Prediction of MHC class II-binding peptides using an evolutionary algorithm and artificial neural network

Motivation: Prediction methods for identifying binding peptides could minimize the number of peptides required to be synthesized and assayed, and thereby facilitate the identification of potential T-cell epitopes. We developed a bioinformatic method for the prediction of peptide binding to MHC class II molecules. Results: Experimental binding data and expert knowledge of anchor positions and binding motifs were combined with an evolutionary algorithm (EA) and an artificial neural network (ANN): binding data extraction --> peptide alignment --> ANN training and classification. This method, termed PERUN, was implemented for the prediction of peptides that bind to HLA-DR4(B1*0401). The respective positive predictive values of PERUN predictions of high-, moderate-, low- and zero-affinity binder-a were assessed as 0.8, 0.7, 0.5 and 0.8 by cross-validation, and 1.0, 0.8, 0.3 and 0.7 by experimental binding. This illustrates the synergy between experimentation and computer modeling, and its application to the identification of potential immunotheraaeutic peptides.

Experimental study of phase equilibria in the system PbO-ZnO-SiO2

An experimental study on the ternary system PbO-ZnO-SiO2, in air by high-temperature equilibration and quenching techniques followed by electron probe X-ray microanalysis was carried out as part of the wider research program on the six-component system PbO-ZnO-SiO2-CaO-FeO-Fe2O3, which combines experimental and thermodynamic computer modeling techniques to characterize zinc and lead industrial slags. Liquidus and solidus data were reported for all primary phase fields in the system PbO-ZnO-SiO2 in the temperature range 640 degrees C to 1400 degrees C (913 to 1673 K).

Experimental study of phase equilibria in the systems Fe-Zn-O and Fe-Zn-Si-O at metallic iron saturation

The reported experimental work on the systems Fe-Zn-O and Fe-Zn-Si-O in equilibrium with metallic iron is part of a wider research program that combines experimental and thermodynamic computer modeling techniques to characterize zinc/lead industrial slags and sinters in the system PbO-ZnO-SiO2-CaO-FeO-Fe2O3. Extensive experimental,investigations using high-temperature equilibration and quenching techniques followed by electron probe X-ray microanalysis (EPMA) were carried out. Special experimental; procedures were developed to enable accurate measurements in these ZnO-containing systems to be performed in equilibrium with metallic iron; The systems Fe-Zn-O and FeZn-Si-O were experimentally investigated in equilibrium with metallic iron in the temperature ranges 900 degreesC to 1200 degreesC (1173 to 1473 K) and from 1000 degreesC to 1350 degreesC (1273 to 1623 K), respectively. The liquidus surface in the system Fe-Zn-Si-O in equilibrium with metallic iron was characterized in the composition ranges 0 to 33 wt pet ZnO and 0 to 40 wt pet SiO2. The wustite (Fe,Zn)O, zincite (Zn,Fe)O, willemite (Zn,Fe)(2)SiO4, arid fayalite: (Fe,Zn)(2)SiO4 solid solutions in equilibrium with metallic iron were measured.

Coupling Mechanical and Electrical Behavior in the Multi-scale Simulation of Polymer-based CNT Nanocomposites

A numeric model has been proposed to investigate the mechanical and electrical properties of a polymeric/carbon nanotube (CNT) composite material subjected to a deformation force. The reinforcing phase affects the behavior of the polymeric matrix and depends on the nanofiber aspect ratio and preferential orientation. The simulations show that the mechanical behavior of a computer generated material (CGM) depends on fiber length and initial orientation in the polymeric matrix. It is also shown how the conductivity of the polymer/CNT composite can be calculated for each time step of applied stress, effectively providing the ability to simulate and predict strain-dependent electrical behavior of CNT nanocomposites.

Molecular determinants of ligand specificity in carbohydrate-binding modules: an NMR and X-ray crystallography integrated study

Dissertação para obtenção do Grau de Doutor em Bioquímica – Ramo Bioquímica Estrutural

Differential roles of T cell receptor alpha and beta chains in ligand binding among H-2Kd-restricted cytolytic T lymphocyte clones specific for a photoreactive Plasmodium berghei circumsporozoite peptide derivative.

