Mutual neutralization in collisions of H+ with Cl.

The cross section and final state distribution for mutual neutralization in collisions of H+ with Cl- have been calculated using an ab initio quantum mechanical approach. It is based on potential energy curves and nonadiabatic coupling elements for the six lowest 1Σ+ states of HCl computed with the multireference configuration interaction method. The reaction is found to be driven by nonadiabatic interactions occurring at relatively small internuclear distances (R < 6 a0). Effects on the mutual neutralization cross section with respect to the asymptotic form of the potential energy curves, inclusion of closed channels, as well as isotopic substitution are investigated. The effect of spin-orbit interaction is investigated using a semiempirical model and found to be small. A simple two-state Landau-Zener calculation fails to predict the cross section

Theoretical studies of collisions involving the H2 reaction complex

In this thesis, collisions involving the H2 reaction complex are studied theoretically and the processes considered are mutual neutralization, double charge transfer, associative ionization, dissociative recombination and resonant ion-pair formation. These processes are examples of reactions that involve several excited states and where the Born-Oppenheimer approximation is not applicable. The H2 system is one of the simplest examples of a diatomic molecule and it thus provides an optimal system on which theory can be tested. The purpose of the present work is to develop a theoretical model in which the cross sections of all of the above processes can be computed, using the same set of potential curves and couplings. This theoretical model is not limited to H2 and may serve as a basis for which more complicated systems can be studied. In this work, calculations that include effects such as rotational couplings and autoionization are carried out on H+ + H- mutual neutralization using this model. These effects have not previously been considered in studies on mutual neutralization for this system. Moreover, the theoretical model is applied in preliminary calculations on double charge transfer, associative ionization and dissociative recombination and future developments are discussed

Theoretical studies of collisions involving the H2 reaction complex

In this thesis, collisions involving the H2 reaction complex are studied theoretically and the processes considered are mutual neutralization, double charge transfer, associative ionization, dissociative recombination and resonant ion-pair formation. These processes are examples of reactions that involve several excited states and where the Born-Oppenheimer approximation is not applicable. The H2 system is one of the simplest examples of a diatomic molecule and it thus provides an optimal system on which theory can be tested. The purpose of the present work is to develop a theoretical model in which the cross sections of all of the above processes can be computed, using the same set of potential curves and couplings. This theoretical model is not limited to H2 and may serve as a basis for which more complicated systems can be studied. In this work, calculations that include effects such as rotational couplings and autoionization are carried out on H+ + H- mutual neutralization using this model. These effects have not previously been considered in studies on mutual neutralization for this system. Moreover, the theoretical model is applied in preliminary calculations on double charge transfer, associative ionization and dissociative recombination and future developments are discussed

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Reverse Engineering of Gene Networks with LASSO and Nonlinear Basis Functions

The quest to determine cause from effect is often referred to as reverse engineering in the context of cellular networks. Here we propose and evaluate an algorithm for reverse engineering a gene regulatory network from time-series kind steady-state data. Our algorithmic pipeline, which is rather standard in its parts but not in its integrative composition, combines ordinary differential equations, parameter estimations by least angle regression, and cross-validation procedures for determining the in-degrees and selection of nonlinear transfer functions. The result of the algorithm is a complete directed net-work, in which each edge has been assigned a score front it bootstrap procedure. To evaluate the performance, we submitted the outcome of the algorithm to the reverse engineering assessment competition DREAM2, where we used the data corresponding to the InSillico1 and InSilico2 networks as input. Our algorithm outperformed all other algorithms when inferring one of the directed gene-to-gene networks.This is the authors’ version of the following article:Mika Gustafsson, Michael Hörnquist, Jesper Lundstrom, Johan Bjorkegren and Jesper Tegnér, Reverse Engineering of Gene Networks with LASSO and Nonlinear Basis Functions, 2009, Annals of the New York Academy of Sciences, Volume 1158 Issue, The Challenges of Systems Biology Community Efforts to Harness Biological Complexity, 265-275.which has been published in final form at: http://dx.doi.org/10.1111/j.1749-6632.2008.03764.xCopyright: Blackwell Publishing Ltdhttp://www.blackwellpublishing.com

Soluble Factors from the Colonic Mucosa of Collagenous Colitis Patients on T Cells: Enhanced Production of IL-17A and IL-10 from Peripheral CD4 + T Cells

Soluble factors from intestinal mucosal cells contribute to immune homeostasis in the gut. We have established an in vitro model to investigate the regulatory role of soluble factors from inflamed intestinal mucosa of collagenous colitis (CC) patients in the differentiation of T cells. Peripheral blood CD4 + T cells from healthy donors were polyclonally activated in the presence of conditioned medium (CM) generated from denuded biopsies (DNB) or isolated lamina propria mononuclear cells (LPMCs) from mucosal biopsies from CC patients compared to noninflamed controls, to determine proliferation and secretion of cytokines involved in T-cell differentiation. Compared to controls, we observed significantly increased production of the proinflammatory cytokines IFN-, IL-17A, IL-6, and IL-1 and the anti-inflammatory cytokines IL-4 and IL-10 in the presence of CC-DNB-CM. The most pronounced effect of CC-LPMC-CM on peripheral CD4 + T cells was a trend towards increased production of IL-17A and IL-10. A trend towards reduced inhibition of T-cell proliferation was noted in the presence of CC-DNB-CM. In conclusion, our in vitro model reveals implications of soluble factors from CC colonic mucosa on peripheral T cells, enhancing their production of both pro-and anti-inflammatory cytokines

Enhanced levels of chemokines and their receptors in the colon of microscopic colitis patients indicate mixed immune cell recruitment

Microscopic colitis (MC), comprising collagenous colitis (CC) and lymphocytic colitis (LC), is a common cause of chronic diarrhea. Various immune cell infiltrations in the epithelium and lamina propria are seen in MC immunopathology. We compared gene and protein expressions of different immune cell attracting chemokines and their receptors in colon biopsies from MC patients in active disease or histopathological remission (CC/LC-HR) with controls, using qRT-PCR and Luminex, respectively. CC and LC patients with active disease demonstrated a mixed chemokine profile with significantly enhanced gene and/or protein expressions of the chemokines CCL2, CCL3, CCL4, CCL5, CCL7, CCL22, CXCL8, CXCL9, CXCL10, CXCL11, and CX3CL1 and the receptors CCR2, CCR3, CCR4, CXCR1, CXCR2, and CX3CR1. Enhanced chemokine/chemokine receptor gene and protein levels in LC-HR patients were similar to LC patients, whereas CC-HR patients demonstrated almost normalized levels. These findings expand the current understanding of the involvement of various immune cells in MC immunopathology and endorse chemokines as potential diagnostic markers as well as therapeutic candidates. Moreover, this study further supports the hypothesis that CC and LC are two different entities due to differences in their immunoregulatory responses