bluuebunny/crossref_metadata_2025 huggingface dataset:
Ontologies for Bioinformatics
Authors: Schuurman Nadine , Leszczynski Agnieszka
Published: October 2017

The past twenty years have witnessed an explosion of biological data in diverse database formats governed by heterogeneous infrastructures. Not only are semantics (attribute terms) different in meaning across databases, but their organization varies widely. Ontologies are a concept imported from computing science to describe different conceptual frameworks that guide the collection, organization and publication of biological data. An ontology is similar to a paradigm but has very strict implications for formatting and meaning in a computational context. The use of ontologies is a means of communicating and resolving semantic and organizational differences between biological databases in order to enhance their integration. The purpose of interoperability (or sharing between divergent storage and semantic protocols) is to allow scientists from around the world to share and communicate with each other. This paper describes the rapid accumulation of biological data, its various organizational structures, and the role that ontologies play in interoperability.
The HapMap Resource is Providing New Insights into Ourselves and its Application to Pharmacogenomics
Authors: Zhang Wei , Ratain Mark J. , Dolan M. Eileen
Published: October 2017

The exploration of quantitative variation in complex traits such as gene expression and drug response in human populations has become one of the major priorities for medical genetics. The International HapMap Project provides a key resource of genotypic data on human lymphoblastoid cell lines derived from four major world populations of European, African, Chinese and Japanese ancestry for researchers to associate with various phenotypic data to find genes affecting health, disease and response to drugs. Recent progress in dissecting genetic contribution to natural variation in gene expression within and among human populations and variation in drug response are two examples in which researchers have utilized the HapMap resource. The HapMap Project provides new insights into the human genome and has applicability to pharmacogenomics studies leading to personalized medicine.
Coarse-Grained Models Reveal Functional Dynamics – II. Molecular Dynamics Simulation at the Coarse-Grained Level – Theories and Biological Applications
Authors: Chng Choon-Peng , Yang Lee-Wei
Published: October 2017

Molecular dynamics (MD) simulation has remained the most indispensable tool in studying equilibrium/non-equilibrium conformational dynamics since its advent 30 years ago. With advances in spectroscopy accompanying solved biocomplexes in growing sizes, sampling their dynamics that occur at biologically interesting spatial/temporal scales becomes computationally intractable; this motivated the use of coarse-grained (CG) approaches. CG-MD models are used to study folding and conformational transitions in reduced resolution and can employ enlarged time steps due to the a bsence of some of the fastest motions in the system. The Boltzmann-Inversion technique, heavily used in parameterizing these models, provides a smoothed-out effective potential on which molecular conformation evolves at a faster pace thus stretching simulations into tens of microseconds. As a result, a complete catalytic cycle of HIV-1 protease or the assembly of lipid-protein mixtures could be investigated by CG-MD to gain biological insights. In this review, we survey the theories developed in recent years, which are categorized into Folding-based and Molecular-Mechanics-based. In addition, physical bases in the selection of CG beads/time-step, the choice of effective potentials, representation of solvent, and restoration of molecular representations back to their atomic details are systematically discussed.
Searching for Factors that Distinguish Disease-Prone and Disease-Resistant Prions via Sequence Analysis
Authors: Kedarisetti Kanaka Durga , Dick Scott , Kurgan Lukasz
Published: October 2017

The exact mechanisms of prion misfolding and factors that predispose an individual to prion diseases are largely unknown. Our approach to identifying candidate factors in-silico relies on contrasting the C-terminal domain of PrPC sequences from two groups of vertebrate species: those that have been found to suffer from prion diseases, and those that have not. We propose that any significant differences between the two groups are candidate factors that may predispose individuals to develop prion disease, which should be further analyzed by wet-lab investigations. Using an array of computational methods we identified possible point mutations that could predispose PrPC to misfold into PrPSc. Our results include confirmatory findings such as the V210I mutation, and new findings including P137M, G142D, G142N, D144P, K185T, V189I, H187Y and T191P mutations, which could impact structural stability. We also propose new hypotheses that give insights into the stability of helix-2 and -3. These include destabilizing effects of Histidine and T188-T193 segment in helix-2 in the disease-prone prions, and a stabilizing effect of Leucine on helix-3 in the disease-resistant prions.
Distribution of Polymorphic and Non-Polymorphic Microsatellite Repeats in Xenopus tropicalis
Authors: Xu Zhenkang , Gutierrez Laura , Hitchens Matthew , Scherer Steve , Sater Amy K. , Wells Dan E.
Published: October 2017

The results of our bioinformatics analysis have found over 91,000 di-, tri-, and tetranucleotide microsatellites in our survey of 25% of the X. tropicalis genome, suggesting there may be over 360,000 within the entire genome. Within the X. tropicalis genome, dinucleotide (78.7%) microsatellites vastly out numbered tri- and tetranucleotide microsatellites. Similarly, AT-rich repeats are overwhelmingly dominant. The four AT-only motifs (AT, AAT, AAAT, and AATT) account for 51,858 out of 91,304 microsatellites found. Individually, AT microsatellites were the most common repeat found, representing over half of all di-, tri-, and tetranucleotide microsatellites. This contrasts with data from other studies, which show that AC is the most frequent microsatellite in vertebrate genomes (Toth et al. 2000). In addition, we have determined the rate of polymorphism for 5,128 non-redundant microsatellites, embedded in unique sequences. Interestingly, this subgroup of microsatellites was determined to have significantly longer repeats than genomic microsatellites as a whole. In addition, microsatellite loci with tandem repeat lengths more than 30 bp exhibited a significantly higher degree of polymorphism than other loci. Pairwise comparisons show that tetranucleotide microsatellites have the highest polymorphic rates. In addition, AAT and ATC showed significant higher polymorphism than other trinucleotide microsatellites, while AGAT and AAAG were significantly more polymorphic than other tetranucleotide microsatellites.
Methodology for Constructing Problem Definitions in Bioinformatics
Authors: Hauth Amy M. , Burger Gertraud
Published: October 2017