To study the interaction of T cell receptor with its ligand, a complex of a major histocompatibility complex molecule and a peptide, we derived H-2Kd-restricted cytolytic T lymphocyte clones from mice immunized with a Plasmodium berghei circumsporozoite peptide (PbCS) 252-260 (SYIPSAEKI) derivative containing photoreactive Nepsilon-[4-azidobenzoyl] lysine in place of Pro-255. This residue and Lys-259 were essential parts of the epitope recognized by these clones. Most of the clones expressed BV1S1A1 encoded beta chains along with specific complementary determining region (CDR) 3beta regions but diverse alpha chain sequences. Surprisingly, all T cell receptors were preferentially photoaffinity labeled on the alpha chain. For a representative T cell receptor, the photoaffinity labeled site was located in the Valpha C-strand. Computer modeling suggested the presence of a hydrophobic pocket, which is formed by parts of the Valpha/Jalpha C-, F-, and G-strands and adjacent CDR3alpha residues and structured to be able to avidly bind the photoreactive ligand side chain. We previously found that a T cell receptor specific for a PbCS peptide derivative containing this photoreactive side chain in position 259 similarly used a hydrophobic pocket located between the junctional CDR3 loops. We propose that this nonpolar domain in these locations allow T cell receptors to avidly and specifically bind epitopes containing non-peptidic side chains.

Preclinical evaluation of implantable cardioverter-defibrillator developed for magnetic resonance imaging use.

BACKGROUND: Many patients with an implantable cardioverter-defibrillator (ICD) have indications for magnetic resonance imaging (MRI). However, MRI is generally contraindicated in ICD patients because of potential risks from hazardous interactions between the MRI and ICD system. OBJECTIVE: The purpose of this study was to use preclinical computer modeling, animal studies, and bench and scanner testing to demonstrate the safety of an ICD system developed for 1.5-T whole-body MRI. METHODS: MRI hazards were assessed and mitigated using multiple approaches: design decisions to increase safety and reliability, modeling and simulation to quantify clinical MRI exposure levels, animal studies to quantify the physiologic effects of MRI exposure, and bench testing to evaluate safety margin. RESULTS: Modeling estimated the incidence of a chronic change in pacing capture threshold >0.5V and 1.0V to be less than 1 in 160,000 and less than 1 in 1,000,000 cases, respectively. Modeling also estimated the incidence of unintended cardiac stimulation to occur in less than 1 in 1,000,000 cases. Animal studies demonstrated no delay in ventricular fibrillation detection and no reduction in ventricular fibrillation amplitude at clinical MRI exposure levels, even with multiple exposures. Bench and scanner testing demonstrated performance and safety against all other MRI-induced hazards. CONCLUSION: A preclinical strategy that includes comprehensive computer modeling, animal studies, and bench and scanner testing predicts that an ICD system developed for the magnetic resonance environment is safe and poses very low risks when exposed to 1.5-T normal operating mode whole-body MRI.

Use of Railroad Flat Cars for Low-Volume Road Bridges, August 1999

In an attempt to solve the bridge problem faced by many county engineers, this investigation focused on a low cost bridge alternative that consists of using railroad flatcars (RRFC) as the bridge superstructure. The intent of this study was to determine whether these types of bridges are structurally adequate and potentially feasible for use on low volume roads. A questionnaire was sent to the Bridge Committee members of the American Association of State Highway and Transportation Officials (AASHTO) to determine their use of RRFC bridges and to assess the pros and cons of these bridges based on others’ experiences. It was found that these types of bridges are widely used in many states with large rural populations and they are reported to be a viable bridge alternative due to their low cost, quick and easy installation, and low maintenance. A main focus of this investigation was to study an existing RRFC bridge that is located in Tama County, IA. This bridge was analyzed using computer modeling and field load testing. The dimensions of the major structural members of the flatcars in this bridge were measured and their properties calculated and used in an analytical grillage model. The analytical results were compared with those obtained in the field tests, which involved instrumenting the bridge and loading it with a fully loaded rear tandem-axle truck. Both sets of data (experimental and theoretical) show that the Tama County Bridge (TCB) experienced very low strains and deflections when loaded and the RRFCs appeared to be structurally adequate to serve as a bridge superstructure. A calculated load rating of the TCB agrees with this conclusion. Because many different types of flatcars exist, other flatcars were modeled and analyzed. It was very difficult to obtain the structural plans of RRFCs; thus, only two additional flatcars were analyzed. The results of these analyses also yielded very low strains and displacements. Taking into account the experiences of other states, the inspection of several RRFC bridges in Oklahoma, the field test and computer analysis of the TCB, and the computer analysis of two additional flatcars, RRFC bridges appear to provide a safe and feasible bridge alternative for low volume roads.

