An iterative method for extracting energy-like quantities from protein structures.

We present a method (ENERGI) for extracting energy-like quantities from a data base of protein structures. In this paper, we use the method to generate pairwise additive amino acid "energy" scores. These scores are obtained by iteration until they correctly discriminate a set of known protein folds from decoy conformations. The method succeeds in lattice model tests and in the gapless threading problem as defined by Maiorov and Crippen [Maiorov, V. N. & Crippen, G. M. (1992) J. Mol. Biol. 227, 876-888]. A more challenging test of threading a larger set of test proteins derived from the representative set of Hobohm and Sander [Hobohm, U. & Sander, C. (1994) Protein Sci. 3, 522-524] is used as a "workbench" for exploring how the ENERGI scores depend on their parameter sets.

Isolation and characterization of microorganisms with probiotic potential

Tese de mestrado em Microbiologia Aplicada, apresentada à Universidade de Lisboa, através da Faculdade de Ciências, 2016

Predicting posttraumatic stress reactions in children prior to traumatic exposure

The present study examined the relations among previously identified risk and protective variables associated with traumatic exposure and evaluated a model of resilience to traumatic events among Latino youth prior to traumatic exposure using structural equation modeling. Model tests were pursued in the context of Full Information Maximum Likelihood (FIML) methods as implemented in Mplus. The model evaluated the role of the following variables: (a) intervening life events; (b) child characteristics; (c) social support from significant others; and (d) children's coping. Data were collected from 181 Latino youth (M age = 9.22, SD = 1.38; 49.0% female) participants. Data analyses revealed that children's perceived available social support and use of coping strategies predicted low state anxiety following exposure to cues of disaster. Life events and preexisting depression symptoms did not significantly predict social support and coping, whereas preexisting anxiety was a significant predictor of perceived social support. This study represents an important initial step towards establishing and empirically evaluating a resilience model. Implications for preparedness interventions and a framework for the etiology of resilient reactions to disaster exposure are discussed.

Cultural intelligence: Extending the nomological network

This dissertation consists of three independent studies, which study the nomological network of cultural intelligence (CI)—a relatively new construct within the fields of cross-cultural psychology and organizational psychology. Since the introduction of this construct, CI now has a generally accepted model comprised of four codependent subfactors. In addition, the focus of preliminary research within the field is on understanding the new construct’s correlates and outcomes. Thus, the goals for this dissertation were (a) to provide an additional evaluation of the factor structure of CI and (b) to examine further the correlates and outcomes that should theoretically be included in its nomological network. Specifically the model tests involved a one-factor, three-factor, and four-factor structure. The examined correlates of CI included the Big Five personality traits, core self-evaluation, social self-efficacy, self-monitoring, emotional intelligence, and cross-cultural experience. The examined outcomes also included overall performance, contextual performance, and cultural adaption in relation to CI. Thus, this dissertation has a series of 20 proposed and statistically evaluated hypotheses. The first study in this dissertation contained the summary of the extant CI literature via meta-analytic techniques. The outcomes of focus were significantly relevant to CI, while the CI correlates had more inconclusive results. The second and third studies contained original data collected from a sample of students and adult workers, respectively. In general, the results between these two studies were parallel. The four-factor structure of CI emerged as the best fit to the data, and several correlates and outcomes indicated significant relation to CI. In addition, the tested incremental validity of CI showed significant results emerging in both studies. Lastly, several exploratory analyses indicated the role of CI as a mediator between relevant antecedent and the outcome of cultural adaption, while the data supported the mediator role of CI. The final chapter includes a thorough discussion of practical implications as well as limitation to the research design.^