Motivation

A recurrent criticism is that certain bioinformatics tools do not account for crucial biology and therefore fail answering the targeted biological question. We posit that the single most important reason for such shortcomings is an inaccurate formulation of the computational problem.

Results

Our paper describes how to define a bioinformatics problem so that it captures both the underlying biology and the computational constraints for a particular problem. The proposed model delineates comprehensively the biological problem and conducts an item-by-item bioinformatics transformation resulting in a germane computational problem. This methodology not only facilitates interdisciplinary information flow but also accommodates emerging knowledge and technologies.
A Computational Model of Quantitative Chromatin Immunoprecipitation (ChIP) Analysis
Authors: Xie Jingping , Crooke Philip S. , McKinney Brett A. , Soltman Joel , Brandt Stephen J.
Published: October 2017

Chromatin immunoprecipitation (ChIP) analysis is widely used to identify the locations in genomes occupied by transcription factors (TFs). The approach involves chemical cross-linking of DNA with associated proteins, fragmentation of chromatin by sonication or enzymatic digestion, immunoprecipitation of the fragments containing the protein of interest, and then PCR or hybridization analysis to characterize and quantify the genomic sequences enriched. We developed a computational model of quantitative ChIP analysis to elucidate the factors contributing to the method's resolution. The most important variables identified by the model were, in order of importance, the spacing of the PCR primers, the mean length of the chromatin fragments, and, unexpectedly, the type of fragment width distribution, with very small DNA fragments and smaller amplicons providing the best resolution of TF binding. One of the major predictions of the model was also validated experimentally.
Comparison of a Label-Free Quantitative Proteomic Method Based on Peptide Ion Current Area to the Isotope Coded Affinity Tag Method
Authors: Ryu Soyoung , Gallis Byron , Goo Young Ah , Shaffer Scott A. , Radulovic Dragan , Goodlett David R.
Published: October 2017

Recently, several research groups have published methods for the determination of proteomic expression profiling by mass spectrometry without the use of exogenously added stable isotopes or stable isotope dilution theory. These so-called label-free, methods have the advantage of allowing data on each sample to be acquired independently from all other samples to which they can later be compared in silico for the purpose of measuring changes in protein expression between various biological states. We developed label free software based on direct measurement of peptide ion current area (PICA) and compared it to two other methods, a simpler label free method known as spectral counting and the isotope coded affinity tag (ICAT) method. Data analysis by these methods of a standard mixture containing proteins of known, but varying, concentrations showed that they performed similarly with a mean squared error of 0.09. Additionally, complex bacterial protein mixtures spiked with known concentrations of standard proteins were analyzed using the PICA label-free method. These results indicated that the PICA method detected all levels of standard spiked proteins at the 90% confidence level in this complex biological sample. This finding confirms that label-free methods, based on direct measurement of the area under a single ion current trace, performed as well as the standard ICAT method. Given the fact that the label-free methods provide ease in experimental design well beyond pair-wise comparison, label-free methods such as our PICA method are well suited for proteomic expression profiling of large numbers of samples as is needed in clinical analysis.
DNA Copy Number Analysis in Gastrointestinal Stromal Tumors Using Gene Expression Microarrays
Authors: Antonescu Cristina R. , Wu Kai , Xing Guoliang Leon , Cao Manqiu , Turpaz Yaron , Leversha Margaret A. , Hubbell Earl , Maki Robert G. , Miyada C. Garrett , Pillai Raji
Published: October 2017

We report a method, Expression-Microarray Copy Number Analysis (ECNA) for the detection of copy number changes using Affymetrix Human Genome U133 Plus 2.0 arrays, starting with as little as 5 ng input genomic DNA. An analytical approach was developed using DNA isolated from cell lines containing various X-chromosome numbers, and validated with DNA from cell lines with defined deletions and amplifications in other chromosomal locations. We applied this method to examine the copy number changes in DNA from 5 frozen gastrointestinal stromal tumors (GIST). We detected known copy number aberrations consistent with previously published results using conventional or BAC-array CGH, as well as novel changes in GIST tumors. These changes were concordant with results from Affymetrix 100K human SNP mapping arrays. Gene expression data for these GIST samples had previously been generated on U133A arrays, allowing us to explore correlations between chromosomal copy number and RNA expression levels. One of the novel aberrations identified in the GIST samples, a previously unreported gain on 1q21.1 containing the PEX11B gene, was confirmed in this study by FISH and was also shown to have significant differences in expression pattern when compared to a control sample. In summary, we have demonstrated the use of gene expression microarrays for the detection of genomic copy number aberrations in tumor samples. This method may be used to study copy number changes in other species for which RNA expression arrays are available, e.g. other mammals, plants, etc., and for which SNPs have not yet been mapped.
Evaluating Microarray-based Classifiers: An Overview
Authors: Boulesteix A.-L. , Strobl C. , Augustin T. , Daumer M.
Published: October 2017

