A sharing-based approach to supporting adaptation in service compositions

Data-related properties of the activities involved in a service composition can be used to facilitate several design-time and run-time adaptation tasks, such as service evolution, distributed enactment, and instance-level adaptation. A number of these properties can be expressed using a notion of sharing. We present an approach for automated inference of data properties based on sharing analysis, which is able to handle service compositions with complex control structures, involving loops and sub-workflows. The properties inferred can include data dependencies, information content, domain-defined attributes, privacy or confidentiality levels, among others. The analysis produces characterizations of the data and the activities in the composition in terms of minimal and maximal sharing, which can then be used to verify compliance of potential adaptation actions, or as supporting information in their generation. This sharing analysis approach can be used both at design time and at run time. In the latter case, the results of analysis can be refined using the composition traces (execution logs) at the point of execution, in order to support run-time adaptation.

Polynomial regression using a perceptron with axo-axonic connections

Social behavior is mainly based on swarm colonies, in which each individual shares its knowledge about the environment with other individuals to get optimal solutions. Such co-operative model differs from competitive models in the way that individuals die and are born by combining information of alive ones. This paper presents the particle swarm optimization with differential evolution algorithm in order to train a neural network instead the classic back propagation algorithm. The performance of a neural network for particular problems is critically dependant on the choice of the processing elements, the net architecture and the learning algorithm. This work is focused in the development of methods for the evolutionary design of artificial neural networks. This paper focuses in optimizing the topology and structure of connectivity for these networks

Artificial analysis of molecular marker loci linked to tree resistance response by an artificial neural network

One of the biggest challenges that software developers face is to make an accurate estimate of the project effort. Radial basis function neural networks have been used to software effort estimation in this work using NASA dataset. This paper evaluates and compares radial basis function versus a regression model. The results show that radial basis function neural network have obtained less Mean Square Error than the regression method.

Sequencing of 3-O sulfate containing heparin decasaccharides with a partial antithrombin III binding site

Heparin- and heparan sulfate-like glycosaminoglycans (HLGAGs) represent an important class of molecules that interact with and modulate the activity of growth factors, enzymes, and morphogens. Of the many biological functions for this class of molecules, one of its most important functions is its interaction with antithrombin III (AT-III). AT-III binding to a specific heparin pentasaccharide sequence, containing an unusual 3-O sulfate on a N-sulfated, 6-O sulfated glucosamine, increases 1,000-fold AT-III's ability to inhibit specific proteases in the coagulation cascade. In this manner, HLGAGs play an important biological and pharmacological role in the modulation of blood clotting. Recently, a sequencing methodology was developed to further structure-function relationships of this important class of molecules. This methodology combines a property-encoded nomenclature scheme to handle the large information content (properties) of HLGAGs, with matrix-assisted laser desorption ionization MS and enzymatic and chemical degradation as experimental constraints to rapidly sequence picomole quantities of HLGAG oligosaccharides. Using the above property-encoded nomenclature-matrix-assisted laser desorption ionization approach, we found that the sequence of the decasaccharide used in this study is ΔU2SHNS,6SI2SHNS,6SI2SHNS,6SIHNAc,6SGHNS,3S,6S (±DDD4–7). We confirmed our results by using integral glycan sequencing and one-dimensional proton NMR. Furthermore, we show that this approach is flexible and is able to derive sequence information on an oligosaccharide mixture. Thus, this methodology will make possible both the analysis of other unusual sequences in HLGAGs with important biological activity as well as provide the basis for the structural analysis of these pharamacologically important group of heparin/heparan sulfates.

Immunoassays with rolling circle DNA amplification: A versatile platform for ultrasensitive antigen detection