Cultural Intelligence: Extending the Nomological Network

This dissertation consists of three independent studies, which study the nomological network of cultural intelligence (CI)—a relatively new construct within the fields of cross-cultural psychology and organizational psychology. Since the introduction of this construct, CI now has a generally accepted model comprised of four codependent subfactors. In addition, the focus of preliminary research within the field is on understanding the new construct’s correlates and outcomes. Thus, the goals for this dissertation were (a) to provide an additional evaluation of the factor structure of CI and (b) to examine further the correlates and outcomes that should theoretically be included in its nomological network. Specifically the model tests involved a one-factor, three-factor, and four-factor structure. The examined correlates of CI included the Big Five personality traits, core self-evaluation, social self-efficacy, self-monitoring, emotional intelligence, and cross-cultural experience. The examined outcomes also included overall performance, contextual performance, and cultural adaption in relation to CI. Thus, this dissertation has a series of 20 proposed and statistically evaluated hypotheses. The first study in this dissertation contained the summary of the extant CI literature via meta-analytic techniques. The outcomes of focus were significantly relevant to CI, while the CI correlates had more inconclusive results. The second and third studies contained original data collected from a sample of students and adult workers, respectively. In general, the results between these two studies were parallel. The four-factor structure of CI emerged as the best fit to the data, and several correlates and outcomes indicated significant relation to CI. In addition, the tested incremental validity of CI showed significant results emerging in both studies. Lastly, several exploratory analyses indicated the role of CI as a mediator between relevant antecedent and the outcome of cultural adaption, while the data supported the mediator role of CI. The final chapter includes a thorough discussion of practical implications as well as limitation to the research design.

Submarine slope failures in gassy soils

Submarine slope stability has become an important concern and a subject of research with increasing demand for offshore developments and technological advancement for harsh and challenging environments. The consequences of submarine slope failure adjacent to oil and gas facilities would have a large financial, safety and regulatory impact. This current research work investigates potential failure of submarine gassy slopes triggered by tidal variations. Due to tidal variations, failure of an unsaturated slope may occur under specific combinations of increasing degree of saturation and soil permeability, and decreasing tidal period. Novel physical model tests in a geotechnical centrifuge were undertaken to examine submarine slope failure mechanisms containing gassy sediments. The model preparation techniques, measurement systems and results are presented. The response observed in the model test is discussed and further developments proposed. The buried PPT’s response of the submarine slope are comparable in terms of attenuation and phase lag with Nagaswaran (1983) and with field measurements of Atigh and Byrne (2004) in terms of phase lag.

Experimental and numerical studies of hydrodynamic interaction of two bodies in waves

This thesis focuses on experimental and numerical studies of the hydrodynamic interaction between two vessels in close proximity in waves. In the model tests, two identical box-like models with round corners were used. Regular waves with the same wave steepness and different wave frequencies were generated. Six degrees of freedom body motions and wave elevations between bodies were measured in a head sea condition. Three initial gap widths were examined. In the numerical computations, a panel-free method based seakeeping program, MAPS0, and a panel method based program, WAMIT, were used for the prediction of body motions and wave elevations. The computed body motions and wave elevations were compared with experimental data.

Validation of an experimental polyurethane model for biomechanical studies on implant supported prosthesis - tension tests

OBJECTIVES: The complexity and heterogeneity of human bone, as well as ethical issues, frequently hinder the development of clinical trials. The purpose of this in vitro study was to determine the modulus of elasticity of a polyurethane isotropic experimental model via tension tests, comparing the results to those reported in the literature for mandibular bone, in order to validate the use of such a model in lieu of mandibular bone in biomechanical studies. MATERIAL AND METHODS: Forty-five polyurethane test specimens were divided into 3 groups of 15 specimens each, according to the ratio (A/B) of polyurethane reagents (PU-1: 1/0.5, PU-2: 1/1, PU-3: 1/1.5). RESULTS: Tension tests were performed in each experimental group and the modulus of elasticity values found were 192.98 MPa (SD=57.20) for PU-1, 347.90 MPa (SD=109.54) for PU-2 and 304.64 MPa (SD=25.48) for PU-3. CONCLUSION: The concentration of choice for building the experimental model was 1/1.

