Use of intrinsic modes in biology: Examples of indicial response of pulmonary blood pressure to ± step hypoxia

Recently, a new method to analyze biological nonstationary stochastic variables has been presented. The method is especially suitable to analyze the variation of one biological variable with respect to changes of another variable. Here, it is illustrated by the change of the pulmonary blood pressure in response to a step change of oxygen concentration in the gas that an animal breathes. The pressure signal is resolved into the sum of a set of oscillatory intrinsic mode functions, which have zero “local mean,” and a final nonoscillatory mode. With this device, we obtain a set of “mean trends,” each of which represents a “mean” in a definitive sense, and together they represent the mean trend systematically with different degrees of oscillatory content. Correspondingly, the oscillatory content of the signal about any mean trend can be represented by a set of partial sums of intrinsic mode functions. When the concept of “indicial response function” is used to describe the change of one variable in response to a step change of another variable, we now have a set of indicial response functions of the mean trends and another set of indicial response functions to describe the energy or intensity of oscillations about each mean trend. Each of these can be represented by an analytic function whose coefficients can be determined by a least-squares curve-fitting procedure. In this way, experimental results are stated sharply by analytic functions.

Residual delay maps unveil global patterns of atmospheric nonlinearity and produce improved local forecasts

We use residual-delay maps of observational field data for barometric pressure to demonstrate the structure of latitudinal gradients in nonlinearity in the atmosphere. Nonlinearity is weak and largely lacking in tropical and subtropical sites and increases rapidly into the temperate regions where the time series also appear to be much noisier. The degree of nonlinearity closely follows the meridional variation of midlatitude storm track frequency. We extract the specific functional form of this nonlinearity, a V shape in the lagged residuals that appears to be a basic feature of midlatitude synoptic weather systems associated with frontal passages. We present evidence that this form arises from the relative time scales of high-pressure versus low-pressure events. Finally, we show that this nonlinear feature is weaker in a well regarded numerical forecast model (European Centre for Medium-Range Forecasts) because small-scale temporal and spatial variation is smoothed out in the grided inputs. This is significant, in that it allows us to demonstrate how application of statistical corrections based on the residual-delay map may provide marked increases in local forecast accuracy, especially for severe weather systems.

The estimation of statistical parameters for local alignment score distributions

The distribution of optimal local alignment scores of random sequences plays a vital role in evaluating the statistical significance of sequence alignments. These scores can be well described by an extreme-value distribution. The distribution’s parameters depend upon the scoring system employed and the random letter frequencies; in general they cannot be derived analytically, but must be estimated by curve fitting. For obtaining accurate parameter estimates, a form of the recently described ‘island’ method has several advantages. We describe this method in detail, and use it to investigate the functional dependence of these parameters on finite-length edge effects.

Creating local bibliographic databases: new tools for evidence-based health care*

The Internet has created new opportunities for librarians to present literature search results to clinicians. In order to take full advantage of these opportunities, libraries need to create locally maintained bibliographic databases. A simple method of creating a local bibliographic database and publishing it on the Web is described. The method uses off-the-shelf software and requires minimal programming. A hedge search strategy for outcome studies of clinical process interventions is created, and Ovid is used to search MEDLINE. The search results are saved and imported into EndNote libraries. The citations are modified, exported to a Microsoft Access database, and published on the Web. Clinicians can use a Web browser to search the database. The bibliographic database contains 13,803 MEDLINE citations of outcome studies. Most searches take between four and ten seconds and retrieve between ten and 100 citations. The entire cost of the software is under $900. Locally maintained bibliographic databases can be created easily and inexpensively. They significantly extend the evidence-based health care services that libraries can offer to clinicians.

A general additive distance with time-reversibility and rate variation among nucleotide sites.

As additivity is a very useful property for a distance measure, a general additive distance is proposed under the stationary time-reversible (SR) model of nucleotide substitution or, more generally, under the stationary, time-reversible, and rate variable (SRV) model, which allows rate variation among nucleotide sites. A method for estimating the mean distance and the sampling variance is developed. In addition, a method is developed for estimating the variance-covariance matrix of distances, which is useful for the statistical test of phylogenies and molecular clocks. Computer simulation shows (i) if the sequences are longer than, say, 1000 bp, the SR method is preferable to simpler methods; (ii) the SR method is robust against deviations from time-reversibility; (iii) when the rate varies among sites, the SRV method is much better than the SR method because the distance is seriously underestimated by the SR method; and (iv) our method for estimating the sampling variance is accurate for sequences longer than 500 bp. Finally, a test is constructed for testing whether DNA evolution follows a general Markovian model.

