Binding free energy differences in a TCR-peptide-MHC complex induced by a peptide mutation: a simulation analysis.

Recognition by the T-cell receptor (TCR) of immunogenic peptides presented by class I major histocompatibility complexes (MHCs) is the determining event in the specific cellular immune response against virus-infected cells or tumor cells. It is of great interest, therefore, to elucidate the molecular principles upon which the selectivity of a TCR is based. These principles can in turn be used to design therapeutic approaches, such as peptide-based immunotherapies of cancer. In this study, free energy simulation methods are used to analyze the binding free energy difference of a particular TCR (A6) for a wild-type peptide (Tax) and a mutant peptide (Tax P6A), both presented in HLA A2. The computed free energy difference is 2.9 kcal/mol, in good agreement with the experimental value. This makes possible the use of the simulation results for obtaining an understanding of the origin of the free energy difference which was not available from the experimental results. A free energy component analysis makes possible the decomposition of the free energy difference between the binding of the wild-type and mutant peptide into its components. Of particular interest is the fact that better solvation of the mutant peptide when bound to the MHC molecule is an important contribution to the greater affinity of the TCR for the latter. The results make possible identification of the residues of the TCR which are important for the selectivity. This provides an understanding of the molecular principles that govern the recognition. The possibility of using free energy simulations in designing peptide derivatives for cancer immunotherapy is briefly discussed.

Ultrastructural analysis of neuronal plasticity in the adult mouse

ABSTRACT Adult neuronal plasticity is a term that corresponds to a set of biological mechanisms allowing a neuronal circuit to respond and adapt to modifications of the received inputs. Mystacial whiskers of the mouse are the starting point of a major sensory pathway that provides the animal with information from its immediate environment. Through whisking, information is gathered that allows the animal to orientate itself and to recognize objects. This sensory system is crucial for nocturnal behaviour during which vision is not of much use. Sensory information of the whiskers are sent via brainstem and thalamus to the primary somatosensory area (S1) of the cerebral cortex in a strictly topological manner. Cell bodies in the layer N of S 1 are arranged in ring forming structures called barrels. As such, each barrel corresponds to the cortical representation in layer IV of a single whisker follicle. This histological feature allows to identify with uttermost precision the part of the cortex devoted to a given whisker and to study modifications induced by different experimental conditions. The condition used in the studies of my thesis is the passive stimulation of one whisker in the adult mouse for a period of 24 hours. It is performed by glueing a piece of metal on one whisker and placing the awake animal in a cage surrounded by an electromagnetic coil that generates magnetic field burst inducing whisker movement at a given frequency during 24 hours. I analysed the ultrastructure of the barrel corresponding the stimulated whisker using serial sections electron microscopy and computer-based three-dimensional reconstructions; analysis of neighbouring, unstimulated barrels as well as those from unstimulated mice served as control. The following elements were structurally analyzed: the spiny dendrites, the axons of excitatory as well as inhibitory cells, their connections via synapses and the astrocytic processes. The density of synapses and spines is upregulated in a barrel corresponding to a stimulated whisker. This upregulation is absent in the BDNF heterozygote mice, indicating that a certain level of activity-dependent released BDNF is required for synaptogenesis in the adult cerebral cortex. Synpaptogenesis is correlated with a modification of the astrocytes that place themselves in closer vicinity of the excitatory synapses on spines. Biochemical analysis revealed that the astrocytes upregulate the expression of transporters by which they internalise glutamate, the neurotransmitter responsible for the excitatory response of cortical neurons. In the final part of my thesis, I show that synaptogenesis in the stimulated barrel is due to the increase in the size of excitatory axonal boutons that become more frequently multisynaptic, whereas the inhibitory axons do not change their morphology but form more synapses with spines apposed to them. Taken together, my thesis demonstrates that all the cellular elements present in the neuronal tissue of the adult brain contribute to activity-dependent cortical plasticity and form part of a mechanism by which the animal responds to a modified sensory experience. Throughout life, the neuronal circuit keeps the faculty to adapt its function. These adaptations are partially transitory but some aspects remain and could be the structural basis of a memory trace in the cortical circuit. RESUME La plasticité neuronale chez l'adulte désigne un ensemble de mécanismes biologiques qui permettent aux circuits neuronaux de répondre et de s'adapter aux modifications des stimulations reçues. Les vibrisses des souris sont un système crucial fournissant des informations sensorielles au sujet de l'environnement de l'animal. L'information sensorielle collectée par les vibrisses est envoyée via le tronc cérébral et le thalamus à l'aire sensorielle primaire (S 1) du cortex cérébral en respectant strictement la somatotopie. Les corps cellulaires dans la couche IV de S 1 sont organisés en anneaux délimitant des structures nommées tonneaux. Chaque tonneau reçoit l'information d'une seule vibrisse et l'arrangement des tonneaux dans le cortex correspond à l'arrangement des vibrisses sur le museau de la souris. Cette particularité histologique permet de sélectionner avec certitude la partie du cortex dévolue à une vibrisse et de l'étudier dans diverses conditions. Le paradigme expérimental utilisé dans cette thèse est la stimulation passive d'une seule vibrisse durant 24 heures. Pour ce faire, un petit morceau de métal est collé sur une vibrisse et la souris est placée dans une cage entourée d'une bobine électromagnétique générant un champ qui fait vibrer le morceau de métal durant 24 heures. Nous analysons l'ultrastructure du cortex cérébral à l'aide de la microscopie électronique et des coupes sériées permettant la reconstruction tridimensionnelle à l'aide de logiciels informatiques. Nous observons les modifications des structures présentes : les dendrites épineuses, les axones des cellules excitatrices et inhibitrices, leurs connections par des synapses et les astrocytes. Le nombre de synapses et d'épines est augmenté dans un tonneau correspondant à une vibrisse stimulée 24 heures. Basé sur cela, nous montrons dans ces travaux que cette réponse n'est pas observée dans des souris hétérozygotes BDNF+/-. Cette neurotrophine sécrétée en fonction de l'activité neuronale est donc nécessaire pour la synaptogenèse. La synaptogenèse est accompagnée d'une modification des astrocytes qui se rapprochent des synapses excitatrices au niveau des épines dendritiques. Ils expriment également plus de transporteurs chargés d'internaliser le glutamate, le neurotransmetteur responsable de la réponse excitatrice des neurones. Nous montrons aussi que les axones excitateurs deviennent plus larges et forment plus de boutons multi-synaptiques à la suite de la stimulation tandis que les axones inhibiteurs ne changent pas de morphologie mais forment plus de synapses avec des épines apposées à leur membrane. Tous les éléments analysés dans le cerveau adulte ont maintenu la capacité de réagir aux modifications de l'activité neuronale et répondent aux modifications de l'activité permettant une constante adaptation à de nouveaux environnements durant la vie. Les circuits neuronaux gardent la capacité de créer de nouvelles synapses. Ces adaptations peuvent être des réponses transitoires aux stimuli mais peuvent aussi laisser une trace mnésique dans les circuits.