For the last eight years, microarray-based class prediction has been the subject of numerous publications in medicine, bioinformatics and statistics journals. However, in many articles, the assessment of classification accuracy is carried out using suboptimal procedures and is not paid much attention. In this paper, we carefully review various statistical aspects of classifier evaluation and validation from a practical point of view. The main topics addressed are accuracy measures, error rate estimation procedures, variable selection, choice of classifiers and validation strategy.
Chromosome 20q Amplification Regulatesin VitroResponse to Kinesin-5 Inhibitor
Authors: Jackson Aimee L. , Mao Mao , Kobayashi Sumire , Ward Teresa , Biery Matthew , Dai Hongyue , Bartz Steven R. , Linsley Peter S.
Published: October 2017

We identified gene expression signatures predicting responsiveness to a Kinesin-5 (KIF11) inhibitor (Kinesin-5i) in cultured colon tumor cell lines. Genes predicting resistance to Kinesin-5i were enriched for those from chromosome 20q, a region of frequent amplification in a number of tumor types. siRNAs targeting genes in this chromosomal region identified AURKA, TPX2 and MYBL2 as genes whose disruption enhances response to Kinesin-5i. Taken together, our results show functional interaction between these genes, and suggest that their overexpression is involved in resistance to Kinesin-5i. Furthermore, our results suggest that patients whose tumors overexpress AURKA due to amplification of 20q will more likely resist treatment with Kinesin-5 inhibitor, and that inactivation of AURKA may sensitize these patients to treatment.
Classifying Variants of Undetermined Significance in BRCA2 with Protein Likelihood Ratios
Authors: Karchin Rachel , Agarwal Mukesh , Sali Andrej , Couch Fergus , Beattie Mary S.
Published: October 2017

Background

Missense (amino-acid changing) variants found in cancer predisposition genes often create difficulties when clinically interpreting genetic testing results. Although bioinformatics has developed approaches to predicting the impact of these variants, many of these approaches have not been readily applicable in the clinical setting. Bioinformatics approaches for predicting the impact of these variants have not yet found their footing in clinical practice because 1) interpreting the medical relevance of predictive scores is difficult; 2) the relationship between bioinformatics “predictors” (sequence conservation, protein structure) and cancer susceptibility is not understood.

Methodology/Principal Findings

We present a computational method that produces a probabilistic likelihood ratio predictive of whether a missense variant impairs protein function. We apply the method to a tumor suppressor gene, BRCA2, whose loss of function is important to cancer susceptibility. Protein likelihood ratios are computed for 229 unclassified variants found in individuals from high-risk breast/ovarian cancer families. We map the variants onto a protein structure model, and suggest that a cluster of predicted deleterious variants in the BRCA2 OB1 domain may destabilize BRCA2 and a protein binding partner, the small acidic protein DSS1. We compare our predictions with variant “re-classifications” provided by Myriad Genetics, a biotechnology company that holds the patent on BRCA2 genetic testing in the U.S., and with classifications made by an established medical genetics model [ 1 ]. Our approach uses bioinformatics data that is independent of these genetics-based classifications and yet shows significant agreement with them. Preliminary results indicate that our method is less likely to make false positive errors than other bioinformatics methods, which were designed to predict the impact of missense mutations in general.

Conclusions/Significance

Missense mutations are the most common disease-producing genetic variants. We present a fast, scalable bioinformatics method that integrates information about protein sequence, conservation, and structure in a likelihood ratio that can be integrated with medical genetics likelihood ratios. The protein likelihood ratio, together with medical genetics likelihood ratios, can be used by clinicians and counselors to communicate the relevance of a VUS to the individual who has that VUS. The approach described here is generalizable to regions of any tumor suppressor gene that have been structurally determined by X-ray crystallography or for which a protein homology model can be built.
An Integrative Analysis of microRNA and mRNA Expression–-A Case Study
Authors: Qin Li-Xuan
Published: October 2017

Background

MicroRNAs are believed to play an important role in gene expression regulation. They have been shown to be involved in cell cycle regulation and cancer. MicroRNA expression profiling became available owing to recent technology advancement. In some studies, both microRNA expression and mRNA expression are measured, which allows an integrated analysis of microRNA and mRNA expression.

Results

We demonstrated three aspects of an integrated analysis of microRNA and mRNA expression, through a case study of human cancer data. We showed that (1) microRNA expression efficiently sorts tumors from normal tissues regardless of tumor type, while gene expression does not; (2) many microRNAs are down-regulated in tumors and these microRNAs can be clustered in two ways: microRNAs similarly affected by cancer and microRNAs similarly interacting with genes; (3) taking let-7f as an example, targets genes can be identified and they can be clustered based on their relationship with let-7f expression.

