Emergence of young human genes after a burst of retroposition in primates.

The origin of new genes through gene duplication is fundamental to the evolution of lineage- or species-specific phenotypic traits. In this report, we estimate the number of functional retrogenes on the lineage leading to humans generated by the high rate of retroposition (retroduplication) in primates. Extensive comparative sequencing and expression studies coupled with evolutionary analyses and simulations suggest that a significant proportion of recent retrocopies represent bona fide human genes. We estimate that at least one new retrogene per million years emerged on the human lineage during the past approximately 63 million years of primate evolution. Detailed analysis of a subset of the data shows that the majority of retrogenes are specifically expressed in testis, whereas their parental genes show broad expression patterns. Consistently, most retrogenes evolved functional roles in spermatogenesis. Proteins encoded by X chromosome-derived retrogenes were strongly preserved by purifying selection following the duplication event, supporting the view that they may act as functional autosomal substitutes during X-inactivation of late spermatogenesis genes. Also, some retrogenes acquired a new or more adapted function driven by positive selection. We conclude that retroduplication significantly contributed to the formation of recent human genes and that most new retrogenes were progressively recruited during primate evolution by natural and/or sexual selection to enhance male germline function.

Inferring ultraviolet anatomical exposure patterns while distinguishing the relative contribution of radiation components

Exposure to solar ultraviolet (UV) radiation is the main causative factor for skin cancer. UV exposure depends on environmental and individual factors, but individual exposure data remain scarce. While ground UV irradiance is monitored via different techniques, it is difficult to translate such observations into human UV exposure or dose because of confounding factors. A multi-disciplinary collaboration developed a model predicting the dose and distribution of UV exposure on the basis of ground irradiation and morphological data. Standard 3D computer graphics techniques were adapted to develop a simulation tool that estimates solar exposure of a virtual manikin depicted as a triangle mesh surface. The amount of solar energy received by various body locations is computed for direct, diffuse and reflected radiation separately. Dosimetric measurements obtained in field conditions were used to assess the model performance. The model predicted exposure to solar UV adequately with a symmetric mean absolute percentage error of 13% and half of the predictions within 17% range of the measurements. Using this tool, solar UV exposure patterns were investigated with respect to the relative contribution of the direct, diffuse and reflected radiation. Exposure doses for various body parts and exposure scenarios of a standing individual were assessed using erythemally-weighted UV ground irradiance data measured in 2009 at Payerne, Switzerland as input. For most anatomical sites, mean daily doses were high (typically 6.2-14.6 Standard Erythemal Dose, SED) and exceeded recommended exposure values. Direct exposure was important during specific periods (e. g. midday during summer), but contributed moderately to the annual dose, ranging from 15 to 24% for vertical and horizontal body parts, respectively. Diffuse irradiation explained about 80% of the cumulative annual exposure dose.

A distributed environment for virtual and/or real experiments for underwater robots

This paper presents the distributed environment for virtual and/or real experiments for underwater robots (DEVRE). This environment is composed of a set of processes running on a local area network composed of three sites: 1) the onboard AUV computer; 2) a surface computer used as human-machine interface (HMI); and 3) a computer used for simulating the vehicle dynamics and representing the virtual world. The HMI can be transparently linked to the real sensors and actuators dealing with a real mission. It can also be linked with virtual sensors and virtual actuators, dealing with a virtual mission. The aim of DEVRE is to assist engineers during the software development and testing in the lab prior to real experiments

Modeling of hybrid systems by piecewise decomposition

Piecewise linear models systems arise as mathematical models of systems in many practical applications, often from linearization for nonlinear systems. There are two main approaches of dealing with these systems according to their continuous or discrete-time aspects. We propose an approach which is based on the state transformation, more particularly the partition of the phase portrait in different regions where each subregion is modeled as a two-dimensional linear time invariant system. Then the Takagi-Sugeno model, which is a combination of local model is calculated. The simulation results show that the Alpha partition is well-suited for dealing with such a system

Modelatge i simulació de quatre centres de processament de dades connectats per WAN

Aquest projecte conté l'estudi de la comunicació entre quatre Centres de Processament de Dades (CPD) per via WAN. L'estudi consisteix en simular aquestes comunicacions en un entorn de proves físic i també en entorn de proves virtual on s'han extret resultats dels protocols de seguretat, d'enrutament, a més dels temps de resposta i limitacions dels equips físics i virtuals.