An analysis of patients' understanding of 'routine' preoperative blood tests and HIV screening. Is no news really good news?

OBJECTIVES: Many patients may believe that HIV screening is included in routine preoperative work-ups. We examined what proportion of patients undergoing preoperative blood testing believed that they had been tested for HIV. METHODS: All patients hospitalized for elective orthopaedic surgery between January and December 2007 were contacted and asked to participate in a 15-min computer-assisted telephone interview (n = 1330). The primary outcome was to determine which preoperative tests patients believed had been performed from a choice of glucose, clotting, HIV serology and cholesterol, and what percentage of patients interpreted the lack of result communication as a normal or negative test. The proportion of patients agreeable to HIV screening prior to future surgery was also determined. RESULTS: A total of 991 patients (75%) completed the questionnaire. Three hundred and seventy-five of these 991 patients (38%) believed incorrectly that they had been tested for HIV preoperatively. Younger patients were significantly more likely to believe that an HIV test had been performed (mean age 46 vs. 50 years for those who did not believe that an HIV test had been performed; P < 0.0001). Of the patients who believed that a test had been performed but received no result, 96% interpreted lack of a result as a negative HIV test. Over 80% of patients surveyed stated that they would agree to routine HIV screening prior to future surgery. A higher acceptance rate was associated with younger age (mean age 47 years for those who would agree vs. 56 years for those who would not; P < 0.0001) and male sex ( P < 0.009). CONCLUSIONS: Many patients believe that a preoperative blood test routinely screens for HIV. The incorrect assumption that a lack of result communication indicates a negative test may contribute to delays in HIV diagnoses.