08025-015 Remsen Source Water Protection Final Report

The City of Remsen is proactively addressing an increase of nitrates in their public water supply before it becomes a financial catastrophe for them. An intensive assessment was conducted by the Iowa DNR Source Water Protection program as one of four pilot projects in the state. This assessment far surpassed standard desktop assessments and gathered monitoring information in-the-field led by a local watershed group. This was incorporated into a computer modeling program to help the local watershed group discuss alternatives. This comprehensive approach clearly identified the source of nitrate infiltration as a cropland area adjacent to the City well field. Many options were evaluated but only one option provided an economical, viable and secure answer to the water supply needs of Remsen for generations to come. The watershed planning group chose to seek the purchase of this critical area of cropland and convert it to a deep rooted mixture of native grasses. This WIRB funding is intended to be used to acquire a small area totaling 21.1 acres. It represents about 22% of the total local project effort. This will be added to the existing City well field of 40.2 acres and another piece of adjacent property, 35.34 acres, that the City recently acquired as part of an overall aggressive program to protect the community water supply. The City has a signed purchase agreement for 14.4 acres of the 21.1 and a strong verbal commitment to obtain the remaining 5.7 acres. This project has been very active for almost 2 years and is ready to implement immediately upon funding notification. The establishment of native grasses, funded by the local chapter of Pheasants Forever, will take approximately the next three years of operation & maintenance.

Haulikkoratamelun minimoinnin suunnittelu

Työn tavoitteena oli tutkia kilpa- ja harjoitusammuntaan käytettävällä haulikkoradalla käytettäväksi soveltuvia passiivisia meluntorjuntamenetelmiä ja suunnitella niistä toimiva kokonaisuus kohderadoille siten, että rata-alueen läheisillä asuinalueilla alitetaan 50 dB LAIMax-taso sekä muilla alueilla ampumaratamelun ohjearvot. Aluksi tarkasteltiin kohderatojen vanhoja menetelmiä ja radan meluntorjunnan kannalta olennaiset suunnat selvitettiin mittauksilla. Myös laukausmelun spektriä tutkittiin mittauksilla. Olemassa oleville menetelmille etsittiin korvaavia ja täydentäviä menetelmiä. Radan sijoittaminen maastoon on tärkeä osa meluntorjuntaa uutta rataa suunniteltaessa, mutta kohteena olleiden ratojen sijoittamista ei voitu enää muuttaa. Koska haulikkoammunnan säännöt eivät mahdollista aliääniammusten tai äänenvaimentimien käyttöä, ei varsinaista melupäästöä pystytä pienentämään. Melulle altistuvan kohteen sisätilojen suojaaminenkin on käytännössä hyödytöntä, koska ampumamelun ohjearvot ovat ulkoalueille. Ainoastaan melun absorptio, etenemisen estäminen ja ohjaaminen ovat kelvollisia menetelmiä kohderadoilla. Rata-alueelle suunniteltiin uudet ratojen väliset meluseinät, joiden ääneneristävyys ja -absorptio on vanhoja seiniä parempi. Taustavallille suunniteltiin jatkamista maavallina ja korottamista meluaitana, joka toimii myös haulienkierrätysjärjestelmän runkona. Alueen maaperä suunniteltiin muutettavaksi akustisesti pehmeämmäksi. Käytettävien menetelmien suunnittelussa tehtiin eri vaihtoehdoille laskennallisia arvioita, tietokonemallinnuksia ja laboratoriokokeita. Myös uusia menetelmiä haulikkoradan meluntorjunnassa tutkittiin. Tutkimusten perusteella näitä menetelmiä tutkitaan jatkossa käytännössä.

