STATISTICAL TEST FOR GENOTYPE AND ENVIRONMENT CONTRIBUTION IN THE GENOTYPES x ENVIRONMENTS INTERACTION MATRIX

The objective of the present work was to propose a method for testing the contribution of each level of the factors in a genotypes x environments (GxE) interaction using multi-environment trials analyses by means of an F test. The study evaluated a data set, with twenty genotypes and thirty-four environments, in a block design with four replications. The sum of squares within rows (genotypes) and columns (environments) of the GxE matrix was simulated, generating 10000 experiments to verify the empirical distribution. Results indicate a noncentral chi-square distribution for rows and columns of the GxE interaction matrix, which was also verified by the Kolmogorov-Smirnov test and Q-Q plot. Application of the F test identified the genotypes and environments that contributed the most to the GxE interaction. In this way, geneticists can select good genotypes in their studies.

Different lead sources in an abandoned uranium mine (Urgeirica - Central Portugal) and its environment impact - isotopic evidence

Different lead sources were identified in a large uranium tailings deposit (5Mton) in the Central Region of Portugal using lead isotopic ratios obtained by ICP-QMS. These ratios helped to clarify the different sources of Pb within the tailings deposit and the impact of the tailings on the surroundings. Ten depth profiles were used for isotopic characterization of the tailings deposit; the lead background signature was evaluated in seven regional rocks (granites) and was defined as being 28 +/- 1 mg kg(-1) for Pb bulk concentration and with isotopic ratios of 1.264(2) for Pb-206/Pb-207 and 1.962(7) for Pb-208/Pb-206. In order to understand Pb isotope distribution within the tailings deposit, simple mixing/mass balance models were used to fit experimental data, involving: (1) the background component; (2) uranium ores (pitchblende) characterized by the ratios Pb-206/Pb-207 of 1.914(3) and Pb-208/Pb-206 of 1.235(2); and (3) an unknown Pb source (named 'Fonte 5') characterized by the ratios Pb-206/Pb-207 of 3.079(7) and Pb-208/Pb-206 of 0.715(1). This unknown source showed high radiogenic ratios found in the water of some tailings depth profiles located in a very specific position in the dump. In terms of isotopic characterization, 69% of the deposit material resulted from the background source, 25% from uranium minerals and only 6% from other uranium mines in the region. Finally, the environment impact revealed that the pollution was focused only in the beginning of the stream and not in the surroundings, nor in the groundwater system. The lead in the water was found only in colloidal form with a clear pitchblende signature. Those data revealed possible remobilization phenomena along the bedside and margins of the watercourse.

Genotype by environment interaction for birth and weaning weights of composite beef cattle in different regions of Brazil

The objectives of the present study were to characterize and define homogenous production environments of composite beef cattle in Brazil in terms of climatic and geographic variables using multivariate exploratory techniques and to use them to assess the presence of G x E for birth weight (BW) and weaning weight (WW). Data from animals born between 1995 and 2008 on 36 farms located in 27 municipalities of the Brazilian states were used. Fifteen years of climate observations (mean minimum and maximum annual temperature and mean annual rainfall) and geographic (latitude, longitude and altitude) data were obtained for each municipality where the farms were located for characterization of the production environments. Hierarchical and nonhierarchical cluster analysis was used to group farms located in regions with similar environmental variables into clusters. Six clusters of farms were formed. The effect of sire-cluster interaction was tested by single-trait analysis using deviance information criterion (DIC). Genetic parameters were estimated by multi-trait analysis considering the same trait to be different in each cluster. According to the values of DIC, the inclusion of sire-cluster effect did not improve the fit of the genetic evaluation model for BW and WW. Estimates of genetic correlations among clusters ranged from -0.02 to 0.92. The low genetic correlation among the most studied regions permits us to suggest that a separate genetic evaluation for some regions should be undertaken. (C) 2012 Elsevier B.V. All rights reserved.

