PeptX: Using Genetic Algorithms to optimize peptides for MHC binding

<p>Abstract</p> <p>Background</p> <p>The binding between the major histocompatibility complex and the presented peptide is an indispensable prerequisite for the adaptive immune response. There is a plethora of different <it>in silico </it>techniques for the prediction of the peptide binding affinity to major histocompatibility complexes. Most studies screen a set of peptides for promising candidates to predict possible T cell epitopes. In this study we ask the question vice versa: Which peptides do have highest binding affinities to a given major histocompatibility complex according to certain <it>in silico </it>scoring functions?</p> <p>Results</p> <p>Since a full screening of all possible peptides is not feasible in reasonable runtime, we introduce a heuristic approach. We developed a framework for Genetic Algorithms to optimize peptides for the binding to major histocompatibility complexes. In an extensive benchmark we tested various operator combinations. We found that (1) selection operators have a strong influence on the convergence of the population while recombination operators have minor influence and (2) that five different binding prediction methods lead to five different sets of "optimal" peptides for the same major histocompatibility complex. The consensus peptides were experimentally verified as high affinity binders.</p> <p>Conclusion</p> <p>We provide a generalized framework to calculate sets of high affinity binders based on different previously published scoring functions in reasonable runtime. Furthermore we give insight into the different behaviours of operators and scoring functions of the Genetic Algorithm.</p

Jets and energy flow in photon-proton collisions at HERA

Properties of the hadronic final state in photoproduction events with large transverse energy are studied at the electron-proton collider HERA. Distributions of the transverse energy, jets and underlying event energy are compared to \overline{p}p data and QCD calculations. The comparisons show that the \gamma p events can be consistently described by QCD models including -- in addition to the primary hard scattering process -- interactions between the two beam remnants. The differential jet cross sections d\sigma/dE_T^{jet} and d\sigma/d\eta^{jet} are measured

Разработка интерактивной моделирующей системы технологии низкотемпературной сепарации газа

We present a study of J ψ meson production in collisions of 26.7 GeV electrons with 820 GeV protons, performed with the H1-detector at the HERA collider at DESY. The J ψ mesons are detected via their leptonic decays both to electrons and muons. Requiring exactly two particles in the detector, a cross section of σ(ep → J ψ X) = (8.8±2.0±2.2) nb is determined for 30 GeV ≤ W γp ≤ 180 GeV and Q 2 ≲ 4 GeV 2 . Using the flux of quasi-real photons with Q 2 ≲ 4 GeV 2 , a total production cross section of σ ( γp → J / ψX ) = (56±13±14) nb is derived at an average W γp =90 GeV. The distribution of the squared momentum transfer t from the proton to the J ψ can be fitted using an exponential exp(− b ∥ t ∥) below a ∥ t ∥ of 0.75 GeV 2 yielding a slope parameter of b = (4.7±1.9) GeV −2

A Measurement of the Proton Structure Function F ⁣2(x,Q2)F_{\!2}(x,Q^2)

A measurement of the proton structure function $F_{\!2}(x,Q^2)$ is reported for momentum transfer squared $Q^2$ between 4.5 $GeV^2$ and 1600 $GeV^2$ and for Bjorken $x$ between $1.8\cdot10^{-4}$ and 0.13 using data collected by the HERA experiment H1 in 1993. It is observed that $F_{\!2}$ increases significantly with decreasing $x$, confirming our previous measurement made with one tenth of the data available in this analysis. The $Q^2$ dependence is approximately logarithmic over the full kinematic range covered. The subsample of deep inelastic events with a large pseudo-rapidity gap in the hadronic energy flow close to the proton remnant is used to measure the "diffractive" contribution to $F_{\!2}$.Comment: 32 pages, ps, appended as compressed, uuencoded fil

Этимологический анализ специальных единиц лексико-семантического поля "интеллектуальные энергетические системы" в системе современного английского языка

В данной статье описываются результаты этимологического анализа лексико-семантического поля "Интеллектуальные энергетические системы" современного английского языка. Этимологический анализ проводится в аспекте "семантической эволюции слова", а также принадлежности слова к собственному или заимствованному языковому материалу

Исследование точности отверстий и их усадки в обрабатываемых дорнованием втулках

В работе рассмотрены область применения ,виды дорнов, схема процесса дорнования отверстия, схема параметры дорнования отверстия, плюсы и минусы дорнования, и оборудование для дорнования. Потом использование конечно-элементного программного обеспечения ANSYS для моделирования процесса обработки. Затем проведено исследование зависимости усадки отверстия от натяга, степени толстостенности, механических свойств материала, а также исследована кривизна обработанных отверстий. В заключении изложены выводы о проделанной работе и представлено уравнение описывающее исследованные зависимости.In the work, the scope of application, types of mandrels, a diagram of the mandrel process of a hole, a diagram of the parameters of a mandrel of a hole, the pros and cons of mandrel, and equipment for mandrel are considered. Then the use of ANSYS finite element software to simulate the processing process. Then the study of the dependence of the hole shrinkage on the tightness, the degree of thickness, the mechanical properties of the material was carried out, and the curvature of the machined holes was also investigated. In the conclusion, the conclusions about the work done are presented and the equation describing the investigated dependences is presented