The study of RNA tertiary interactions in tRNA structure and function

Le rôle des deux paires de bases universelles inverse Hoogsteen U : A ( RHUAs ) présentent chez les ARNt standards , une dans la boucle T et l'autre dans le noyau de la forme en L , a été étudiée. Pour chacun des RHUAs , un criblage génétique spécialisé in vivo chez les bactéries , le système suppresseur ambre ( pour l'étude de la RHUA dans la boucle T ) et le système d'ARNt de la sélénocystéine ( tRNASec ) ( pour l'étude de la RHUA dans le noyau ) , ont été utilisé pour générer des variants fonctionnels à partir de multiples librairies combinatoires . Ces variants ont ensuite été séquencé et soumis à une analyse systématique qui comprend la modélisation informatique et un type d'analyse phylogénétique. Les résultats du système suppresseur ambre ont montré un ensemble de variants fonctionnels qui ne nécessitent pas le motif RHUA dans la boucle T et qui ont remplacé la méthode standard de l'interaction entre les boucles D et T avec une double hélice interboucle , ILDH . D'autres études ont abouti à la détermination d'un modèle In silico de l'alternative à la norme standard de la boucle T, sous le nom de type III . Les résultats du système tRNASec ont révélé que pour cette ARNt exceptionnel, l'absence de RHUA ( dans le noyau ) assure une flexibilité accrue qui est spécifiquement nécessaire pour la fonction de tRNASec . Ainsi, les ARNt standards , à la différence de tRNASec , avec la présence universelle de RHUA dans le noyau , a été naturellement sélectionnée pour être rigide . Pris ensemble, la RHUA joue un rôle essentiel dans la stabilisation des interactions tertiaires.

Complete filling of zeolite frameworks with polyalkynes formed in situ by transition-metal ion catalysts

We report the use of transition-metal-exchanged zeolites as media for the catalytic formation and encapsulation of both polyethyne and polypropyne, and computer modeling studies on the composites so formed. Alkyne gas was absorbed into the pores of zeolite Y (Faujasite) exchanged with transition-metal cations [Fe(II), Co(II), Cu(II), Ni(II), and Zn(II)]. Ni(II) and Zn(II) were found to be the most efficient for the production of poly-ynes. These cations were also found to be effective in polymer generation when exchanged in zeolites mordenite and beta. The resulting powdered samples were characterized by FTIR, Raman, diffuse reflectance electronic spectroscopy, TEM, and elemental analysis, revealing, nearly complete loading of the zeolite channels for the majority of the samples. Based on the experimental carbon content, we have derived the percentage of channel filling, and the proportion of the channels containing a single polymer chain for mordenite. Experimentally, the channels for Y are close to complete filling for polyethyne (PE) and polypropyne (PP), and this is also true for polyethyne in mordenite. Computer modeling studies using Cerius2 show that the channels of mordenite can only accept a single polymer chain of PP, in which case these channels are also completely filled.

Influência das tensões tectônicas na permeabilidade da formação Açu - Bacia Potiguar