A fast marching level set method for monotonically advancing fronts.

A fast marching level set method is presented for monotonically advancing fronts, which leads to an extremely fast scheme for solving the Eikonal equation. Level set methods are numerical techniques for computing the position of propagating fronts. They rely on an initial value partial differential equation for a propagating level set function and use techniques borrowed from hyperbolic conservation laws. Topological changes, corner and cusp development, and accurate determination of geometric properties such as curvature and normal direction are naturally obtained in this setting. This paper describes a particular case of such methods for interfaces whose speed depends only on local position. The technique works by coupling work on entropy conditions for interface motion, the theory of viscosity solutions for Hamilton-Jacobi equations, and fast adaptive narrow band level set methods. The technique is applicable to a variety of problems, including shape-from-shading problems, lithographic development calculations in microchip manufacturing, and arrival time problems in control theory.

cAMP compartmentation is responsible for a local activation of cardiac Ca2+ channels by beta-adrenergic agonists.

The role of cAMP subcellular compartmentation in the progress of beta-adrenergic stimulation of cardiac L-type calcium current (ICa) was investigated by using a method based on the use of whole-cell patch-clamp recording and a double capillary for extracellular microperfusion. Frog ventricular cells were sealed at both ends to two patch-clamp pipettes and positioned approximately halfway between the mouths of two capillaries that were separated by a 5-micron thin wall. ICa could be inhibited in one half or the other by omitting Ca2+ from one solution or the other. Exposing half of the cell to a saturating concentration of isoprenaline (ISO, 1 microM) produced a nonmaximal increase in ICa (347 +/- 70%; n = 4) since a subsequent application of ISO to the other part induced an additional effect of nearly similar amplitude to reach a 673 +/- 130% increase. However, half-cell exposure to forskolin (FSK, 30 microM) induced a maximal stimulation of ICa (561 +/- 55%; n = 4). This effect was not the result of adenylyl cyclase activation due to FSK diffusion in the nonexposed part of the cell. To determine the distant effects of ISO and FSK on ICa, the drugs were applied in a zero-Ca solution. Adding Ca2+ to the drug-containing solutions allowed us to record the local effect of the drugs. Dose-response curves for the local and distant effects of ISO and FSK on ICa were used as an index of cAMP concentration changes near the sarcolemma. We found that ISO induced a 40-fold, but FSK induced only a 4-fold, higher cAMP concentration close to the Ca2+ channels, in the part of the cell exposed to the drugs, than it did in the rest of the cell. cAMP compartmentation was greatly reduced after inhibition of phosphodiesterase activity with 3-isobutyl-methylxanthine, suggesting the colocalization of enzymes involved in the cAMP cascade. We conclude that beta-adrenergic receptors are functionally coupled to nearby Ca2+ channels via local elevations of cAMP.

Thermodynamic parameters for the helix-coil transition of oligopeptides: molecular dynamics simulation with the peptide growth method.

The helix-coil transition equilibrium of polypeptides in aqueous solution was studied by molecular dynamics simulation. The peptide growth simulation method was introduced to generate dynamic models of polypeptide chains in a statistical (random) coil or an alpha-helical conformation. The key element of this method is to build up a polypeptide chain during the course of a molecular transformation simulation, successively adding whole amino acid residues to the chain in a predefined conformation state (e.g., alpha-helical or statistical coil). Thus, oligopeptides of the same length and composition, but having different conformations, can be incrementally grown from a common precursor, and their relative conformational free energies can be calculated as the difference between the free energies for growing the individual peptides. This affords a straightforward calculation of the Zimm-Bragg sigma and s parameters for helix initiation and helix growth. The calculated sigma and s parameters for the polyalanine alpha-helix are in reasonable agreement with the experimental measurements. The peptide growth simulation method is an effective way to study quantitatively the thermodynamics of local protein folding.