Simulació de processos de combustió de sòlids prims

L'objecte del projecte consisteix en investigar les capacitats del programari dedinàmica de fluids computacional FLUENT per simular processos transitoris de combustióquan es cremen sòlids. Com el programari FLUENT no incorpora cap mòdul de combustióde sòlids prims, s'hauran de realitzar les funcions d'usuari adients per tal d'incorporar lesequacions i les condicions de contorns que són rellevants en aquests tipus de problemes. Elmodel resultant es validarà amb dades experimentals per a la combustió de fulls decel•lulosa en flames bidimensionals. També es durà a terme una anàlisi de sensibilitat de lasolució variant els paràmetres del model. En funció dels resultats de la validació es durà aterme una extensió del model per a situacions tridimensionals

A Tool for optimum design of Waste Water Treatment Plants under uncertainty

L’objectiu principal és presentar un nou prototipus d’eina per al disseny de les plantes de tractament d’aigües residuals utilitzant models mecànics dinàmics quantificant la incertesa

Modelització i simulació del motor d'inducció en règim transitori amb PSIM

El present treball pretén modelitzar i simular el motor d’inducció trifàsic en règim transitori amb PSIM 6.0 Demo(la versió del programa que s’utilitza actualment a l’Escola Politècnica Superior de la UdG), però també s’estudia el model en règim permanent, per tal de comparar a nivell teòric els resultats dels dos règims. Primer cal entendre i implementar el model del motor d’inducció, i així obtenir l'esquema equivalent en règim transitori, per després poder-lo simular. Abans de dur a terme la simulació, cal obtenir els paràmetres del circuit equivalent del motor real per introduir-los al programa informàtic, amb la finalitat de tenir precisió en les respostes. Aquests valors s’obtindran mitjançant assajos necessaris al laboratori. Posteriorment, es fan simulacions i pràctiques reals amb el motor treballen en diferents condicions per veure el seu comportament, i així poder comparar els resultats de la simulació amb els valors reals. També s’implementa un estudi de la influencia dels paràmetres interns en el funcionament del motor. Així es podrà visualitzar i comparar les respostes de diferents variables en cadascunes de les simulacions que es duguin a terme. Finalment, seria interessant la introducció de la màquina d’inducció trifàsica actuant com a generador en la simulació.Aquest és un estudi en el qual se simula la màquina d'inducció trifàsic en règim transitori i en règim permanent mitjançant l'ús del PSIM, que és el programa informàtic de simulació

Modelling short-term ultraviolet exposure as an alternative to individual dosimetry

Background: Excessive exposure to solar Ultra-Violet (UV) light is the main cause of most skin cancers in humans. Factors such as the increase of solar irradiation at ground level (anthropic pollution), the rise in standard of living (vacation in sunny areas), and (mostly) the development of outdoor activities have contributed to increase exposure. Thus, unsurprisingly, incidence of skin cancers has increased over the last decades more than that of any other cancer. Melanoma is the most lethal cutaneous cancer, while cutaneous carcinomas are the most common cancer type worldwide. UV exposure depends on environmental as well as individual factors related to activity. The influence of individual factors on exposure among building workers was investigated in a previous study. Posture and orientation were found to account for at least 38% of the total variance of relative individual exposure. A high variance of short-term exposure was observed between different body locations, indicating the occurrence of intense, subacute exposures. It was also found that effective short-term exposure ranged between 0 and 200% of ambient irradiation, suggesting that ambient irradiation is a poor predictor of effective exposure. Various dosimetric techniques enable to assess individual effective exposure, but dosimetric measurements remain tedious and tend to be situation-specific. As a matter of facts, individual factors (exposure time, body posture and orientation in the sun) often limit the extrapolation of exposure results to similar activities conducted in other conditions. Objective: The research presented in this paper aims at developing and validating a predictive tool of effective individual exposure to solar UV. Methods: Existing computer graphic techniques (3D rendering) were adapted to reflect solar exposure conditions and calculate short-term anatomical doses. A numerical model, represented as a 3D triangular mesh, is used to represent the exposed body. The amount of solar energy received by each "triangle is calculated, taking into account irradiation intensity, incidence angle and possible shadowing from other body parts. The model take into account the three components of the solar irradiation (direct, diffuse and albedo) as well as the orientation and posture of the body. Field measurements were carried out using a forensic mannequin at the Payerne MeteoSwiss station. Short-term dosimetric measurements were performed in 7 anatomical locations for 5 body postures. Field results were compared to the model prediction obtained from the numerical model. Results: The best match between prediction and measurements was obtained for upper body parts such as shoulders (Ratio Modelled/Measured; Mean = 1.21, SD = 0.34) and neck (Mean = 0.81, SD = 0.32). Small curved body parts such as forehead (Mean = 6.48, SD = 9.61) exhibited a lower matching. The prediction is less accurate for complex postures such as kneeling (Mean = 4.13, SD = 8.38) compared to standing up (Mean = 0.85, SD = 0.48). The values obtained from the dosimeters and the ones computed from the model are globally consistent. Conclusion: Although further development and validation are required, these results suggest that effective exposure could be predicted for a given activity (work or leisure) in various ambient irradiation conditions. Using a generic modelling approach is of high interest in terms of implementation costs as well as predictive and retrospective capabilities.