We describe an adaptation of the rolling circle amplification (RCA) reporter system for the detection of protein Ags, termed “immunoRCA.” In immunoRCA, an oligonucleotide primer is covalently attached to an Ab; thus, in the presence of circular DNA, DNA polymerase, and nucleotides, amplification results in a long DNA molecule containing hundreds of copies of the circular DNA sequence that remain attached to the Ab and that can be detected in a variety of ways. Using immunoRCA, analytes were detected at sensitivities exceeding those of conventional enzyme immunoassays in ELISA and microparticle formats. The signal amplification afforded by immunoRCA also enabled immunoassays to be carried out in microspot and microarray formats with exquisite sensitivity. When Ags are present at concentrations down to fM levels, specifically bound Abs can be scored by counting discrete fluorescent signals arising from individual Ag–Ab complexes. Multiplex immunoRCA also was demonstrated by accurately quantifying Ags mixed in different ratios in a two-color, single-molecule-counting assay on a glass slide. ImmunoRCA thus combines high sensitivity and a very wide dynamic range with an unprecedented capability for single molecule detection. This Ag-detection method is of general applicability and is extendable to multiplexed immunoassays that employ a battery of different Abs, each labeled with a unique oligonucleotide primer, that can be discriminated by a color-coded visualization system. ImmunoRCA-profiling based on the simultaneous quantitation of multiple Ags should expand the power of immunoassays by exploiting the increased information content of ratio-based expression analysis.

Kabat Database and its applications: future directions

The Kabat Database was initially started in 1970 to determine the combining site of antibodies based on the available amino acid sequences. The precise delineation of complementarity determining regions (CDR) of both light and heavy chains provides the first example of how properly aligned sequences can be used to derive structural and functional information of biological macromolecules. This knowledge has subsequently been applied to the construction of artificial antibodies with prescribed specificities, and to many other studies. The Kabat database now includes nucleotide sequences, sequences of T cell receptors for antigens (TCR), major histocompatibility complex (MHC) class I and II molecules, and other proteins of immunological interest. While new sequences are continually added into this database, we have undertaken the task of developing more analytical methods to study the information content of this collection of aligned sequences. New examples of analysis will be illustrated on a yearly basis. The Kabat Database and its applications are freely available at http://immuno.bme.nwu.edu.

The human XPG gene: gene architecture, alternative splicing and single nucleotide polymorphisms

Defects in the XPG DNA repair endonuclease gene can result in the cancer-prone disorders xeroderma pigmentosum (XP) or the XP–Cockayne syndrome complex. While the XPG cDNA sequence was known, determination of the genomic sequence was required to understand its different functions. In cells from normal donors, we found that the genomic sequence of the human XPG gene spans 30 kb, contains 15 exons that range from 61 to 1074 bp and 14 introns that range from 250 to 5763 bp. Analysis of the splice donor and acceptor sites using an information theory-based approach revealed three splice sites with low information content, which are components of the minor (U12) spliceosome. We identified six alternatively spliced XPG mRNA isoforms in cells from normal donors and from XPG patients: partial deletion of exon 8, partial retention of intron 8, two with alternative exons (in introns 1 and 6) and two that retained complete introns (introns 3 and 9). The amount of alternatively spliced XPG mRNA isoforms varied in different tissues. Most alternative splice donor and acceptor sites had a relatively high information content, but one has the U12 spliceosome sequence. A single nucleotide polymorphism has allele frequencies of 0.74 for 3507G and 0.26 for 3507C in 91 donors. The human XPG gene contains multiple splice sites with low information content in association with multiple alternatively spliced isoforms of XPG mRNA.

Noninvasive functional optical spectroscopy of human breast tissue

Near infrared diffuse optical spectroscopy and diffuse optical imaging are promising methods that eventually may enhance or replace existing technologies for breast cancer screening and diagnosis. These techniques are based on highly sensitive, quantitative measurements of optical and functional contrast between healthy and diseased tissue. In this study, we examine whether changes in breast physiology caused by exogenous hormones, aging, and fluctuations during the menstrual cycle result in significant alterations in breast tissue optical contrast. A noninvasive quantitative diffuse optical spectroscopy technique, frequency-domain photon migration, was used. Measurements were performed on 14 volunteer subjects by using a hand-held probe. Intrinsic tissue absorption and reduced scattering parameters were calculated from frequency-domain photon migration data. Wavelength-dependent absorption (at 674, 803, 849, and 956 nm) was used to determine tissue concentration of oxyhemoglobin, deoxyhemoglobin, total hemoglobin, tissue hemoglobin oxygen saturation, and bulk water content. Results show significant and dramatic differences in optical properties between menopausal states. Average premenopausal intrinsic tissue absorption and reduced scattering values at each wavelength are 2.5- to 3-fold higher and 16–28% greater, respectively, than absorption and scattering for postmenopausal subjects. Absorption and scattering properties for women using hormone replacement therapy are intermediate between premenopausal and postmenopausal populations. Physiological properties show differences in mean total hemoglobin (7.0 μM, 11.8 μM, and 19.2 μM) and water concentration relative to pure water (10.9%, 15.3%, and 27.3%) for postmenopausal, hormone replacement therapy, and premenopausal subjects, respectively. Because of their unique, quantitative information content, diffuse optical methods may play an important role in breast diagnostics and improving our understanding of breast disease.