Discussion

Our findings in this paper were made using novel applications of existing statistical methods: hierarchical clustering was applied with a new distance measure–the co-clustering frequency–to identify sample clusters that are stable; microRNA-gene correlation profiles were subject to hierarchical clustering to identify microRNAs that similarly interact with genes and hence are likely functionally related; the clustering of regression models method was applied to identify microRNAs similarly related to cancer while adjusting for tissue type and genes similarly related to microRNA while adjusting for disease status. These analytic methods are applicable to interrogate multiple types of -omics data in general.
Uncovering Biological Network Function via Graphlet Degree Signatures
Authors: Milenković Tijana , Pržulj Nataša
Published: October 2017

Motivation

Proteins are essential macromolecules of life and thus understanding their function is of great importance. The number of functionally unclassified proteins is large even for simple and well studied organisms such as baker's yeast. Methods for determining protein function have shifted their focus from targeting specific proteins based solely on sequence homology to analyses of the entire proteome based on protein-protein interaction (PPI) networks. Since proteins interact to perform a certain function, analyzing structural properties of PPI networks may provide useful clues about the biological function of individual proteins, protein complexes they participate in, and even larger subcellular machines.

Results

We design a sensitive graph theoretic method for comparing local structures of node neighborhoods that demonstrates that in PPI networks, biological function of a node and its local network structure are closely related. The method summarizes a protein's local topology in a PPI network into the vector of graphlet degrees called the signature of the protein and computes the signature similarities between all protein pairs. We group topologically similar proteins under this measure in a PPI network and show that these protein groups belong to the same protein complexes, perform the same biological functions, are localized in the same subcellular compartments, and have the same tissue expressions. Moreover, we apply our technique on a proteome-scale network data and infer biological function of yet unclassified proteins demonstrating that our method can provide valuable guidelines for future experimental research such as disease protein prediction.

Availability

Data is available upon request.
The Anti-tumour Agent, Cisplatin, and its Clinically Ineffective Isomer, Transplatin, Produce Unique Gene Expression Profiles in Human Cells
Authors: Galea Anne M. , Murray Vincent
Published: October 2017

Cisplatin is a DNA-damaging anti-cancer agent that is widely used to treat a range of tumour types. Despite its clinical success, cisplatin treatment is still associated with a number of dose-limiting toxic side effects. The purpose of this study was to clarify the molecular events that are important in the anti-tumour activity of cisplatin, using gene expression profiling techniques. Currently, our incomplete understanding of this drug's mechanism of action hinders the development of more efficient and less harmful cisplatin-based chemotherapeutics. In this study the effect of cisplatin on gene expression in human foreskin fibroblasts has been investigated using human 19K oligonucleotide microarrays. In addition its clinically inactive isomer, transplatin, was also tested. Dual-fluor microarray experiments comparing treated and untreated cells were performed in quadruplicate. Cisplatin treatment was shown to significantly up- or down-regulate a consistent subset of genes. Many of these genes responded similarly to treatment with transplatin, the therapeutically inactive isomer of cisplatin. However, a smaller proportion of these transcripts underwent differential expression changes in response to the two isomers. Some of these genes may constitute part of the DNA damage response induced by cisplatin that is critical for its anti-tumour activity. Ultimately, the identification of gene expression responses unique to clinically active compounds, like cisplatin, could thus greatly benefit the design and development of improved chemotherapeutics.
Multifraction reduction III: The case of interval monoids
Authors: Dehornoy Patrick , Wehrung Friedrich
Published: October 2017

We investigate gcd-monoids, which are cancellative monoids in which any two elements admit a left and a right gcd, and the associated reduction of multifractions (arXiv:1606.08991 and 1606.08995), a general approach to the word problemfor the enveloping group. Here we consider the particular case of interval monoids associated with finite posets. In this way, we construct gcd-monoids, in which reduction of multifractions has prescribed properties not yet known to be compatible: semi-convergence of reductionwithout convergence, semi-convergence up to some level but not beyond, non-embeddability into the enveloping group (a strong negation of semi-convergence).
Young tableaux and representations of Hecke algebras of type ADE
Authors: Poulain d'Andecy Loïc
Published: October 2017

We introduce and study some affine Hecke algebras of type ADE, generalising the affine Hecke algebras of GL. We construct irreducible calibrated representations and describe the calibrated spectrum. This is done in terms of new families of combinatorial objects equipped with actions of the corresponding Weyl groups. These objects are built from and generalise the usual standard Young tableaux, and are controlled by the considered affine Hecke algebras. By restriction and limiting procedure, we obtain several combinatorial models for representations of finite Hecke algebras and Weyl groups of type ADE. Representations are constructed by explicit formulas, in a seminormal form.
Kernel Estimates for Schrödinger Type Operators with Unbounded Diffusion and Potential Terms
Authors: Canale Anna , Rhandi Abdelaziz , Tacelli Cristian
Published: October 2017

