Use of the FACTS solvation model for protein-ligand docking calculations. Application to EADock.

Protein-ligand docking has made important progress during the last decade and has become a powerful tool for drug development, opening the way to virtual high throughput screening and in silico structure-based ligand design. Despite the flattering picture that has been drawn, recent publications have shown that the docking problem is far from being solved, and that more developments are still needed to achieve high successful prediction rates and accuracy. Introducing an accurate description of the solvation effect upon binding is thought to be essential to achieve this goal. In particular, EADock uses the Generalized Born Molecular Volume 2 (GBMV2) solvent model, which has been shown to reproduce accurately the desolvation energies calculated by solving the Poisson equation. Here, the implementation of the Fast Analytical Continuum Treatment of Solvation (FACTS) as an implicit solvation model in small molecules docking calculations has been assessed using the EADock docking program. Our results strongly support the use of FACTS for docking. The success rates of EADock/FACTS and EADock/GBMV2 are similar, i.e. around 75% for local docking and 65% for blind docking. However, these results come at a much lower computational cost: FACTS is 10 times faster than GBMV2 in calculating the total electrostatic energy, and allows a speed up of EADock by a factor of 4. This study also supports the EADock development strategy relying on the CHARMM package for energy calculations, which enables straightforward implementation and testing of the latest developments in the field of Molecular Modeling.

Model of single-electron decay from a strongly isolated quantum dot

Recent measurements of electron escape from a nonequilibrium charged quantum dot are interpreted within a two-dimensional (2D) separable model. The confining potential is derived from 3D self-consistent Poisson-Thomas-Fermi calculations. It is found that the sequence of decay lifetimes provides a sensitive test of the confining potential and its dependence on electron occupation

Development of LRFD Procedures for Bridge Pile Foundations in Iowa: Volume II: Field Testing of Steel Piles in Clay, Sand, and Mixed Soils and Data Analysis, September 2011

In response to the mandate on Load and Resistance Factor Design (LRFD) implementations by the Federal Highway Administration (FHWA) on all new bridge projects initiated after October 1, 2007, the Iowa Highway Research Board (IHRB) sponsored these research projects to develop regional LRFD recommendations. The LRFD development was performed using the Iowa Department of Transportation (DOT) Pile Load Test database (PILOT). To increase the data points for LRFD development, develop LRFD recommendations for dynamic methods, and validate the results ofLRFD calibration, 10 full-scale field tests on the most commonly used steel H-piles (e.g., HP 10 x 42) were conducted throughout Iowa. Detailed in situ soil investigations were carried out, push-in pressure cells were installed, and laboratory soil tests were performed. Pile responses during driving, at the end of driving (EOD), and at re-strikes were monitored using the Pile Driving Analyzer (PDA), following with the CAse Pile Wave Analysis Program (CAPWAP) analysis. The hammer blow counts were recorded for Wave Equation Analysis Program (WEAP) and dynamic formulas. Static load tests (SLTs) were performed and the pile capacities were determined based on the Davisson’s criteria. The extensive experimental research studies generated important data for analytical and computational investigations. The SLT measured loaddisplacements were compared with the simulated results obtained using a model of the TZPILE program and using the modified borehole shear test method. Two analytical pile setup quantification methods, in terms of soil properties, were developed and validated. A new calibration procedure was developed to incorporate pile setup into LRFD.

Optimal dividend strategies for a compound Poisson risk process under transaction costs and power utility

We characterize the value function of maximizing the total discounted utility of dividend payments for a compound Poisson insurance risk model when strictly positive transaction costs are included, leading to an impulse control problem. We illustrate that well known simple strategies can be optimal in the case of exponential claim amounts. Finally we develop a numerical procedure to deal with general claim amount distributions.