Dimensionat de la instal·lació de climatització d'un edifici de vivendes mitjançant el programa de simulació HvacCad : estudi comparatiu amb els mètodes tradicionals de càlcul

L’objecte d’aquest treball és fer una posta a punt d’un programa de simulació. En el nostre cas el programa s’anomena HvacCad. A partir d’aquest programa trobarem les càrregues tèrmiques d’un edifici de vivendes exemple tant per a l’ hivern com a l’estiu. Paral•lelament a aquests càlculs farem els mateixos però amb un full de càlcul convencional, anomenat Aguilar, així podrem comparar els resultats obtinguts. No realitzarem el càlcul de la instal•lació de climatització, només trobarem la potència màxima dels aparells

Ab initio absorption spectrum of NiO combining molecular dynamics with the embedded cluster approach in a discrete reaction field

We developed a procedure that combines three complementary computational methodologies to improve the theoretical description of the electronic structure of nickel oxide. The starting point is a Car-Parrinello molecular dynamics simulation to incorporate vibrorotational degrees of freedom into the material model. By means ofcomplete active space self-consistent field second-order perturbation theory (CASPT2) calculations on embedded clusters extracted from the resulting trajectory, we describe localized spectroscopic phenomena on NiO with an efficient treatment of electron correlation. The inclusion of thermal motion into the theoretical description allowsus to study electronic transitions that, otherwise, would be dipole forbidden in the ideal structure and results in a natural reproduction of the band broadening. Moreover, we improved the embedded cluster model by incorporating self-consistently at the complete active space self-consistent field (CASSCF) level a discrete (or direct) reaction field (DRF) in the cluster surroundings. The DRF approach offers an efficient treatment ofelectric response effects of the crystalline embedding to the electronic transitions localized in the cluster. We offer accurate theoretical estimates of the absorption spectrum and the density of states around the Fermi level of NiO, and a comprehensive explanation of the source of the broadening and the relaxation of the charge transferstates due to the adaptation of the environment

Sex-biased dispersal in a migratory bat: a characterization using sex-specific demographic parameters.

We studied the noctule bat (Nyctalus noctula), in which the mitochondrial F(ST) is about 10 times that revealed by nuclear markers, to address two questions. We first verified whether random dispersal of one sex is compatible with highly contrasted mitochondrial and nuclear population structures. Using computer simulations, we then assessed the power of multilocus population differentiation tests when the expected population structure departs only slightly from panmixia. Using an island model with sex-specific demographic parameters, we found that random male dispersal is consistent with the population structure observed in the noctule. However, other parameter combinations are also compatible with the data. We computed the minimum sex bias in dispersal (at least 69% of the dispersing individuals are males), a result that would not be available if we had used more classical population genetic models. The power of multilocus population differentiation tests was unexpectedly high, the tests being significant in almost 100% of the replicates, although the observed population structure infered from nuclear markers was extremely low (F(ST) = 0.6%).

A hierarchical approach to model parameter optimization for developmental systems.

In the context of Systems Biology, computer simulations of gene regulatory networks provide a powerful tool to validate hypotheses and to explore possible system behaviors. Nevertheless, modeling a system poses some challenges of its own: especially the step of model calibration is often difficult due to insufficient data. For example when considering developmental systems, mostly qualitative data describing the developmental trajectory is available while common calibration techniques rely on high-resolution quantitative data. Focusing on the calibration of differential equation models for developmental systems, this study investigates different approaches to utilize the available data to overcome these difficulties. More specifically, the fact that developmental processes are hierarchically organized is exploited to increase convergence rates of the calibration process as well as to save computation time. Using a gene regulatory network model for stem cell homeostasis in Arabidopsis thaliana the performance of the different investigated approaches is evaluated, documenting considerable gains provided by the proposed hierarchical approach.

Control de glicèmia en pacients crítics mitjançant CGMS

L’estudi que es realitza en aquest projecte/treball final de carrera queda englobat dins del grup de recerca MICE (Modal Intervals Control and Engeneering), el qual realitzainvestigacions entorn al control de glucèmia. Aquest grup de recerca vinculat a la Universitat de Girona col•labora amb l’Hospital Universitari Dr. Josep Trueta de Girona. La temàtica principal tractarà de realitzar el control de glucèmia en pacients crítics, que es troben ingressats en la unitat de cures intensives de qualsevol hospital. Com a conseqüència d’aquesta problemàtica, s’ha implementat en un entorn virtual, un pacient el qual simula la situació d’un pacient real en la unitat de cures intensives. El model emprat per a la obtenció del model de pacient virtual és el desenvolupat per Chase et al. (2005), el qual mitjançant variables com l’alimentació enteral i la sensibilitat insulínica, es podien realitzar assajos reals per a validar protocols de control ‘in silico’ per posteriorment realitzar assajos amb població real

A variational approach for calculating Franck-Condon factors including mode-mode anharmonic coupling

We have implemented our new procedure for computing Franck-Condon factors utilizing vibrational configuration interaction based on a vibrational self-consistent field reference. Both Duschinsky rotations and anharmonic three-mode coupling are taken into account. Simulations of the first ionization band of Cl O2 and C4 H4 O (furan) using up to quadruple excitations in treating anharmonicity are reported and analyzed. A developer version of the MIDASCPP code was employed to obtain the required anharmonic vibrational integrals and transition frequencies