Computational methods for prediction of T-cell epitopes - a framework for modelling, testing, and applications

Computational models complement laboratory experimentation for efficient identification of MHC-binding peptides and T-cell epitopes. Methods for prediction of MHC-binding peptides include binding motifs, quantitative matrices, artificial neural networks, hidden Markov models, and molecular modelling. Models derived by these methods have been successfully used for prediction of T-cell epitopes in cancer, autoimmunity, infectious disease, and allergy. For maximum benefit, the use of computer models must be treated as experiments analogous to standard laboratory procedures and performed according to strict standards. This requires careful selection of data for model building, and adequate testing and validation. A range of web-based databases and MHC-binding prediction programs are available. Although some available prediction programs for particular MHC alleles have reasonable accuracy, there is no guarantee that all models produce good quality predictions. In this article, we present and discuss a framework for modelling, testing, and applications of computational methods used in predictions of T-cell epitopes. (C) 2004 Elsevier Inc. All rights reserved.

Fast and efficient synthesis of pyrano[3,2-c]quinolines catalyzed by niobium(V) chloride

A highly efficient two-step method for the synthesis of pyranoquinoline derivatives from imino-Diels-Alder reactions between aldimines and 3,4-dihydro-2H-pyran using niobium(V) chloride as catalyst under mild conditions is described.

Recognition of cyclic, acyclic, exocyclic, and spiro Acetals via structurally diagnostic ion/molecule reactions with the (CH3)(2)N-C+=O acylium ion

Reactions of the model acylium ion (CH3)(2)N-C+=O with acyclic, exocyclic, and Spiro acetals of the general formula (RO)-O-1-(CRR4)-R-3-OR2-upole mass spectrometry. Characteristic intrinsic reactivities were observed for each of these classes of acetals. The two most Characteristic intrinsic reactivities were observed for each of these classes of acetals. The two most common reactions observed were hydride and alkoxy anion [(RO-)-O-1 and (RO-)-O-2] abstraction. Other specific reactions were also observed: (a) a secondary polar [4(+) + 2] cycloaddition for acetals bearing alpha,beta-unsaturated R-3 or R-4 substituents and (b) OH- abstraction for exocyclic and spiro acetals. These structurally diagnostic reactions, in conjunction with others observed previously for cyclic acetals, are shown to reveal the class of the acetal molecule and its ring type and substituents and to permit their recognition and distinction from other classes of isomeric molecules.

Differential adjustment in gill Na(+)/K(+)- and V-ATPase activities and transporter mRNA expression during osmoregulatory acclimation in the cinnamon shrimp Macrobrachium amazonicum (Decapoda, Palaemonidae)

We evaluate osmotic and chloride (Cl(-)) regulatory capability in the diadromous shrimp Macrobrachium amazonicum, and the accompanying alterations in hemolymph osmolality and [Cl(-)], gill Na(+)/K(+)-ATPase activity, and expression of gill Na(+)/K(+)-ATPase alpha-subunit and V-ATPase B subunit mRNA during salinity (S) acclimation. We also characterize V-ATPase kinetics and the organization of transport-related membrane systems in the gill epithelium. Macrobrachium amazonicum strongly hyper-regulates hemolymph osmolality and [Cl(-)] in freshwater and in salinities up to 25 parts per thousand S. During a 10-day acclimation period to 25 parts per thousand S, hemolymph became isosmotic and hypo-chloremic after 5 days, [Cl(-)] alone remaining hyporegulated thereafter. Gill Na(+)/K(+)-ATPase alpha-subunit mRNA expression increased 6.5 times initial values after 1 h, then decreased to 3 to 4 times initial values by 24 h and to 1.5 times initial values after 10 days at 25 parts per thousand S. This increased expression was accompanied by a sharp decrease at 5 h then recovery of initial Na(+)/K(+)-ATPase activity within 24 h, declining again after 5 days, which suggests transient Cl(-) secretion. V-ATPase B-subunit mRNA expression increased 1.5-fold within 1 h, then reduced sharply to 0.3 times initial values by 5 h, and remained unchanged for the remainder of the 10-day period. V-ATPase activity dropped sharply and was negligible after a 10-day acclimation period to 21 parts per thousand S, revealing a marked downregulation of ion uptake mechanisms. The gill epithelium consists of thick, apical pillar cell flanges, the perikarya of which are coupled to an intralamellar septum. These two cell types respectively exhibit extensive apical evaginations and deep membrane invaginations, both of which are associated with numerous mitochondria, characterizing an ion transporting epithelium. These changes in Na(+)/K(+)- and V-ATPase activities and in mRNA expression during salinity acclimation appear to underpin ion uptake and Cl(-) secretion by the palaemonid shrimp gill.