We prove that the heat kernel associated to the Schrödinger type operator

A:=(1+|x|^\alpha)\Delta-|x|^\beta

satisfies the estimate

k(t,x,y)\leq c_1e^{\lambda_0t}e^{c_2t^{-b}}\frac{(|x||y|)^{-\frac{N-1}{2}-\frac{\beta-\alpha}{4}}}{1+|y|^\alpha} e^{-\frac{\sqrt{2}}{\beta-\alpha+2}|x|^{\frac{\beta-\alpha+2}{2}}} e^{-\frac{\sqrt{2}}{\beta-\alpha+2}|y|^{\frac{\beta-\alpha+2}{2}}}

for

t>0,|x|,|y|\ge 1

, where

c_1,c_2

are positive constants and

b=\frac{\beta-\alpha+2}{\beta+\alpha-2}

provided that

N>2,\,\alpha\geq 2

and

\beta>\alpha-2

. We also obtain an estimate of the eigenfunctions of

A

.
Solvability of Hammerstein Integral Equations with Applications to Boundary Value Problems
Authors: Bugajewska Daria , Infante Gennaro , Kasprzak Piotr
Published: October 2017

In this paper we present some new results regarding the solvability of nonlinear Hammerstein integral equations in a special cone of continuous functions. The proofs are based on a certain fixed point theorem of Leggett and Williams type. We give an application of the abstract result to prove the existence of nontrivial solutions of a periodic boundary value problem. We also investigate, via a version of Krasnosel'skiĭ's theorem for the sum of two operators, the solvability of perturbed Hammerstein integral equations in the space of continuous functions of bounded variation in the sense of Jordan. As an application of these results, we study the solvability of a boundary value problem subject to integral boundary conditions of Riemann–Stieltjes type. Some examples are presented in order to illustrate the obtained results.
Existence of Cylindrically Symmetric Ground States to a Nonlinear Curl-Curl Equation with Non-Constant Coefficients
Authors: Hirsch Andreas , Reichel Wolfgang
Published: October 2017

We consider the nonlinear curl-curl problem

\nabla\times\nabla\times U + V(x) U=f(x, |U|^2)U

in

\mathbb R^3

related to the nonlinear Maxwell equations with Kerr-type nonlinear material laws. We prove the existence of a symmetric ground-state type solution for a bounded, cylindrically symmetric coefficient

V

and subcritical cylindrically symmetric nonlinearity

f

. The new existence result extends the class of problems for which ground-state type solutions are known. It is based on compactness properties of symmetric functions due to Lions [J. Funct. Anal. 41 (1981)(2), 236–275], new rearrangement type inequalities by Brock [Proc. Indian Acad. Sci. Math. Sci. 110 (2000), 157–204] and the recent extension of the Nehari-manifold technique from Szulkin and Weth [Handbook of Nonconvex Analysis and Applications (2010), pp. 597–632].
Multivariate Wave-Packet Transforms
Authors: Ghaani Farashahi Arash
Published: October 2017

This paper presents a study for square-integrability of classical multivariate wave-packets in

L^2({\mathbb{R}^d})

via group representation theory. The abstract notions of multivariate wave-packet groups and multivariate wave-packet representations will be introduced and as the main result, we prove an admissibility condition on closed subgroups of GL

(d, \mathbb R)

, which guarantees the square integrability of classical multivariate wave-packet representations on

L^2({\mathbb{R}^d})

. Finally, we present application of our results in the case of different admissible subgroups.
Efeitos da ventilação mecânica não invasiva sobre a função pulmonar em pacientes no pós-operatório de cirurgia de revascularização do miocárdio
Authors: Ataide Ailyn Amoury , Ferraz Larissa Ainette , Rocha Larissa Salgado de Oliveira , Falcão Luiz Fábio Magno , Normando Valéria Marques Ferreira , Avila Paulo Eduardo Santos , Santos Márcio Clementino de Sousa , Rocha Rodrigo Santiago Barbosa
Published: October 2017

Introdução: A cirurgia cardíaca é responsável por diminuir os quadros sintomáticos e promover qualidade de vida dos pacientes com doença arterial coronariana. No entanto, complicações pulmonares são observadas com frequência e representam importante causa de morbidade e mortalidade para pacientes no pós-operatório imediato de cirurgia cardíaca, fato que pode ser minimizado pela fisioterapia com a utilização da ventilação mecânica não invasiva (VMNI).Objetivo: Verificar os efeitos da ventilação mecânica não invasiva sobre valores espirométricos em pacientes no pós-operatório de cirurgia de revascularização do miocárdio. Metodologia: Participaram 27 pacientes no primeiro pós operatório de cirurgia de revascularização do miocárdio. Foi realizada a espirometria antes e após aplicação em sessão única da ventilação mecânica não invasiva na modalidade BIPAP com pressão inspiratória de 15 cmH2O e pressão expiratória de 5 cmH2O.Resultados: Houve aumento do VEF1 (p<0,0001) e do CVF (p<0,0001) após aplicação da VMNI, no entanto quanto ao Índice de Tiffeneau não houve diferença estatística em relação aos valores encontrados antes e após aplicação da VMNI (p=0,1455). Conclusão: O uso da VMNI no pós-operatório de cirurgia de revascularização do miocárdio melhorou a função pulmonar.
Fisioterapia convencional versus conceito Balance sobre alterações sensório-motoras da neuropatia diabética
Authors: Magno Lizandra Dias , Moraes Anderson Antunes da Costa , Cruz Bianca Silva da , Rocha Rodrigo Santiago Barbosa , Santos Luciane Lobato Sobral , Rocha Larissa Salgado de Oliveira
Published: October 2017