Protein-protein interaction: a genetic selection for compensating mutations at the barnase-barstar interface.

Barnase and barstar are trivial names of the extracellular RNase and its intracellular inhibitor produced by Bacillus amyloliquefaciens. Inhibition involves the formation of a very tight one-to-one complex of the two proteins. With the crystallographic solution of the structure of the barnase-barstar complex and the development of methods for measuring the free energy of binding, the pair can be used to study protein-protein recognition in detail. In this report, we describe the isolation of suppressor mutations in barstar that compensate for the loss in interaction energy caused by a mutation in barnase. Our suppressor search is based on in vivo selection for barstar variants that are able to protect host cells against the RNAse activity of those barnase mutants not properly inhibited by wild-type barstar. This approach utilizes a plasmid system in which barnase expression is tightly controlled to keep the mutant barnase gene silent. When expression of barnase is turned on, failure to form a complex between the mutant barnase and barstar has a lethal effect on host cells unless overcome by substitution of the wild-type barstar by a functional suppressor derivative. A set of barstar suppressors has been identified for barnase mutants with substitutions in two amino acid positions (residues 102 and 59), which are critically involved in both RNase activity and barstar binding. The mutations selected as suppressors could not have been predicted on the basis of the known protein structures. The single barstar mutation with the highest information content for inhibition of barnase (H102K) has the substitution Y30W. The reduction in binding caused by the R59E mutation in barnase can be partly reversed by changing Glu-76 of barstar, which forms a salt bridge with the Arg-59 in the wild-type complex, to arginine, thus completing an interchange of the two charges.

O ensino contábil para empreendimentos econômicos solidários: um estudo na Incubadora Social da Universidade Federal de Goiás

A pesquisa permeia a contabilidade e autogestão existentes nos empreendimentos econômicos solidários, em que o modelo de gestão é democrático e participativo e requer ferramentas contábeis compatíveis com suas características. O objetivo é verificar se a aplicação de técnica de ensino-aprendizagem contábil baseada nas rotinas gerenciais e demandas dos usuários contribui com a decodificação da informação contábil, colaborando com o controle gerencial dos empreendimentos. Assim, foi feito experimento em que no pré-teste foi analisado o entendimento contábil no que tange ao conteúdo informacional, sua utilidade e domínio. No pós-teste foi feita análise dos efeitos da aplicação da técnica sobre esses entendimentos. O estudo foi realizado com 16 cooperativas pertencentes à Incubadora Social da Universidade Federal de Goiás e a coleta de dados foi realizada por meio de entrevistas estruturadas, observações e análise de registros. Estas foram transcritas e analisadas pelo método de análise de conteúdo, que consistiu em organizar categorias conceituais representantes do entendimento contábil testado, designada pela ocorrência ou expressão nos dados transcritos. A análise dos resultados foi feita pelo teste não-paramétrico, Postos Sinalizados de Wilcoxon. Os resultados apresentados não demonstraram diferenças significativas com relação ao entendimento contábil dos diretores e não diretores antes e depois da intervenção. Limitações como amostra e a rotatividade de pessoas na cooperativa denotam a necessidade de haver formações recorrentes para os cooperados. Para futuras pesquisas fica o tempo de curso ser prolongado permitindo a participação recorrente e de mais cooperados. Como implicações práticas têm-se a percepção dos cooperados na necessidade de ter e entender as ferramentas e controles para administrar à cooperativa.