Optimisation of data analysis method for a fluidized bed combustion test rig

Nowadays the used fuel variety in power boilers is widening and new boiler constructions and running models have to be developed. This research and development is done in small pilot plants where more faster analyse about the boiler mass and heat balance is needed to be able to find and do the right decisions already during the test run. The barrier on determining boiler balance during test runs is the long process of chemical analyses of collected input and outputmatter samples. The present work is concentrating on finding a way to determinethe boiler balance without chemical analyses and optimise the test rig to get the best possible accuracy for heat and mass balance of the boiler. The purpose of this work was to create an automatic boiler balance calculation method for 4 MW CFB/BFB pilot boiler of Kvaerner Pulping Oy located in Messukylä in Tampere. The calculation was created in the data management computer of pilot plants automation system. The calculation is made in Microsoft Excel environment, which gives a good base and functions for handling large databases and calculations without any delicate programming. The automation system in pilot plant was reconstructed und updated by Metso Automation Oy during year 2001 and the new system MetsoDNA has good data management properties, which is necessary for big calculations as boiler balance calculation. Two possible methods for calculating boiler balance during test run were found. Either the fuel flow is determined, which is usedto calculate the boiler's mass balance, or the unburned carbon loss is estimated and the mass balance of the boiler is calculated on the basis of boiler's heat balance. Both of the methods have their own weaknesses, so they were constructed parallel in the calculation and the decision of the used method was left to user. User also needs to define the used fuels and some solid mass flowsthat aren't measured automatically by the automation system. With sensitivity analysis was found that the most essential values for accurate boiler balance determination are flue gas oxygen content, the boiler's measured heat output and lower heating value of the fuel. The theoretical part of this work concentrates in the error management of these measurements and analyses and on measurement accuracy and boiler balance calculation in theory. The empirical part of this work concentrates on the creation of the balance calculation for the boiler in issue and on describing the work environment.

RiskDiff: A web tool for the analysis of the difference due to risk and demographic factors for incidence or mortality data.

Background Analysing the observed differences for incidence or mortality of a particular disease between two different situations (such as time points, geographical areas, gender or other social characteristics) can be useful both for scientific or administrative purposes. From an epidemiological and public health point of view, it is of great interest to assess the effect of demographic factors in these observed differences in order to elucidate the effect of the risk of developing a disease or dying from it. The method proposed by Bashir and Estève, which splits the observed variation into three components: risk, population structure and population size is a common choice at practice. Results A web-based application, called RiskDiff has been implemented (available at http://rht.iconcologia.net/riskdiff.htm webcite), to perform this kind of statistical analyses, providing text and graphical summaries. Code from the implemented functions in R is also provided. An application to cancer mortality data from Catalonia is used for illustration. Conclusions Combining epidemiological with demographical factors is crucial for analysing incidence or mortality from a disease, especially if the population pyramids show substantial differences. The tool implemented may serve to promote and divulgate the use of this method to give advice for epidemiologic interpretation and decision making in public health.

Relation between sequence and structure of HIV-1 protease inhibitor complexes: a model system for the analysis of protein flexibility.

The flexibility of different regions of HIV-1 protease was examined by using a database consisting of 73 X-ray structures that differ in terms of sequence, ligands or both. The root-mean-square differences of the backbone for the set of structures were shown to have the same variation with residue number as those obtained from molecular dynamics simulations, normal mode analyses and X-ray B-factors. This supports the idea that observed structural changes provide a measure of the inherent flexibility of the protein, although specific interactions between the protease and the ligand play a secondary role. The results suggest that the potential energy surface of the HIV-1 protease is characterized by many local minima with small energetic differences, some of which are sampled by the different X-ray structures of the HIV-1 protease complexes. Interdomain correlated motions were calculated from the structural fluctuations and the results were also in agreement with molecular dynamics simulations and normal mode analyses. Implications of the results for the drug-resistance engendered by mutations are discussed briefly.

The maximum voltage drop in an on-chip power distribution network: analysis of square, triangular and hexagonal power pad arrangements

A mathematical model of the voltage drop which arises in on-chip power distribution networks is used to compare the maximum voltage drop in the case of different geometric arrangements of the pads supplying power to the chip. These include the square or Manhattan power pad arrangement, which currently predominates, as well as equilateral triangular and hexagonal arrangements. In agreement with the findings in the literature and with physical and SPICE models, the equilateral triangular power pad arrangement is found to minimize the maximum voltage drop. This headline finding is a consequence of relatively simple formulas for the voltage drop, with explicit error bounds, which are established using complex analysis techniques, and elliptic functions in particular.

"Soap-Bubble" visualization and quantitative analysis of 3D coronary magnetic resonance angiograms.