Objetivo: Avaliar sensibilidade, equilíbrio e qualidade de vida em diabéticos neuropatas, comparando os efeitos de dois protocolos de Fisioterapia. Método: Dez voluntários divididos em dois grupos - Grupo Fisioterapia Convencional (GC) e Grupo Balance (GB), submetidos a dois protocolos distintos com duração de 1 hora/dia, totalizando 12 sessões, avaliados em dois momentos pelos instrumentos: Teste de Marcha Tandem (TMT) e Escala de Equilíbrio de Berg (EEB) para o equilíbrio; estesiometria, a fim de delinear a sensibilidade periférica e a escala Neuroqol, para qualidade de vida (QV). A análise estatística foi realizada por meio dos testes T de Student e Qui-quadrado no pré e pós-tratamento (p ≤0,05). Resultados: O GC obteve resultado significante no pós-tratamento somente na avaliação da EEB (p=0,03), enquanto o GB apresentou valores maiores no período pós-tratamento em todas as variáveis avaliadas, com melhoras quantitativas na sensibilidade (p=0,02), equilíbrio pelo TMT (p=0,03) e EEB (p=0,04), além da QV (p=0,04). No que diz respeito à comparação entre os grupos, os resultados significativos foram apenas para variáveis EEB (p=0,03) e TMT (p=0,04) no pós-tratamento. Conclusão: A Fisioterapia possui grande valia no tratamento da neuropatia diabética, interferindo sobre as disfunções de sensibilidade e equilíbrio, perpassando pela qualidade de vida. Dessa forma, a utilização de novas técnicas, como o Balance, apresenta boa efetividade e deve ser estimulada, a fim de prevenir complicações inerentes à doença e garantir qualidade de vida aos indivíduos diabéticos.
Study of anti-inflammatory and analgesic properties of 3-benzoyl-propionic acid
Authors: Avila Paulo Eduardo Santos , Sena Chubert Bernardo Castro de , Machi Barbarella de Matos , Pinto Laine Celestino , Montenegro Raquel Carvalho , Borges Rosivaldo dos Santos , Bastos Gilmara de Nazareth Tavares , Nascimento José Luiz Martins do
Published: October 2017

Inflammation is an attempt by the body to remove noxious stimuli and initiate thus a cascade of responses in order to promote healing. There are a variety of inflammatory mechanisms involved in infections, chronic diseases and other tissue damage. Understanding these mechanisms and the search for new anti-inflammatory drugs with greater specificity and fewer side effects, underlying the development and improvement of new protocols and standardization of experimental inflammatory models to understand better these issues. The aim of this study was to evaluate the anti-inflammatory and analgesic activity of 3-benzoyl-propionic acid (3BPA) and its potential toxicological effect. To test the 3BPA as new anti-inflammatory and analgesic drug, the use carrageenan air pouch model 1% by in vitro model of cell culture to test genocytotoxicity. In the in vitro model the 3BPA presented low level of genotoxic and low cytotoxicity risk, shown by comet assay and no damage to the plasma membrane by hemolytic test erythrocytes. In the study of anti-inflammatory activityin vivo by the air pouch method were conducted nitrite dose trials, PGE2 levels and cell migration. To verify analgesic effects of 3BPA drugin vivo tests of abdominal contortions induced by acetic acid and formalin were performed. Regard to the anti-inflammatory activity, 3BPA showed intense activity shown in marked reduction of cell migration and levels of NO, with large populations of neutrophils and reduction of PGE 2 values at a dose of 0.5mg/kg. In studies of antinociceptive activity, 3BPA reduced the number of writhes and the time lick the neurogenic and inflammatory phases of the formalin test. The results of this study also advanced substantially with respect to anti-inflammatory and analgesic properties of 3BPA by providing evidence of their likely mechanism of action, through the evaluation of antinociceptive activity, as well as the anti-inflammatory activity in vitro and in vivo, where the 3BPA showed no genotoxic effect.
Baixas doses de hidrocortisona possuem ação protetora no choque hemorrágico em ratos
Authors: Tavares Marcelo Luiz Couto , Monteiro Andrew Moraes , Feijó Daniel Haber , Mainardi Carolina Ribeiro , Ribeiro Junior Rubens Fernando Gonçalves , Dias Daniela Vale , Brito Marcus Vinicius Henriques
Published: October 2017

Objetivo: Verificar os efeitos de baixa dose de hidrocortisona no choque hemorrágico em ratos. Método: Vinte ratos Wistar, machos, foram randomicamente distribuídos em 04 grupos: Grupo Sham (GS); Grupo Choque (GC), animais submetidos ao choque hemorrágico; Grupo Solução Salina Hipertônica 7,5% (GSH 7,5%), com reposição volêmica de solução salina a 7,5% após choque hemorrágico; Grupo Hidrocortisona (GH), animais que receberam hidrocortisona após o choque. Foram analisadas amostras de gasometrias e variações da pressão arterial média (PAM) antes da indução do choque e após os tratamentos. Amostras de intestino delgado foram colhidas para analisar alterações histológicas. Resultados: APAM foi elevada para níveis estatisticamente significantes após receber os tratamentos nos grupos GSH 7,5% (p=0,0001) e GH (p=0,0058), sendo a melhora mais efetiva no primeiro quando comparados ao GC. Quanto à gasometria, a hidrocortisona elevou o pH do sangue arterial em comparação ao GC (p=0,0372), diminuiu a PaCO2 (p=0,0008), manteve níveis maiores de íons bicarbonato (p=0,0395), níveis menores de lactato (p=0,002). O GH (p=0,02) e o GSH 7,5% (p=0,0147) apresentaram menos lesões histológicas que o GC. Conclusão: Baixas doses de hidrocortisona tiveram ação protetora no choque hemorrágico em ratos.
Corrosion of Post-Tensioned Tendons with Deficient Grout, Part 2: Segregated Grout with Elevated Sulfate Content
Authors: Permeh S. , Krishna Vigneshwaran K.K. , Echeverría M. , Lau K. , Lasa I.
Published: October 2017