Vaginal progesterone in women with an asymptomatic sonographic short cervix in the midtrimester decreases preterm delivery and neonatal morbidity: a systematic review and metaanalysis of individual patient data

OBJECTIVE: To determine whether the use of vaginal progesterone in asymptomatic women with a sonographic short cervix (<= 25 mm) in the midtrimester reduces the risk of preterm birth and improves neonatal morbidity and mortality. STUDY DESIGN: Individual patient data metaanalysis of randomized controlled trials. RESULTS: Five trials of high quality were included with a total of 775 women and 827 infants. Treatment with vaginal progesterone was associated with a significant reduction in the rate of preterm birth <33 weeks (relative risk [RR], 0.58; 95% confidence interval [CI], 0.42-0.80), <35 weeks (RR, 0.69; 95% CI, 0.55-0.88), and <28 weeks (RR, 0.50; 95% CI, 0.30-0.81); respiratory distress syndrome (RR, 0.48; 95% CI, 0.30-0.76); composite neonatal morbidity and mortality (RR, 0.57; 95% CI, 0.40-0.81); birthweight <1500 g (RR, 0.55; 95% CI, 0.38-0.80); admission to neonatal intensive care unit (RR, 0.75; 95% CI, 0.59-0.94); and requirement for mechanical ventilation (RR, 0.66; 95% CI, 0.44-0.98). There were no significant differences between the vaginal progesterone and placebo groups in the rate of adverse maternal events or congenital anomalies. CONCLUSION: Vaginal progesterone administration to asymptomatic women with a sonographic short cervix reduces the risk of preterm birth and neonatal morbidity and mortality.

Calculations of the spectral shifts and line profiles of alkaline earth atoms in liquid helium environment

Liquid configurations generated by Metropolis Monte Carlo simulations are used in time-dependent density functional theory calculations of the spectral line shifts and line profiles of the lowest lying excitation of the alkaline earth atoms, Be, Mg, Ca, Sr and Ba embedded in liquid helium. The results are in very good agreement with the available experimental data. Special attention is given to the calculated spectroscopic shift and the associated line broadening. The analysis specifies the inhomogeneous broadening of the three separate contributions due to the splitting of the s -> p transition of the alkaline earth atom in the liquid environment. (C) 2012 Elsevier B. V. All rights reserved.

A new species of the Bokermannohyla circumdata group (Anura: Hylidae) from southeastern Brazil, with bioacoustic data on seven species of the genus

We describe a new species of the Bokermannohyla circumdata group from the Estacao de Pesquisa e Desenvolvimento Ambiental Galheiro (EPDA-Galheiro) (19 degrees 12'S; 47 degrees 08'W), Municipality of Perdizes, State of Minas Gerais, a mid-altitudinal (similar or equal to 850 m above sea level) riparian forest environment in the Cerrado of southeastern Brazil. Bokermannohyla napolii sp. nov. is allied to the large-sized species of the group, diagnosed on the basis of adult morphology/morphometrics, and mainly vocalizations. Adult specimens of the new species are most closely related to those of B. luctuosa and B. circumdata, but can be differentiated from the former by having distal subarticular tubercle of finger III bifid/divided in males, and finger IV bifid/divided in males and females; and from both B. luctuosa and B. circumdata by a distinctive advertisement call structure. We also provide bioacoustic data on seven other species of the genus, including previously unknown advertisement calls of B. circumdata and B. carvalhoi, and re-description of the advertisement calls of B. luctuosa, B. ibitiguara, B. nanuzae, B. sazimai, and B. hylax.

Gene by environment QTL mapping through multiple trait analyses in blood pressure salt-sensitivity: identification of a novel QTL in rat chromosome 5

Background The genetic mechanisms underlying interindividual blood pressure variation reflect the complex interplay of both genetic and environmental variables. The current standard statistical methods for detecting genes involved in the regulation mechanisms of complex traits are based on univariate analysis. Few studies have focused on the search for and understanding of quantitative trait loci responsible for gene × environmental interactions or multiple trait analysis. Composite interval mapping has been extended to multiple traits and may be an interesting approach to such a problem. Methods We used multiple-trait analysis for quantitative trait locus mapping of loci having different effects on systolic blood pressure with NaCl exposure. Animals studied were 188 rats, the progenies of an F2 rat intercross between the hypertensive and normotensive strain, genotyped in 179 polymorphic markers across the rat genome. To accommodate the correlational structure from measurements taken in the same animals, we applied univariate and multivariate strategies for analyzing the data. Results We detected a new quantitative train locus on a region close to marker R589 in chromosome 5 of the rat genome, not previously identified through serial analysis of individual traits. In addition, we were able to justify analytically the parametric restrictions in terms of regression coefficients responsible for the gain in precision with the adopted analytical approach. Conclusion Future work should focus on fine mapping and the identification of the causative variant responsible for this quantitative trait locus signal. The multivariable strategy might be valuable in the study of genetic determinants of interindividual variation of antihypertensive drug effectiveness.