Análisis de la información en la prevención del consumo de drogas y otras adicciones

Tradicionalmente gran parte de los programas preventivos de drogas y otras adicciones dirigidos a preadolescentes y adolescentes, se han apoyado en la información como estrategia fundamental para disuadir el consumo, utilizando argumentos basados en las consecuencias del deterioro al ser consumidores de sustancias, así como en el abuso de otras conductas adictivas no químicas. El enfoque clásico se apoya en que los jóvenes toman sus decisiones de consumir, o no, en base a una elaboración racional, por tanto en el caso de estar informados de los riesgos que asumen al consumir optarían por no hacerlo. Es fundamental incidir en la importancia que adquieren tres cuestiones alrededor de la información: el nivel y calidad de la información que tienen los jóvenes, el nivel y calidad de la información que tienen los padres y la búsqueda de las fuentes de información sobre drogas y su nivel de credibilidad. Posiblemente los modelos de transmisión y contenido de información que utiliza la publicidad comercial podrían ser más adecuados y eficaces que los del recurso al miedo en el ámbito de los comportamientos de salud, y por supuesto, de las adicciones en general. La tendencia de los promotores de mensajes de salud sigue siendo la de transmitir las consecuencias y los riesgos, en la línea de la apelación al miedo. Presumimos que se alcanzaría una mayor eficiencia con mensajes positivos, reforzando los estilos de vida saludables.

Methods of Visualization and Analysis of Cardiac Depolarization in the Three Dimensional Space

Research analysis of electrocardiograms (ECG) today is carried out mostly using time depending signals of different leads shown in the graphs. Definition of ECG parameters is performed by qualified personnel, and requiring particular skills. To support decoding the cardiac depolarization phase of ECG there are methods to analyze space-time convolution charts in three dimensions where the heartbeat is described by the trajectory of its electrical vector. Based on this, it can be assumed that all available options of the classical ECG analysis of this time segment can be obtained using this technique. Investigated ECG visualization techniques in three dimensions combined with quantitative methods giving additional features of cardiac depolarization and allow a better exploitation of the information content of the given ECG signals.

Prognostic Value of Secretoneurin in Critically Ill Patients With Infections.

OBJECTIVES Secretoneurin is produced in neuroendocrine cells, and the myocardium and circulating secretoneurin levels provide incremental prognostic information to established risk indices in cardiovascular disease. As myocardial dysfunction contributes to poor outcome in critically ill patients, we wanted to assess the prognostic value of secretoneurin in two cohorts of critically ill patients with infections. DESIGN Two prospective, observational studies. SETTING Twenty-four and twenty-five ICUs in Finland. PATIENTS A total of 232 patients with severe sepsis (cohort #1) and 94 patients with infections and respiratory failure (cohort #2). INTERVENTIONS None. MEASUREMENTS AND MAIN RESULTS We measured secretoneurin levels by radioimmunoassay in samples obtained early after ICU admission and compared secretoneurin with other risk indices. In patients with severe sepsis, admission secretoneurin levels (logarithmically transformed) were associated with hospital mortality (odds ratio, 3.17 [95% CI, 1.12-9.00]; p = 0.030) and shock during the hospitalization (odds ratio, 2.17 [1.06-4.46]; p = 0.034) in analyses that adjusted for other risk factors available on ICU admission. Adding secretoneurin levels to age, which was also associated with hospital mortality in the multivariate model, improved the risk prediction as assessed by the category-free net reclassification index: 0.35 (95% CI, 0.06-0.64) (p = 0.02). In contrast, N-terminal pro-B-type natriuretic peptide levels were not associated with mortality in the multivariate model that included secretoneurin measurements, and N-terminal pro-B-type natriuretic peptide did not improve patient classification on top of age. Secretoneurin levels were also associated with hospital mortality after adjusting for other risk factors and improved patient classification in cohort #2. In both cohorts, the optimal cutoff for secretoneurin levels at ICU admission to predict hospital mortality was ≈ 175 pmol/L, and higher levels were associated with mortality also when adjusting for Simplified Acute Physiology Score II and Sequential Organ Failure Assessment scores. CONCLUSIONS Secretoneurin levels provide incremental information to established risk indices for the prediction of mortality and shock in critically ill patients with severe infections.

Mollusca Non-Grata: The influence of top-down control and residence time on the abundance, distribution, and behavior of non-native marine snails in Washington State

Thesis (Ph.D.)--University of Washington, 2016-06

A Knowledge-based System for Intelligent Support in Pharmacogenomics Evidence Assessment: Ontology-driven Evidence Representation, Retrieval, Classification and Interpretation

Thesis (Ph.D.)--University of Washington, 2016-06