Corrosion failure of post-tensioning (PT) tendons with pre-packaged thixotropic grout has been documented in Florida bridges. Analysis of the deficient grout in Florida PT bridges, where severe corrosion developed, indicated elevated sulfate ion concentration, high pore water pH, low chloride ion content, and enhanced moisture content. Limited information is available on the corrosion behavior of PT strand in grout materials with elevated sulfate ion content. In this work, the corrosion performance of steel strands embedded in deficient grout was evaluated. The deficient grout was cast in large scale test assemblies that would represent geometry and material conditions found in Florida bridges, where PT strand corrosion occurred. Large scale mock up tendons (developed by the modified inclined tube [MIT] test) of about 4.57 m long were cast using expired grout materials, excess of 15% water, and sulfate ion concentrations to create deficiencies and corrosion conditions in the grout environment. Corrosion measurements such as corrosion potential (Ecorr) and corrosion current density (icorr), as well as potentiodynamic polarization tests were performed on the steel probes located along the MIT samples in contact with the deficient grout. Grout characterization parameters included the determination of the grout resistance (Rs), as well as the moisture and sulfate ion content. Also, visual inspection of the MIT samples (steel strand and steel corrosion probes) after a time was performed, as well as the corrosion products characterization. Testing confirmed that enhanced corrosion can occur in the deficient grout with high free sulfate ion accumulation.
Statistical analysis of severe magnetic fluctuations in the near-Earth plasma sheet observed by THEMIS-E
Authors: Xu Heqiucen , Shiokawa Kazuo , Frühauff Dennis
Published: October 2017

Abstract. We statistically analyzed severe magnetic fluctuations in the nightside near-Earth plasma sheet at 6–12 RE (Earth radii; 1 RE = 6371 km), because they are important for non-magnetohydrodynamics (non-MHD) effects in the magnetotail and are considered to be necessary for current disruption in the inside-out substorm model. We used magnetic field data from 2013 and 2014 obtained by the Time History of Events and Macroscale Interactions during Substorms E (THEMIS-E) satellite (sampling rate: 4 Hz). A total of 1283 severe magnetic fluctuation events were identified that satisfied the criteria σB∕B > 0. 5, where σB and B are the standard deviation and the average value of magnetic field intensity during the time interval of the local proton gyroperiod, respectively. We found that the occurrence rates of severe fluctuation events are 0.00118, 0.00899, and 0.0238 % at 6–8, 8–10, and 10–12 RE, respectively, and most events last for no more than 15 s. From these occurrence rates, we estimated the possible scale sizes of current disruption by severe magnetic fluctuations as 3.83 RE3 by assuming that four substorms with 5 min intervals of current disruption occur every day. The fluctuation events occurred most frequently at the ZGSM (Z distance in the geocentric solar magnetospheric coordinate system) close to the model neutral sheet within 0.2 RE. Most events occur in association with sudden decreases in the auroral electrojet lower (AL) index and magnetic field dipolarization, indicating that they are related to substorms. Sixty-two percent of magnetic fluctuation events were accompanied by ion flow with velocity V > 100 km s−1, indicating that the violation of ion gyromotion tends to occur during high-speed flow in the near-Earth plasma sheet. The superposed epoch analysis also indicated that the flow speed increases before the severe magnetic fluctuations. We discuss how both the inside-out and outside-in substorm models can explain this increase in flow speeds before magnetic fluctuation events.
Combining satellite data and appropriate objective functions for improved spatial pattern performance of a distributed hydrologic model
Authors: Demirel Mehmet C. , Mai Juliane , Mendiguren Gorka , Koch Julian , Samaniego Luis , Stisen Simon
Published: October 2017