SEM analysis and push-out bond strength of fiberglass posts luted with different cements of glass-ionomer in humid environment: pilot test

The objective of this study was to evaluate the push-out bond strength of fiberglass resin reinforced bonded with five ionomer cements. Also, the interface between cement and dentin was inspected by means of SEM. Fifty human canines were chose after rigorous scrutiny process, endodontically treated and divided randomly into five groups (n = 3) according to cement tested: Group I – Ionoseal (VOCO), Group II – Fugi I (GC), Group III – Fugi II Improved (GC), Group IV – Rely X Luting 2 (3M ESPE), Group V – Ketac Cem (3M ESPE). The post-space was prepared to receive a fiberglass post, which was tried before cementation process. No dentin or post surface pretreatment was carried out. After post bonding, all roots were cross-sectioned to acquire 3 thin-slices (1 mm) from three specific regions of tooth (cervical, medium and apical). A Universal test machine was used to carry out the push-out test with cross-head speed set to 0.5mm/mim. All failed specimens were observed under optical microscope to identify the failure mode. Representative specimens from each group was inspected under SEM. The data were analyzed by Kolmogorov-Smirnov and Levene’s tests and by two-way ANOVA, and Tukey’s port hoc test at a significance level of 5%. It was compared the images obtained for determination of types of failures more occurred in different levels. SEM inspection displayed that all cements filled the space between post and dentin, however, some imperfections such bubles and voids were noticed in all groups in some degree of extension. The push-out bond strength showed that cement Ketac Cem presented significant higher results when compared to the Ionoseal (P = 0.02). There were no statistical significant differences among other cements.

Computational framework to support integration of biomolecular and clinical data within a translational approach

Background The use of the knowledge produced by sciences to promote human health is the main goal of translational medicine. To make it feasible we need computational methods to handle the large amount of information that arises from bench to bedside and to deal with its heterogeneity. A computational challenge that must be faced is to promote the integration of clinical, socio-demographic and biological data. In this effort, ontologies play an essential role as a powerful artifact for knowledge representation. Chado is a modular ontology-oriented database model that gained popularity due to its robustness and flexibility as a generic platform to store biological data; however it lacks supporting representation of clinical and socio-demographic information. Results We have implemented an extension of Chado – the Clinical Module - to allow the representation of this kind of information. Our approach consists of a framework for data integration through the use of a common reference ontology. The design of this framework has four levels: data level, to store the data; semantic level, to integrate and standardize the data by the use of ontologies; application level, to manage clinical databases, ontologies and data integration process; and web interface level, to allow interaction between the user and the system. The clinical module was built based on the Entity-Attribute-Value (EAV) model. We also proposed a methodology to migrate data from legacy clinical databases to the integrative framework. A Chado instance was initialized using a relational database management system. The Clinical Module was implemented and the framework was loaded using data from a factual clinical research database. Clinical and demographic data as well as biomaterial data were obtained from patients with tumors of head and neck. We implemented the IPTrans tool that is a complete environment for data migration, which comprises: the construction of a model to describe the legacy clinical data, based on an ontology; the Extraction, Transformation and Load (ETL) process to extract the data from the source clinical database and load it in the Clinical Module of Chado; the development of a web tool and a Bridge Layer to adapt the web tool to Chado, as well as other applications. Conclusions Open-source computational solutions currently available for translational science does not have a model to represent biomolecular information and also are not integrated with the existing bioinformatics tools. On the other hand, existing genomic data models do not represent clinical patient data. A framework was developed to support translational research by integrating biomolecular information coming from different “omics” technologies with patient’s clinical and socio-demographic data. This framework should present some features: flexibility, compression and robustness. The experiments accomplished from a use case demonstrated that the proposed system meets requirements of flexibility and robustness, leading to the desired integration. The Clinical Module can be accessed in http://dcm.ffclrp.usp.br/caib/pg=iptrans webcite.