The behavior of the fluid flux in oil fields is influenced by different factors and it has a big impact on the recovery of hydrocarbons. There is a need of evaluating and adapting the actual technology to the worldwide reservoirs reality, not only on the exploration (reservoir discovers) but also on the development of those that were already discovered, however not yet produced. The in situ combustion (ISC) is a suitable technique for these recovery of hydrocarbons, although it remains complex to be implemented. The main objective of this research was to study the application of the ISC as an advanced oil recovery technique through a parametric analysis of the process using vertical wells within a semi synthetic reservoir that had the characteristics from the brazilian northwest, in order to determine which of those parameters could influence the process, verifying the technical and economical viability of the method on the oil industry. For that analysis, a commercial reservoir simulation program for thermal processes was used, called steam thermal and advanced processes reservoir simulator (STARS) from the computer modeling group (CMG). This study aims, through the numerical analysis, find results that help improve mainly the interpretation and comprehension of the main problems related to the ISC method, which are not yet dominated. From the results obtained, it was proved that the mediation promoted by the thermal process ISC over the oil recovery is very important, with rates and cumulated production positively influenced by the method application. It was seen that the application of the method improves the oil mobility as a function of the heating when the combustion front forms inside the reservoir. Among all the analyzed parameters, the activation energy presented the bigger influence, it means, the lower the activation energy the bigger the fraction of recovered oil, as a function of the chemical reactions speed rise. It was also verified that the higher the enthalpy of the reaction, the bigger the fraction of recovered oil, due to a bigger amount of released energy inside the system, helping the ISC. The reservoir parameters: porosity and permeability showed to have lower influence on the ISC. Among the operational parameters that were analyzed, the injection rate was the one that showed a stronger influence on the ISC method, because, the higher the value of the injection rate, the higher was the result obtained, mainly due to maintaining the combustion front. In connection with the oxygen concentration, an increase of the percentage of this parameter translates into a higher fraction of recovered oil, because the quantity of fuel, helping the advance and the maintenance of the combustion front for a longer period of time. About the economic analysis, the ISC method showed to be economically feasible when evaluated through the net present value (NPV), considering the injection rates: the higher the injection rate, the higher the financial incomes of the final project

Estudo paramétrico da segregação gravitacional na injeção contínua de vapor

Steam injection is the most used method of additional recovery for the extraction of heavy oil. In this type procedure is common to happen gravitational segregation and this phenomenon can affect the production of oil and therefore, it shoulds be considered in the projects of continuous steam injection. For many years, the gravitational segregation was not adequately considered in the calculation procedures in Reservoir Engineering. The effect of the gravity causes the segregation of fluids inside the porous media according to their densities. The results of simulation arising from reservoirs could provide the ability to deal with the gravity, and it became apparent that the effects of the gravity could significantly affect the performance of the reservoir. It know that the gravitational segregation can happen in almost every case where there is injection of light fluid, specially the steam, and occurs with greater intensity for viscous oil reservoirs. This work discusses the influence of some parameters of the rock-reservoir in segregation as viscosity, permeability, thickness, cover gas, porosity. From a model that shows the phenomenon with greater intensity, optimized some operational parameters as the rate flow rate steam, distance between the wells injector-producer, and interval of completion which contributed to the reduction in gravity override, thus increasing the oil recovery. It was shown a greater technical-economic viability for the model of distance between the wells 100 m. The analysis was performed using the simulator of CMG (Computer Modeling Group-Stars 2007.11, in which was observed by iterating between studied variables in heavy oil reservoirs with similar characteristics to Brazilian Northeast

Estudo paramétrico da injeção de vapor em reservatórios delgados

Exploration of heavy oil reservoirs is increasing every year in worldwide, because the discovery of light oil reservoirs is becoming increasingly rare. This fact has stimulated the research with the purpose of becoming viable, technically and economically, the exploration of such oil reserves. In Brazil, in special in the Northeast region, there is a large amount of heavy oil reservoir, where the recovery by the so called secondary methods Water injection or gas injection is inefficient or even impracticable in some reservoirs with high viscosity oils (heavy oils). In this scenario, steam injection appears as an interesting alternative for recover of these kinds of oil reservoirs. Its main mechanism consists of oil viscosity reduction through steam injection, increasing reservoir temperature. This work presents a parametric simulation study of some operational and reservoir variables that had influence on oil recovery in thin reservoirs typically found in Brazilian Northeast Basins, that use the steam injection as improved oil recovery method. To carry out simulations, it was used the commercial software STARS (Steam, Thermal, and Advanced Processes Reservoir Simulator) from CMG (Computer Modeling Group) version 2007.11. Reservoirs variables studied were horizontal permeability, vertical and horizontal permeability ratio, water zone and pay zone thickness ratio, pay zone thickness and thermal conductivity of the rock. Whereas, operational parameters studied were distance between wells and steam injection rate. Results showed that reservoir variables that had more influence on oil recovery were horizontal permeability and water zone and pay zone thickness ratio. In relation to operational variables, results showed that short distances between wells and low steam injection rates improved oil recovery