Obtenção de gel mucoadesivo de nistatina para o tratamento da candidíase oral. Desenvolvimento e caracterização de dispersões sólidas de nistatina

A nistatina (NYS) é o fármaco de primeira escolha no tratamento da candidíase oral, que frequentemente acomete mais os indivíduos imunocomprometidos e pacientes com outras desordens (diabetes não tratada, neoplasias, imunodeficiências). No mercado brasileiro, a NYS é encontrada na forma de suspensão oral aquosa, onde o procedimento para sua administração consiste em bochechar o medicamento. Apesar de haver a indicação de que se mantenha o contato direto entre fármaco e a mucosa oral, na qual se encontra a Candida spp., o que aumentaria expressivamente o sucesso terapêutico, a suspensão não apresenta tal propriedade. Assim, a NYS que é fármaco com ação efetiva contra a candidíase oral, é considerada pertencente à Classe IV do Sistema de Classificação Biofarmacêutica, ou seja, apresenta baixa solubilidade e baixa permeabilidade. A baixa solubilidade pode comprometer sua disponibilidade na cavidade oral, e consequentemente, sua ação farmacológica. Diante desse quadro, o objetivo do presente trabalho foi o desenvolvimento de dispersões sólidas de NYS para o tratamento da candidíase oral, e sua posterior incorporação em gel mucoadesivo oral, favorecendo a formulação no local de ação. As dispersões sólidas são sistemas farmacêuticos, onde um fármaco pouco solúvel em água encontra-se dispersado em um carreador, no estado sólido. Os carreadores normalmente são hidrofílicos, o que permite que esses sistemas sejam empregados para aumentar a solubilidade aquosa do fármaco. Assim, foram desenvolvidas as dispersões sólidas de NYS, pelo método de eliminação do solvente, empregando como carreadores, lactose, HPMC, poloxamer 407 e poloxamer 188. Essas foram submetidas à caracterização por análise térmica, usando os ensaios de calorimetria exploratória diferencial (DSC) e termogravimetria/termogravimetria derivada (TG/DTG). Dentre essas dispersões sólidas, aquelas que se mostraram com comportamento térmico sugerindo a formação de um novo \"sistema\", foram analisadas por meio de ensaio de solubilidade. Dessa forma, a formulação NYS DS G2 (49) se destacou, pois apresentou maior solubilidade em água (4,484 mg/mL); em pH 5,5 (4,249 mg/mL) e em pH 7,0 (4,293 mg/mL), ou seja, houve um aumento de 1,426 vezes em água; 4,227 vezes em pH 5,5; e 2,743 vezes em pH 7,0. Essa formulação foi, por fim avaliada por difração de raio-X e espectroscopia de infravermelho com transformada de Fourier, técnicas que corroboraram com a análise térmica quanto à indicação de formação da dispersão sólida. Por sua vez, essa dispersão sólida foi incorporada em 4 bases de géis mucoadesivos de carbopol ® 934 PNF, alterando apenas a concentração do polímero (0,5; 1,0; 1,5; 2,0 %p/p). Foi observado que a liberação de NYS DS G2 (49) foi superior, quando comparada à liberação de NYS MP a partir do gel, e através do ensaio de mucoadesão, percebeu-se que os géis desenvolvidos apresentaram propriedades mucoadesivas compatíveis com relatos na literatura, independentemente da quantidade de carbopol ® empregada. As características reológicas foram distintas, e foi observado que as formulações Gel A e Gel B, que possuem menor quantidade de polímero, tiverem um indicativo de comportamento de fluido newtoniano, diferente dos demais, o que pode não ser desejado para esse tipo de forma farmacêutica tópica e semi-sólida. Ao final desse trabalho, pode-se concluir que foi possível desenvolver um sistema farmacêutico na forma de dispersão sólida com maior solubilidade que a NYS pura, e sua incorporação em uma forma farmacêutica mucoadesiva, e que a liberação da NYS na forma DS foi muito superior que o fármaco na forma \"convencional\", o que permite que a NYS esteja mais disponível na cavidade oral, e também junto à mucosa bucal, o que levaria a efeito farmacológico mais efetivo do antifúngico.

Robust fitting of Zernike polynomials to noisy point clouds defined over connected domains of arbitrary shape

A new method for fitting a series of Zernike polynomials to point clouds defined over connected domains of arbitrary shape defined within the unit circle is presented in this work. The method is based on the application of machine learning fitting techniques by constructing an extended training set in order to ensure the smooth variation of local curvature over the whole domain. Therefore this technique is best suited for fitting points corresponding to ophthalmic lenses surfaces, particularly progressive power ones, in non-regular domains. We have tested our method by fitting numerical and real surfaces reaching an accuracy of 1 micron in elevation and 0.1 D in local curvature in agreement with the customary tolerances in the ophthalmic manufacturing industry.