Development of LRFD Design Procedures for Bridge Piles in Iowa – Field Testing of Steel H-Piles in Clay, Sand, and Mixed Soils and Data Analysis (Volume II), TR-583, 2011

In response to the mandate on Load and Resistance Factor Design (LRFD) implementations by the Federal Highway Administration (FHWA) on all new bridge projects initiated after October 1, 2007, the Iowa Highway Research Board (IHRB) sponsored these research projects to develop regional LRFD recommendations. The LRFD development was performed using the Iowa Department of Transportation (DOT) Pile Load Test database (PILOT). To increase the data points for LRFD development, develop LRFD recommendations for dynamic methods, and validate the results of LRFD calibration, 10 full-scale field tests on the most commonly used steel H-piles (e.g., HP 10 x 42) were conducted throughout Iowa. Detailed in situ soil investigations were carried out, push-in pressure cells were installed, and laboratory soil tests were performed. Pile responses during driving, at the end of driving (EOD), and at re-strikes were monitored using the Pile Driving Analyzer (PDA), following with the CAse Pile Wave Analysis Program (CAPWAP) analysis. The hammer blow counts were recorded for Wave Equation Analysis Program (WEAP) and dynamic formulas. Static load tests (SLTs) were performed and the pile capacities were determined based on the Davisson’s criteria. The extensive experimental research studies generated important data for analytical and computational investigations. The SLT measured load-displacements were compared with the simulated results obtained using a model of the TZPILE program and using the modified borehole shear test method. Two analytical pile setup quantification methods, in terms of soil properties, were developed and validated. A new calibration procedure was developed to incorporate pile setup into LRFD.

Social inequalities of functioning and perceived health in Switzerland: a representative cross-sectional analysis.

Many people worldwide live with a disability, i.e. limitations in functioning. The prevalence is expected to increase due to demographic change and the growing importance of non-communicable disease and injury. To date, many epidemiological studies have used simple dichotomous measures of disability, even though the WHO's International Classification of Functioning, Disability, and Health (ICF) provides a multi-dimensional framework of functioning. We aimed to examine associations of socio-economic status (SES) and social integration in 3 core domains of functioning (impairment, pain, limitations in activity and participation) and perceived health. We conducted a secondary analysis of representative cross-sectional data of the Swiss Health Survey 2007 including 10,336 female and 8,424 male Swiss residents aged 15 or more. Guided by a theoretical ICF-based model, 4 mixed effects Poisson regressions were fitted in order to explain functioning and perceived health by indicators of SES and social integration. Analyses were stratified by age groups (15-30, 31-54, ≥55 years). In all age groups, SES and social integration were significantly associated with functional and perceived health. Among the functional domains, impairment and pain were closely related, and both were associated with limitations in activity and participation. SES, social integration and functioning were related to perceived health. We found pronounced social inequalities in functioning and perceived health, supporting our theoretical model. Social factors play a significant role in the experience of health, even in a wealthy country such as Switzerland. These findings await confirmation in other, particularly lower resourced settings.

Measuring the relative effect of factors affecting species distribution model predictions

1. Species distribution models are increasingly used to address conservation questions, so their predictive capacity requires careful evaluation. Previous studies have shown how individual factors used in model construction can affect prediction. Although some factors probably have negligible effects compared to others, their relative effects are largely unknown. 2. We introduce a general "virtual ecologist" framework to study the relative importance of factors involved in the construction of species distribution models. 3. We illustrate the framework by examining the relative importance of five key factors-a missing covariate, spatial autocorrelation due to a dispersal process in presences/absences, sample size, sampling design and modeling technique-in a real study framework based on plants in a mountain landscape at regional scale, and show that, for the parameter values considered here, most of the variation in prediction accuracy is due to sample size and modeling technique. Contrary to repeatedly reported concerns, spatial autocorrelation has only comparatively small effects. 4. This study shows the importance of using a nested statistical framework to evaluate the relative effects of factors that may affect species distribution models.

Psychosexual development in men with congenital hypogonadotropic hypogonadism on long-term treatment: a mixed methods study.