Validation of an experimental polyurethane model for biomechanical studies on implant-supported prosthesis: compression tests

OBJECTIVES: The complexity and heterogeneity of human bone, as well as ethical issues, most always hinder the performance of clinical trials. Thus, in vitro studies become an important source of information for the understanding of biomechanical events on implant-supported prostheses, although study results cannot be considered reliable unless validation studies are conducted. The purpose of this work was to validate an artificial experimental model based on its modulus of elasticity, to simulate the performance of human bone in vivo in biomechanical studies of implant-supported prostheses. MATERIAL AND METHODS: In this study, fast-curing polyurethane (F16 polyurethane, Axson) was used to build 40 specimens that were divided into five groups. The following reagent ratios (part A/part B) were used: Group A (0.5/1.0), Group B (0.8/1.0), Group C (1.0/1.0), Group D (1.2/1.0), and Group E (1.5/1.0). A universal testing machine (Kratos model K - 2000 MP) was used to measure modulus of elasticity values by compression. RESULTS: Mean modulus of elasticity values were: Group A - 389.72 MPa, Group B - 529.19 MPa, Group C - 571.11 MPa, Group D - 470.35 MPa, Group E - 437.36 MPa. CONCLUSION: The best mechanical characteristics and modulus of elasticity value comparable to that of human trabecular bone were obtained when A/B ratio was 1:1.

Model Independent Tests of Skyrmions and Their Holographic Cousins

We describe a new exact relation for large N(c) QCD for the long-distance behavior of baryon form factors in the chiral limit. This model-independent relation is used to test the consistency of the structure of several baryon models. All 4D semiclassical chiral soliton models satisfy the relation, as does the Pomarol-Wulzer holographic model of baryons as 5D Skyrmions. However, remarkably, we find that the holographic model treating baryons as instantons in the Sakai-Sugimoto model does not satisfy the relation.

Model specification tests in nonparametric stochastic regression models

In this paper, we consider testing for additivity in a class of nonparametric stochastic regression models. Two test statistics are constructed and their asymptotic distributions are established. We also conduct a small sample study for one of the test statistics through a simulated example. (C) 2002 Elsevier Science (USA).

Thermal tests on the LISA pathfinder engineering model

Report for the scientific sojourn carried out at Albert Einstein Institut in Germany, from April to July 2006.

Oxidation of silicon: further tests for the interfacial silicon emission model

The classical description of Si oxidation given by Deal and Grove has well-known limitations for thin oxides (below 200 Ã). Among the large number of alternative models published so far, the interfacial emission model has shown the greatest ability to fit the experimental oxidation curves. It relies on the assumption that during oxidation Si interstitials are emitted to the oxide to release strain and that the accumulation of these interstitials near the interface reduces the reaction rate there. The resulting set of differential equations makes it possible to model diverse oxidation experiments. In this paper, we have compared its predictions with two sets of experiments: (1) the pressure dependence for subatmospheric oxygen pressure and (2) the enhancement of the oxidation rate after annealing in inert atmosphere. The result is not satisfactory and raises serious doubts about the model’s correctness

Social preferences: Some simple tests and a new model

Departures from pure self interest in economic experiments have recently inspired models of "social preferences". We conduct experiments on simple two-person and three-person games with binary choices that test these theories more directly than the array of games conventionally considered. Our experiments show strong support for the prevalence of "quasi-maximin" preferences: People sacrifice to increase the payoffs for all recipients, but especially for the lowest-payoff recipients. People are also motivated by reciprocity: While people are reluctant to sacrifice to reciprocate good or bad behavior beyond what they would sacrifice for neutral parties, they withdraw willingness to sacrifice to achieve a fair outcome when others are themselves unwilling to sacrifice. Some participants are averse to getting different payoffs than others, but based on our experiments and reinterpretation of previous experiments we argue that behavior that has been presented as "difference aversion" in recent papers is actually a combination of reciprocal and quasi-maximin motivations. We formulate a model in which each player is willing to sacrifice to allocate the quasi-maximin allocation only to those players also believed to be pursuing the quasi-maximin allocation, and may sacrifice to punish unfair players.