Propriedades magnéticas de trímeros de FexCo1-x depositados em Pt(111)

Quais propriedades magnéticas são modificadas quando se agrupam átomos de Fe/Co para formar estruturas quasi-2D, se comparadas aos nanofios (quasi-1D) de FexCo1-x? E como estas propriedades reagem com a variação da proporção de Fe/Co nos aglomerados? A fim de responder a estas questões, trímeros de FexCo1-x depositados em Pt(111) são investigados utilizando o método de primeiros princípios Real Space-Linear Muffin-Tin Orbital-Atomic Sphere Approximation (RS-LMTO-ASA) no âmbito da Teoria do Funcional da Densidade (DFT). Diferentes configurações de trímeros triangulares são consideradas, variando-se as posições e a concentração dos átomos de Fe/Co. Neste trabalho, demonstra-se a ocorrência de uma tendência não-linear estritamente decrescente dos momentos orbitais médios como função da concentração de Fe, distinta do encontrado tanto para os nanofios de FexCo1-x (dependência linear) quanto para a monocamada correspondente (dependência não-linear). Os resultados obtidos mostram ainda que os momentos orbitais variam com o ambiente local e com a direção de magnetização, especialmente quando associados aos átomos de Co, em concordância com publicações anteriores. A mudança de dimensionalidade quasi-1D (nanofios) para quasi-2D (trímeros compactos) não afeta o comportamento dos momentos de spin, que permanecem descritos por uma função linear com respeito à proporção de Fe/Co. Ambos o formato e a concentração de Fe nos sistemas apresentam um papel importante nos valores de energia de anisotropia magnética. Em adição, observou-se que o subtrato de Pt opera ativamente na definição das propriedades magnéticas dos aglomerados. Embora todas as configurações lineares e compactas dos aglomerados de FexCo1-x sejam estáveis e exibam interações fortemente ferromagnéticas entre os primeiros vizinhos, nem todas revelaram o ordenamento colinear como estado fundamental, apresentando uma interação de Dzyaloshinskii-Moriya não-desprezível induzida pelo acoplamento spin-órbita. Estes casos específicos são: o trímero triangular de Co puro e o trímero linear (nanofio) de Fe puro, para o qual foi verificado o acoplamento do tipo Ruderman-Kittel-Kasuya-Yosida entre os átomos de Fe constituintes. Os resultados obtidos contribuem para o entendimento de quais mecanismos definem o magnetismo nos trímeros de FexCo1-x/Pt(111), e discutem as questões presentes atualmente na literatura no contexto destes sistemas.

Multiple Perspectives on Academic Service-Learning Partnerships at the American University in Cairo: A Mixed Method Study

This mixed method study aimed to redress the gap in the literature on academic service-learning partnerships, especially in Eastern settings. It utilized Enos and Morton's (2003) theoretical framework to explore these partnerships at the American University in Cairo (AUC). Seventy-nine community partners, administrators, faculty members, and students from a diverse range of age, citizenship, racial, educational, and professional backgrounds participated in the study. Qualitative interviews were conducted with members of these four groups, and a survey with both close-ended and open-ended questions administered to students yielded 61 responses. Qualitative analyses revealed that the primary motivators for partners' engagement in service-learning partnerships included contributing to the community, enhancing students' learning and growth, and achieving the civic mission of the University. These partnerships were characterized by short-term relationships with partners' aspiring to progress toward long-term commitments. The challenges to these partnerships included issues pertaining to the institution, partnering organizations, culture, politics, pedagogy, students, and faculty members. Key strategies for improving these partnerships included institutionalizing service-learning in the University and cultivating an institutional culture supportive of community engagement. Quantitative analyses showed statistically significant relationships between students' scores on the Community Awareness and Interpersonal Effectiveness scales and their overall participation in community service activities inside and outside the classroom, as well as a statistically significant difference between their scores on the Community Awareness scale and department offering service-learning courses. The study's outcomes underscore the role of the local culture in shaping service-learning partnerships, as well as the role of both curricular and extracurricular activities in boosting students' awareness of their community and interpersonal effectiveness. Cultivating a culture of community engagement and building support mechanisms for engaged scholarship are among the critical steps required by public policy-makers in Egypt to promote service-learning in Egyptian higher education. Institutionalizing service-learning partnerships at AUC and enhancing the visibility of these partnerships on campus and in the community are essential to the future growth of these collaborations. Future studies should explore factors affecting community partners' satisfaction with these partnerships, top-down and bottom-up support to service-learning, the value of reflection to faculty members, and the influence of students' economic backgrounds on their involvement in service-learning partnerships.