INTRODUCTION: Congenital hypogonadotropic hypogonadism (CHH) is a rare, genetic, reproductive endocrine disorder characterized by absent puberty and infertility. Limited information is available on the psychosocial impact of CHH and psychosexual development in these patients. AIM: The aim of this study was to determine the impact of CHH on psychosexual development in men on long-term treatment. METHODS: A sequential mixed methods explanatory design was used. First, an online survey (quantitative) was used to quantify the frequency of psychosexual problems among CHH men. Second, patient focus groups (qualitative) were conducted to explore survey findings in detail and develop a working model to guide potential nursing and interdisciplinary interventions. MAIN OUTCOME MEASURES: Patient characteristics, frequency of body shame, difficulty with intimate relationships, and never having been sexually active were assessed. Additionally, we collected subjective patient-reported outcomes regarding the impact of CHH on psychological/emotional well-being, intimate relationships, and sexual activity. RESULTS: A total of 101 CHH men on long-term treatment (>1 year) were included for the analysis of the online survey (mean age 37 ± 11 years, range 19-66, median 36). Half (52/101, 51%) of the men had been seen at a specialized academic center and 37/101 (37%) reported having had fertility-inducing treatment. A high percentage of CHH men experience psychosexual problems including difficulty with intimate relationships (70%) and body image concerns/body shame (94/101, 93%), and the percentage of men never having been sexually active is five times the rate in a reference group (26% vs. 5.4%, P < 0.001). Focus groups revealed persisting body shame and low self-esteem despite long-term treatment that has lasting impact on psychosexual functioning. CONCLUSIONS: CHH men frequently experience psychosexual problems that pose barriers to intimate relationships and initiating sexual activity. These lingering effects cause significant distress and are not ameliorated by long-term treatment. Psychosexual assessment in CHH men with appropriate psychological support and treatment should be warranted in these patients. Dwyer AA, Quinton R, Pitteloud N, and Morin D. Psychosexual development in men with congenital hypogonadotropic hypogonadism on long-term treatment: A mixed methods study. Sex Med 2015;3:32-41.

Case management for emergency department frequent users : a randomized controlled trial

Background: Emergency department frequent users (EDFUs) account for a disproportionally high number of emergency department (ED) visits, contributing to overcrowding and high health-care costs. At the Lausanne University Hospital, EDFUs account for only 4.4% of ED patients, but 12.1% of all ED visits. Our study tested the hypothesis that an interdisciplinary case management intervention red. Methods: In this randomized controlled trial, we allocated adult EDFUs (5 or more visits in the previous 12 months) who visited the ED of the University Hospital of Lausanne, Switzerland between May 2012 and July 2013 either to an intervention (N=125) or a standard emergency care (N=125) group and monitored them for 12 months. Randomization was computer generated and concealed, and patients and research staff were blinded to the allocation. Participants in the intervention group, in addition to standard emergency care, received case management from an interdisciplinary team at baseline, and at 1, 3, and 5 months, in the hospital, in the ambulatory care setting, or at their homes. A generalized, linear, mixed-effects model for count data (Poisson distribution) was applied to compare participants' numbers of visits to the ED during the 12 months (Period 1, P1) preceding recruitment to the numbers of visits during the 12 months monitored (Period 2, P2).

Narrative discourse in interviews to linguistically mixed couples

This article deals with self-referential storytelling in sociolinguistic interviews. It analyzes the personal stories in ten interviews to linguistically heterogeneous couples. For this purpose, it is applied the model of linguistic analysis of drama (Bruner & Weisser 1991) and it identifies and interprets discursive markers of autobiographical storytelling. Therefore it takes into consideration the elements referred to agents and to their actions, to the sequences of events, to the canon or rule, and to the narrator's perspective. At the same time, it proposes to extend our approach to the existence itself of the participants. Resumen.-"Discurso narrativo en entrevistas a parejas lingüísticamente mixtas". Este artículo trata de las narraciones autorreferenciales en entrevistas sociolingüísticas sobre concepciones y usos de las lenguas en familias lingüísticamente mixtas. Analiza los relatos que aparecen en diez entrevistas a padres y madres que forman parejas lingüísticamente heterogéneas. Aplica el modelo de análisis lingüístico del dramatismo (Bruner & Weisser 1991). Identifica e interpreta los marcadores discursivos de la narración autobiográfica. Con este propósito considera los constituyentes que se refieren a los agentes y sus acciones, a las secuencias de sucesos, al canon o norma y a la perspectiva del narrador. Y propone la ampliación del estudio a los guiones de vida de lo actores. Palabras clave: entrevista, relato, narración, pareja, política lingüística de la familia, multilingüismo, marcador discursivo.

