achieve timely project implementation the Decatur SWCD has cooperated with the IDNR Watershed Improvement Section, Fisheries Bureau, and IDALS-DSC to assess extant water quality and watershed conditions, coalesced a diverse team of committed partners and secured matching funding from multiple sources.