Expression profiling and sequence diversity of novel DREB genes from common bean (Phaseolus vulgaris L.) and their association with drought-related traits

Common bean is a major dietary component in several countries, but its productivity is negatively affected by abiotic stresses. Dissecting candidate genes involved in abiotic stress tolerance is a paramount step toward the improvement of common bean performance under such constraints. Thereby, this thesis presents a systematic analysis of the DEHYDRATION RESPONSIVE ELEMENT-BINDING (DREB) gene subfamily, which encompasses genes that regulate several processes during stress responses, but with limited information for common bean. First, a series of in silico analyses with sequences retrieved from the P. vulgaris genome on Phytozome supported the categorization of 54 putative PvDREB genes distributed within six phylogenetic subgroups (A-1 to A-6), along the 11 chromosomes. Second, we cloned four novel PvDREB genes and determined their inducibility-factors, including the dehydration-, salinity- and cold-inducible genes PvDREB1F and PvDREB5A, and the dehydration- and cold-inducible genes PvDREB2A and PvDREB6B. Afterwards, nucleotide polymorphisms were searched through Sanger sequencing along those genes, revealing a high number of single nucleotide polymorphisms within PvDREB6B by the comparison of Mesoamerican and Andean genotypes. The nomenclature of PvDREB6B is discussed in details. Furthermore, we used the BARCBean6K_3 SNP platform to identify and genotype the closest SNP to each one of the 54 PvDREB genes. We selected PvDREB6B for a broader study encompassing a collection of wild common bean accessions of Mesoamerican origin. The population structure of the wild beans was accessed using sequence polymorphisms of PvDREB6B. The genetic clusters were partially associated with variation in latitude, altitude, precipitation and temperature throughout the areas such beans are distributed. With an emphasis on drought stress, an adapted tube-screening method in greenhouse conditions enabled the phenotyping of several drought-related traits in the wild collection. Interestingly, our data revealed a correlation between root depth, plant height and biomass and the environmental data of the location of the accessions. Correlation was also observed between the population structure determined through PvDREB6B and the environmental data. An association study combining data from the SNP array and DREB polymorphisms enabled the detection of SNP associated with drought-related traits through a compressed mixed linear model (CMLM) analysis. This thesis highlighted important features of DREB genes in common bean, revealing candidates for further strategies aimed at improvement of abiotic stress tolerance, with emphasis on drought tolerance

An evolutive approach for the delineation of local labour markets

This paper presents a new approach to the delineation of local labour markets based on evolutionary computation. The main objective is the regionalisation of a given territory into functional regions based on commuting flows. According to the relevant literature, such regions are defined so that (a) their boundaries are rarely crossed in daily journeys to work, and (b) a high degree of intra-area movement exists. This proposal merges municipalities into functional regions by maximizing a fitness function that measures aggregate intra-region interaction under constraints of inter-region separation and minimum size. Real results are presented based on the latest database from the Census of Population in the Region of Valencia. Comparison between the results obtained through the official method which currently is most widely used (that of British Travel-to-Work Areas) and those from our approach is also presented, showing important improvements in terms of both the number of different market areas identified that meet the statistical criteria and the degree of aggregate intra-market interaction.

A memetic algorithm for the delineation of local labour markets

Given a territory composed of basic geographical units, the delineation of local labour market areas (LLMAs) can be seen as a problem in which those units are grouped subject to multiple constraints. In previous research, standard genetic algorithms were not able to find valid solutions, and a specific evolutionary algorithm was developed. The inclusion of multiple ad hoc operators allowed the algorithm to find better solutions than those of a widely-used greedy method. However, the percentage of invalid solutions was still very high. In this paper we improve that evolutionary algorithm through the inclusion of (i) a reparation process, that allows every invalid individual to fulfil the constraints and contribute to the evolution, and (ii) a hillclimbing optimisation procedure for each generated individual by means of an appropriate reassignment of some of its constituent units. We compare the results of both techniques against the previous results and a greedy method.