Ethnic identity construction in Chiapas: examining the role of higher intercultural education model = La construcción de la identidad étnica en Chiapas : examinando el rol de un modelo de educación superior intercultural

This study explored ethnic identity among 410 mestizo students who were attending one of three universities, which varied in their ethnic composition and their educative model. One of these universities was private and had mostly mestizo students such as the public one did. The third educative context, also public, had an intercultural model of education and the students were mixed among mestizo and indigenous. The Multigroup Ethnic Identity Measure (MEIM) was administered to high school students in order to compare their scores on ethnic identity and its components: affi rmation, belonging or commitment and exploration. Principle components factor analysis with varimax rotation and tests of mean group differences are performed. The results showed signifi cant differences between the studied groups. Scores on ethnic identity and its components were signifi cantly higher among mestizos group from University with intercultural model of education than mestizos from public and private universities of the same region. Implications of these fi ndings for education are considered, as they are the strengths as well as the limitations of this research

SSPBE: um programa para solução numérica da equação de Poisson-Boltzmann em simetria esférica com modelo de adsorção

A Fortran77 program, SSPBE, designed to solve the spherically symmetric Poisson-Boltzmann equation using cell model for ionic macromolecular aggregates or macroions is presented. The program includes an adsorption model for ions at the aggregate surface. The working algorithm solves the Poisson-Boltzmann equation in the integral representation using the Picard iteration method. Input parameters are introduced via an ASCII file, sspbe.txt. Output files yield the radial distances versus mean field potentials and average molar ion concentrations, the molar concentration of ions at the cell boundary, the self-consistent degree of ion adsorption from the surface and other related data. Ion binding to ionic, zwitterionic and reverse micelles are presented as representative examples of the applications of the SSPBE program.

Asymptotic analysis of stock price densities and implied volatilities in mixed stochastic models

In this paper, we obtain sharp asymptotic formulas with error estimates for the Mellin con- volution of functions de ned on (0;1), and use these formulas to characterize the asymptotic behavior of marginal distribution densities of stock price processes in mixed stochastic models. Special examples of mixed models are jump-di usion models and stochastic volatility models with jumps. We apply our general results to the Heston model with double exponential jumps, and make a detailed analysis of the asymptotic behavior of the stock price density, the call option pricing function, and the implied volatility in this model. We also obtain similar results for the Heston model with jumps distributed according to the NIG law.

Comparison of a deterministic and a data driven model to describe MBR fouling

Membrane bioreactors (MBRs) are a combination of activated sludge bioreactors and membrane filtration, enabling high quality effluent with a small footprint. However, they can be beset by fouling, which causes an increase in transmembrane pressure (TMP). Modelling and simulation of changes in TMP could be useful to describe fouling through the identification of the most relevant operating conditions. Using experimental data from a MBR pilot plant operated for 462days, two different models were developed: a deterministic model using activated sludge model n°2d (ASM2d) for the biological component and a resistance in-series model for the filtration component as well as a data-driven model based on multivariable regressions. Once validated, these models were used to describe membrane fouling (as changes in TMP over time) under different operating conditions. The deterministic model performed better at higher temperatures (>20°C), constant operating conditions (DO set-point, membrane air-flow, pH and ORP), and high mixed liquor suspended solids (>6.9gL-1) and flux changes. At low pH (<7) or periods with higher pH changes, the data-driven model was more accurate. Changes in the DO set-point of the aerobic reactor that affected the TMP were also better described by the data-driven model. By combining the use of both models, a better description of fouling can be achieved under different operating conditions

Model-based study of a chemical-looping combustion process

Chemical-looping combustion (CLC) is a novel combustion technology with inherent separation of the greenhouse gas CO2. The technique typically employs a dual fluidized bed system where a metal oxide is used as a solid oxygen carrier that transfers the oxygen from combustion air to the fuel. The oxygen carrier is looping between the air reactor, where it is oxidized by the air, and the fuel reactor, where it is reduced by the fuel. Hence, air is not mixed with the fuel, and outgoing CO2 does not become diluted by the nitrogen, which gives a possibility to collect the CO2 from the flue gases after the water vapor is condensed. CLC is being proposed as a promising and energy efficient carbon capture technology, since it can achieve both an increase in power station efficiency simultaneously with low energy penalty from the carbon capture. The outcome of a comprehensive literature study concerning the current status of CLC development is presented in this thesis. Also, a steady state model of the CLC process, based on the conservation equations of mass and energy, was developed. The model was used to determine the process conditions and to calculate the reactor dimensions of a 100 MWth CLC system with bunsenite (NiO) as oxygen carrier and methane (CH4) as fuel. This study has been made in Oxygen Carriers and Their Industrial Applications research project (2008 – 2011), funded by the Tekes – Functional Material program. I would like to acknowledge Tekes and participating companies for funding and all project partners for good and comfortable cooperation.