Impact of urban atmospheric environment on hospital admissions in the elderly

OBJECTIVE: To analyze the impact of intra-urban atmospheric conditions on circulatory and respiratory diseases in elder adults. METHODS: Cross-sectional study based on data from 33,212 hospital admissions in adults over 60 years in the city of São Paulo, southeastern Brazil, from 2003 to 2007. The association between atmospheric variables from Congonhas airport and bioclimatic index, Physiological Equivalent Temperature, was analyzed according to the district's socioenvironmental profile. Descriptive statistical analysis and regression models were used. RESULTS: There was an increase in hospital admissions due to circulatory diseases as average and lowest temperatures decreased. The likelihood of being admitted to the hospital increased by 12% with 1ºC decrease in the bioclimatic index and with 1ºC increase in the highest temperatures in the group with lower socioenvironmental conditions. The risk of admission due to respiratory diseases increased with inadequate air quality in districts with higher socioenvironmental conditions. CONCLUSIONS: The associations between morbidity and climate variables and the comfort index varied in different groups and diseases. Lower and higher temperatures increased the risk of hospital admission in the elderly. Districts with lower socioenvironmental conditions showed greater adverse health impacts.

Semantic integration of gene expression analysis tools and data sources using software connectors

Abstract Background The study and analysis of gene expression measurements is the primary focus of functional genomics. Once expression data is available, biologists are faced with the task of extracting (new) knowledge associated to the underlying biological phenomenon. Most often, in order to perform this task, biologists execute a number of analysis activities on the available gene expression dataset rather than a single analysis activity. The integration of heteregeneous tools and data sources to create an integrated analysis environment represents a challenging and error-prone task. Semantic integration enables the assignment of unambiguous meanings to data shared among different applications in an integrated environment, allowing the exchange of data in a semantically consistent and meaningful way. This work aims at developing an ontology-based methodology for the semantic integration of gene expression analysis tools and data sources. The proposed methodology relies on software connectors to support not only the access to heterogeneous data sources but also the definition of transformation rules on exchanged data. Results We have studied the different challenges involved in the integration of computer systems and the role software connectors play in this task. We have also studied a number of gene expression technologies, analysis tools and related ontologies in order to devise basic integration scenarios and propose a reference ontology for the gene expression domain. Then, we have defined a number of activities and associated guidelines to prescribe how the development of connectors should be carried out. Finally, we have applied the proposed methodology in the construction of three different integration scenarios involving the use of different tools for the analysis of different types of gene expression data. Conclusions The proposed methodology facilitates the development of connectors capable of semantically integrating different gene expression analysis tools and data sources. The methodology can be used in the development of connectors supporting both simple and nontrivial processing requirements, thus assuring accurate data exchange and information interpretation from exchanged data.

Models of the Distribution of Persistent Organic Pollutants in the Marine Environment

Persistent organic pollutants (POPs) is a group of chemicals that are toxic, undergo long-range transport and accumulate in biota. Due to their persistency the distribution and recirculation in the environment often continues for a long period of time. Thereby they appear virtually everywhere within the biosphere, and poses a toxic stress to living organisms. In this thesis, attempts are made to contribute to the understanding of factors that influence the distribution of POPs with focus on processes in the marine environment. The bioavailability and the spatial distribution are central topics for the environmental risk management of POPs. In order to study these topics, various field studies were undertaken. To determine the bioavailable fraction of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs), polychlorinated naphthalenes (PCNs), and polychlorinated biphenyls (PCBs) the aqueous dissolved phase were sampled and analysed. In the same samples, we also measured how much of these POPs were associated with suspended particles. Different models, which predicted the phase distribution of these POPs, were then evaluated. It was found that important water characteristics, which influenced the solid-water phase distribution of POPs, were particulate organic matter (POM), particulate soot (PSC), and dissolved organic matter (DOM). The bioavailable dissolved POP-phase in the water was lower when these sorbing phases were present. Furthermore, sediments were sampled and the spatial distribution of the POPs was examined. The results showed that the concentration of PCDD/Fs, and PCNs were better described using PSC- than using POM-content of the sediment. In parallel with these field studies, we synthesized knowledge of the processes affecting the distribution of POPs in a multimedia mass balance model. This model predicted concentrations of PCDD/Fs throughout our study area, the Grenlandsfjords in Norway, within factors of ten. This makes the model capable to validate the effect of suitable remedial actions in order to decrease the exposure of these POPs to biota in the Grenlandsfjords which was the aim of the project. Also, to evaluate the influence of eutrophication on the marine occurrence PCB data from the US Musselwatch and Benthic Surveillance Programs are examined in this thesis. The dry weight based concentrations of PCB in bivalves were found to correlate positively to the organic matter content of nearby sediments, and organic matter based concentrations of PCB in sediments were negatively correlated to the organic matter content of the sediment.