In order to compare coronary magnetic resonance angiography (MRA) data obtained with different scanning methodologies, adequate visualization and presentation of the coronary MRA data need to be ensured. Furthermore, an objective quantitative comparison between images acquired with different scanning methods is desirable. To address this need, a software tool ("Soap-Bubble") that facilitates visualization and quantitative comparison of 3D volume targeted coronary MRA data was developed. In the present implementation, the user interactively specifies a curved subvolume (enclosed in the 3D coronary MRA data set) that closely encompasses the coronary arterial segments. With a 3D Delaunay triangulation and a parallel projection, this enables the simultaneous display of multiple coronary segments in one 2D representation. For objective quantitative analysis, frequently explored quantitative parameters such as signal-to-noise ratio (SNR); contrast-to-noise ratio (CNR); and vessel length, sharpness, and diameter can be assessed. The present tool supports visualization and objective, quantitative comparisons of coronary MRA data obtained with different scanning methods. The first results obtained in healthy adults and in patients with coronary artery disease are presented.

Theoretical Analysis and Simulations of Vertically Vibrated Granular Materials

The dynamical properties ofshaken granular materials are important in many industrial applications where the shaking is used to mix, segregate and transport them. In this work asystematic, large scale simulation study has been performed to investigate the rheology of dense granular media, in the presence of gas, in a three dimensional vertical cylinder filled with glass balls. The base wall of the cylinder is subjected to sinusoidal oscillation in the vertical direction. The viscoelastic behavior of glass balls during a collision, have been studied experimentally using a modified Newton's Cradle device. By analyzing the results of the measurements, using numerical model based on finite element method, the viscous damping coefficient was determinedfor the glass balls. To obtain detailed information about the interparticle interactions in a shaker, a simplified model for collision between particles of a granular material was proposed. In order to simulate the flow of surrounding gas, a formulation of the equations for fluid flow in a porous medium including particle forces was proposed. These equations are solved with Large Eddy Simulation (LES) technique using a subgrid-model originally proposed for compressible turbulent flows. For a pentagonal prism-shaped container under vertical vibrations, the results show that oscillon type structures were formed. Oscillons are highly localized particle-like excitations of the granular layer. This self-sustaining state was named by analogy with its closest large-scale analogy, the soliton, which was first documented by J.S. Russell in 1834. The results which has been reportedbyBordbar and Zamankhan(2005b)also show that slightly revised fluctuation-dissipation theorem might apply to shaken sand, which appears to be asystem far from equilibrium and could exhibit strong spatial and temporal variations in quantities such as density and local particle velocity. In this light, hydrodynamic type continuum equations were presented for describing the deformation and flow of dense gas-particle mixtures. The constitutive equation used for the stress tensor provides an effective viscosity with a liquid-like character at low shear rates and a gaseous-like behavior at high shear rates. The numerical solutions were obtained for the aforementioned hydrodynamic equations for predicting the flow dynamics ofdense mixture of gas and particles in vertical cylindrical containers. For a heptagonal prism shaped container under vertical vibrations, the model results were found to predict bubbling behavior analogous to those observed experimentally. This bubbling behavior may be explained by the unusual gas pressure distribution found in the bed. In addition, oscillon type structures were found to be formed using a vertically vibrated, pentagonal prism shaped container in agreement with computer simulation results. These observations suggest that the pressure distribution plays a key rolein deformation and flow of dense mixtures of gas and particles under vertical vibrations. The present models provide greater insight toward the explanation of poorly understood hydrodynamic phenomena in the field of granular flows and dense gas-particle mixtures. The models can be generalized to investigate the granular material-container wall interactions which would be an issue of high interests in the industrial applications. By following this approach ideal processing conditions and powder transport can be created in industrial systems.

An Analysis of Eye Scanpath Entropy in a Progressively Forming Virtual Environment

A sign of presence in virtual environments is that people respond to situations and events as if they were real, where response may be considered at many different levels, ranging from unconscious physiological responses through to overt behavior,emotions, and thoughts. In this paper we consider two responses that gave different indications of the onset of presence in a gradually forming environment. Two aspects of the response of people to an immersive virtual environment were recorded: their eye scanpath, and their skin conductance response (SCR). The scenario was formed over a period of 2 min, by introducing an increasing number of its polygons in random order in a head-tracked head-mounted display. For one group of experimental participants (n 8) the environment formed into one in which they found themselves standing on top of a 3 m high column. For a second group of participants (n 6) the environment was otherwise the same except that the column was only 1 cm high, so that they would be standing at normal ground level. For a third group of participants (n 14) the polygons never formed into a meaningful environment. The participants who stood on top of the tall column exhibited a significant decrease in entropy of the eye scanpath and an increase in the number of SCR by 99 s into the scenario, at a time when only 65% of the polygons had been displayed. The ground level participants exhibited a similar decrease in scanpath entropy, but not the increase in SCR. The random scenario grouping did not exhibit this decrease in eye scanpath entropy. A drop in scanpath entropy indicates that the environment had cohered into a meaningful perception. An increase in the rate of SCR indicates the perception of an aversive stimulus. These results suggest that on these two dimensions (scanpath entropy and rate of SCR) participants were responding realistically to the scenario shown in the virtual environment. In addition, the response occurred well before the entire scenario had been displayed, suggesting that once a set of minimal cues exists within a scenario,it is enough to form a meaningful perception. Moreover, at the level of the sympathetic nervous system, the participants who were standing on top of the column exhibited arousal as if their experience might be real. This is an important practical aspect of the concept of presence.