Abstract. Satellite based earth observations offer great opportunities to improve spatial model predictions by means of spatial pattern oriented model evaluations. In this study, observed spatial patterns of actual evapotranspiration (AET) are utilized for spatial model calibration tailored to target the pattern performance of the model. The proposed calibration framework combines temporally aggregated observed spatial patterns with a new spatial performance metric and a flexible spatial parameterisation scheme. The mesoscale Hydrologic Model (mHM) is used to simulate streamflow and AET and has been selected due to its soil parameter distribution approach based on pedotransfer functions and the build in multiscale parameter regionalization. In addition two new domain specific spatial parameter distribution options have been incorporated in the model in order to increase the flexibility of root fraction coefficient and potential evapotranspiration correction parameterisations, based on soil type and vegetation density. These parametrisations are utilized as they are most relevant for simulated AET patterns from the hydrologic model. Due to the fundamental challenges encountered when evaluating spatial pattern performance using standard metrics, we developed a simple but highly discriminative spatial metric i.e. comprised of three easily interpretable components measuring co-location, variation and distribution of the spatial data. The study shows that with flexible spatial model parameterisation used in combination with the appropriate objective functions, the simulated spatial patterns of actual evapotranspiration become substantially more similar to the satellite based estimates. Overall 26 parameters are identified for calibration through a sequential screening approach based on a combination of streamflow and spatial pattern metrics. The robustness of the calibrations is tested using an ensemble of nine calibrations based on different seed numbers using the shuffled complex evolution optimizer. The calibration results reveal a limited trade-offs between streamflow dynamics and spatial patterns illustrating the benefit of combining separate observation types and objective functions. At the same time, the simulated spatial patterns of AET significantly improved when including an objective function based on observed AET patterns and a novel spatial performance metric compared to traditional streamflow only calibration. Since the overall water balance is usually a crucial goal in the hydrologic modelling, spatial pattern oriented optimization should always be accompanied by traditional discharge measurements. In such a multi-objective framework, the current study promotes the use of a novel bias-insensitive spatial pattern metric, which exploits the key information contained in the observed patterns while allowing the water balance to be informed by discharge observations.
Assessment of Forest Fire Rating Systems in Typical Mediterranean Forest, Crete, Greece
Authors: Elhag Mohamed , Boteva Slivena
Published: October 2017

Abstract. The Fire Weather Index (FWI) module was tested under the Mediterranean- type conditions of Crete (Greece) for the two fire seasons 2008–2009. High correlations were found between the Fine Fuel Moisture Code (FFMC) and the Duff Moisture Code (DMC. The Drought Code (DC) was insignificantly correlated with the soil moisture content. No significant correlation was found between the area burned by wildfires and any component of the FWI system during the studied period, unlike fire occurrence with which most of the components were highly correlated. Meanwhile, the Keetch-Byram Drought Index (KBDI) of the American Forest Fire Danger Rating System (NFFDRS) was also examined under the same conditions. It provided a useful means of monitoring general wetting and drying cycles, but is inadequate for indicating daily fire danger throughout the fire season in our region. Weak correlations between the KBDI- the fire occurrence and the area burned were found for the two fire seasons studied-2008–2009. Correlations between the KBDI and litter, duff and soil did not give statistically sound results. On the contrary, the KBDI seemed to predict with high accuracy the moisture content of three annual plants (Piplatherum miliaceum, Parietaria diffusa, Avena sterillis) with a shallow rooting system of Pinus halepensis forest understory in the region. This indicated that the index was adequate, to a certain extent, to represent the upper soil layers' water status, while it is unsuitable to predict needles moisture content of Pinus halepensis, which has a deep rooting system.
Linking source with consequences of coastal storm impacts for climate change and risk reduction scenarios for Mediterranean sandy beaches
Authors: Sanuy Marc , Duo Enrico , Jäger Wiebke S. , Ciavola Paolo , Jiménez José A.
Published: October 2017

Abstract. Integrated risk assessment approaches to support coastal managers’ decisions when designing plans are increasingly becoming an urgent need. To enable efficient coastal management, possible present and future scenarios must be included, disaster risk reduction (DRR) measures integrated, and multiple hazards dealt with. In this work, the Bayesian Network approach to coastal risk assessment was applied and tested at two Mediterranean sandy coasts (Tordera Delta in Spain and Lido degli Estensi–Spina in Italy). Process-oriented models are used to predict hazards at the receptor scale based on a large number of storm characteristics. Hazards are converted into impacts through vulnerability relations. A Bayesian Network integrates all results to link forcing characteristics with expected impacts through conditional probabilities. The tool has been proven successful in reproducing current coastal responses at both sites. It has also shown great utility for scenario comparisons, and is able to output significant impact change trends, despite the inherent uncertainties of the approach. This work highlights the advantages of using such a tool for present and future coastal risk assessment and planning.
Impacts of a lengthening open water season on Alaskan coastal communities
Authors: Rolph Rebecca J. , Mahoney Andrew R. , Walsh John , Loring Philip A.
Published: October 2017

Abstract. It is often remarked that Arctic coastal communities are on the frontlines of the impacts related to the rapidly diminishing ice pack. These impacts can have direct effects on communities, such as reduced access to subsistence hunting species, or increased wave height and coastal erosion. There are also indirect effects driven by external socioeconomic systems, such as increased maritime activity, which may provide local economic benefits while increasing potential for disruption to subsistence activities. Here, we use the Historical Sea Ice Atlas (HSIA) dataset to assess the potential direct and indirect impacts from sea ice change for selected Alaska communities. The HSIA provides sea ice concentration for the Bering, Chukchi and Beaufort Seas on a 0.25-degree grid for the period 1953–2013. We estimate the timing of freeze-up and break-up, which is reported by local residents to be of critical importance for subsistence hunting activities and food security. We calculate the open water season length and extend the existing timeseries of the Barnett Severity Index (BSI), which assesses the impact of ice conditions on maritime traffic destined for the Beaufort Sea. We find consistent trends toward later freeze-up and earlier break-up, leading to a lengthened open water period. In Utqiavik (formerly Barrow), there is evidence of a navigational regime change in the 1990s when the pack ice edge started to routinely retreat beyond this most northern community.