Dynamical aspects of atmospheric data assimilation in the tropics

A faithful depiction of the tropical atmosphere requires three-dimensional sets of observations. Despite the increasing amount of observations presently available, these will hardly ever encompass the entire atmosphere and, in addition, observations have errors. Additional (background) information will always be required to complete the picture. Valuable added information comes from the physical laws governing the flow, usually mediated via a numerical weather prediction (NWP) model. These models are, however, never going to be error-free, why a reliable estimate of their errors poses a real challenge since the whole truth will never be within our grasp. The present thesis addresses the question of improving the analysis procedures for NWP in the tropics. Improvements are sought by addressing the following issues: - the efficiency of the internal model adjustment, - the potential of the reliable background-error information, as compared to observations, - the impact of a new, space-borne line-of-sight wind measurements, and - the usefulness of multivariate relationships for data assimilation in the tropics. Most NWP assimilation schemes are effectively univariate near the equator. In this thesis, a multivariate formulation of the variational data assimilation in the tropics has been developed. The proposed background-error model supports the mass-wind coupling based on convectively-coupled equatorial waves. The resulting assimilation model produces balanced analysis increments and hereby increases the efficiency of all types of observations. Idealized adjustment and multivariate analysis experiments highlight the importance of direct wind measurements in the tropics. In particular, the presented results confirm the superiority of wind observations compared to mass data, in spite of the exact multivariate relationships available from the background information. The internal model adjustment is also more efficient for wind observations than for mass data. In accordance with these findings, new satellite wind observations are expected to contribute towards the improvement of NWP and climate modeling in the tropics. Although incomplete, the new wind-field information has the potential to reduce uncertainties in the tropical dynamical fields, if used together with the existing satellite mass-field measurements. The results obtained by applying the new background-error representation to the tropical short-range forecast errors of a state-of-art NWP model suggest that achieving useful tropical multivariate relationships may be feasible within an operational NWP environment.

Coupling between upper ocean layer variability and size-fractionated phytoplankton in a non-nutrient-limited environment

[EN] We describe the coupling between upper ocean layer variability and size-fractionated phytoplankton distribution in the non-nutrient-limited Bransfield Strait region (BS) of Antarctica. For this purpose we use hydrographic and size-fractionated chlorophyll a data from a transect that crossed 2 fronts and an eddy, together with data from 3 stations located in a deeply mixed region, the Antarctic Sound (AS). In the BS transect, small phytoplankton (<20 μm equivalent spherical diameter [ESD]) accounted for 80% of total chl a and their distribution appeared to be linked to cross-frontal variability. On the deepening upper mixed layer (UML) sides of both fronts we observed a deep subducting column-like structure of small phytoplankton biomass. On the shoaling UML sides of both fronts, where there were signs of restratification, we observed a local shallow maximum of small phytoplankton biomass. We propose that this observed phytoplankton distribution may be a response to the development of frontal vertical circulation cells. In the deep, turbulent environment of the AS, larger phytoplankton (>20 μm ESD) accounted for 80% of total chl a. The proportion of large phytoplankton increases as the depth of the upper mixed layer (ZUML), and the corresponding rate of vertical mixing, increases. We hypothesize that this change in phytoplankton composition with varying ZUML is related to the competition for light, and results from modification of the light regime caused by vertical mixing.

Data and behavioral contracts for web services

The recent trend in Web services is fostering a computing scenario where loosely coupled parties interact in a distributed and dynamic environment. Such interactions are sequences of xml messages and in order to assemble parties – either statically or dynamically – it is important to verify that the “contracts” of the parties are “compatible”. The Web Service Description Language (wsdl) is a standard used for describing one-way (asynchronous) and request/response (synchronous) interactions. Web Service Conversation Language extends wscl contracts by allowing the description of arbitrary, possibly cyclic sequences of exchanged messages between communicating parties. Unfortunately, neither wsdl nor wscl can effectively define a notion of compatibility, for the very simple reason that they do not provide any formal characterization of their contract languages. We define two contract languages for Web services. The first one is a data contract language and allow us to describe a Web service in terms of messages (xml documents) that can be sent or received. The second one is a behavioral contract language and allow us to give an abstract definition of the Web service conversation protocol. Both these languages are equipped with a sort of “sub-typing” relation and, therefore, they are suitable to be used for querying Web services repositories. In particular a query for a service compatible with a given contract may safely return services with “greater” contract.