REGSTATTOOLS: freeware statistical tools for the analysis of disease population databases used in health and social studies

Background: The repertoire of statistical methods dealing with the descriptive analysis of the burden of a disease has been expanded and implemented in statistical software packages during the last years. The purpose of this paper is to present a web-based tool, REGSTATTOOLS http://regstattools.net intended to provide analysis for the burden of cancer, or other group of disease registry data. Three software applications are included in REGSTATTOOLS: SART (analysis of disease"s rates and its time trends), RiskDiff (analysis of percent changes in the rates due to demographic factors and risk of developing or dying from a disease) and WAERS (relative survival analysis). Results: We show a real-data application through the assessment of the burden of tobacco-related cancer incidence in two Spanish regions in the period 1995-2004. Making use of SART we show that lung cancer is the most common cancer among those cancers, with rising trends in incidence among women. We compared 2000-2004 data with that of 1995-1999 to assess percent changes in the number of cases as well as relative survival using RiskDiff and WAERS, respectively. We show that the net change increase in lung cancer cases among women was mainly attributable to an increased risk of developing lung cancer, whereas in men it is attributable to the increase in population size. Among men, lung cancer relative survival was higher in 2000-2004 than in 1995-1999, whereas it was similar among women when these time periods were compared. Conclusions: Unlike other similar applications, REGSTATTOOLS does not require local software installation and it is simple to use, fast and easy to interpret. It is a set of web-based statistical tools intended for automated calculation of population indicators that any professional in health or social sciences may require.

Family Size Evolution in Drosophila Chemosensory Gene Families: A Comparative Analysis with a Critical Appraisal of Methods

Gene turnover rates and the evolution of gene family sizes are important aspects of genome evolution. Here, we use curated sequence data of the major chemosensory gene families from Drosophila-the gustatory receptor, odorant receptor, ionotropic receptor, and odorant-binding protein families-to conduct a comparative analysis among families, exploring different methods to estimate gene birth and death rates, including an ad hoc simulation study. Remarkably, we found that the state-of-the-art methods may produce very different rate estimates, which may lead to disparate conclusions regarding the evolution of chemosensory gene family sizes in Drosophila. Among biological factors, we found that a peculiarity of D. sechellia's gene turnover rates was a major source of bias in global estimates, whereas gene conversion had negligible effects for the families analyzed herein. Turnover rates vary considerably among families, subfamilies, and ortholog groups although all analyzed families were quite dynamic in terms of gene turnover. Computer simulations showed that the methods that use ortholog group information appear to be the most accurate for the Drosophila chemosensory families. Most importantly, these results reveal the potential of rate heterogeneity among lineages to severely bias some turnover rate estimation methods and the need of further evaluating the performance of these methods in a more diverse sampling of gene families and phylogenetic contexts. Using branch-specific codon substitution models, we find further evidence of positive selection in recently duplicated genes, which attests to a nonneutral aspect of the gene birth-and-death process.

Performance Analysis of Two Quantum Reaction Dynamics Codes: Time-Dependent and Time-Independent Strategies

The computer simulation of reaction dynamics has nowadays reached a remarkable degree of accuracy. Triatomic elementary reactions are rigorously studied with great detail on a straightforward basis using a considerable variety of Quantum Dynamics computational tools available to the scientific community. In our contribution we compare the performance of two quantum scattering codes in the computation of reaction cross sections of a triatomic benchmark reaction such as the gas phase reaction Ne + H2+ %12. NeH++ H. The computational codes are selected as representative of time-dependent (Real Wave Packet [ ]) and time-independent (ABC [ ]) methodologies. The main conclusion to be drawn from our study is that both strategies are, to a great extent, not competing but rather complementary. While time-dependent calculations advantages with respect to the energy range that can be covered in a single simulation, time-independent approaches offer much more detailed information from each single energy calculation. Further details such as the calculation of reactivity at very low collision energies or the computational effort related to account for the Coriolis couplings are analyzed in this paper.