Temperature effect on the sorption of cholate anions on calcined LDH

Layered Double Hydroxides are a class of materials that can be described as positively charged layers of divalent and trivalent cations in the centre of edge-sharing octahedra. Cholesterol derivatives such as cholic acid are substances that play an important role in the digestion of fat components by the organism. This work presents a study on the intercalation of cholate anions in calcined MgAl-CO(3)-HDL. Isotherm experiments were performed at three different temperatures to evaluate the capacity of anion removal by sorption in the calcined LDH. The plateau was reached in all conditions. Increasing temperature results in decreasing cholate sorption. Characteristic peaks of LDH regenerated with OH(-) anions were observed at lower cholate concentrations. A peak in 2 theta equals to 7.5 degrees and peaks between 15 degrees and 20 degrees are observed. Those peaks are the same as the ones observed in the pure sodium cholate PXRD. At higher cholate concentrations the sorbed solids present PXRD related to an additional layered phase, which is related to intercalation of cholate anions with basal spacing equal to 34.3 angstrom. Thus, the cholate anions are also intercalated with a bilayer molecular arrangement at equilibrium concentrations at the isotherms plateau. (C) 2009 Elsevier Ltd. All rights reserved.

On recent developments in the theory of abstract differential equations with fractional derivatives

This note is motivated from some recent papers treating the problem of the existence of a solution for abstract differential equations with fractional derivatives. We show that the existence results in [Agarwal et al. (2009) [1], Belmekki and Benchohra (2010) [2], Darwish et al. (2009) [3], Hu et al. (2009) [4], Mophou and N`Guerekata (2009) [6,7], Mophou (2010) [8,9], Muslim (2009) [10], Pandey et al. (2009) [11], Rashid and El-Qaderi (2009) [12] and Tai and Wang (2009) [13]] are incorrect since the considered variation of constant formulas is not appropriate. In this note, we also consider a different approach to treat a general class of abstract fractional differential equations. (C) 2010 Elsevier Ltd. All rights reserved.

EXISTENCE RESULTS FOR ABSTRACT DEGENERATE NEUTRAL FUNCTIONAL DIFFERENTIAL EQUATIONS

In this paper we discuss the existence of solutions for a class of abstract degenerate neutral functional differential equations. Some applications to partial differential equations are considered.

Global solutions for abstract neutral differential equations

We study the existence of global solutions for a class of abstract neutral differential equation defined on the whole real axis. Some concrete applications related to ordinary and partial differential equations are considered. (C) 2009 Elsevier Ltd. All rights reserved.

Global solutions for abstract impulsive differential equations

In this paper, we study the existence of solutions on the whole of R for a class of impulsive abstract differential equations. An application to partial differential equations is presented. (C) 2009 Elsevier Ltd. All rights reserved.

The existence of solutions for impulsive neutral functional differential equations

This work deals with the existence of mild solutions for a class of impulsive functional differential equations of the neutral type associated with the family of linear closed (not necessarily bounded) operators {A(t) : t is an element of 1}. (C) 2009 Elsevier Ltd. All rights reserved.

Existence results for abstract impulsive second-order neutral functional differential equations

We establish the existence of mild solutions for a class of impulsive second-order partial neutral functional differential equations with infinite delay in a Banach space. (C) 2009 Published by Elsevier Ltd

Existence results for partial neutral functional differential equations with state-dependent delay

In this paper we study the existence of mild solutions for a class of first order abstract partial neutral differential equations with state-dependent delay. (C) 2008 Elsevier Ltd. All rights reserved.

Existence of solutions for second order partial neutral functional differential equations

We establish existence of mild solutions for a class of abstract second-order partial neutral functional differential equations with unbounded delay in a Banach space.

Global solutions for abstract impulsive neutral differential equations

We study the existence of mild solutions for a class of impulsive neutral functional differential equation defined on the whole real axis. Some concrete applications to ordinary and partial neutral differential equations with impulses are considered. (C) 2010 Elsevier Ltd. All rights reserved.

Effects of Self-Assembled Materials Prepared from V(2)O(5) for Lithium Ion Electroinsertion

Self-assembled materials consisting of V(2)O(5), polyallylamine (PAR) and silver nanoparticles (AgNPs) were obtained by the layer-by-layer (LbL) method, aiming at their application as electrodes for lithium-ion batteries and electrochromic devices. The method employed herein allowed for linear growth of visually homogeneous films composed of V(2)O(5), V(2)O(5)/PAH, and V(2)O(5)/PAH/AgNP with 15 bilayers. According to the Fourier transform infrared spectra, interaction between the oxygen atom of the vanadyl group and the amino group should be responsible for the growth of these films. This interaction also enabled establishment of an electrostatic shield between the lithium ions and the sites with higher negative charge, thereby raising the ionic mobility and consequently increasing the energy storage capacity and reducing the response time. According to the site-saturation model and the electrochemical and spectroelectrochemical results, the presence of PAH in the self-assembled host matrix decreased the number of V(2)O(5) electroactive sites. Thus, AgNPs were stabilized in PAR and inserted into the nanoarchitecture, so as to enhance the specific capacity. This should provide new conducting pathways and connect isolated V(2)O(5) particles in the host matrix. Therefore, new nanoarchitectures for specific interactions were formed spontaneously and chosen as examples in this work, aiming to demonstrate the potentiality of the adopted self-assembled method for enhancing the charge transport rate into the host matrices. The obtained materials displayed suitable properties for use as electrodes in lithium batteries and electrochromic devices.