Structural analysis of TCR-ligand interactions studied on H-2Kd-restricted cloned CTL specific for a photoreactive peptide derivative.

To study the interaction of the TCR with its ligand, the complex of a MHC molecule and an antigenic peptide, we modified a TCR contact residue of a H-2Kd-restricted antigenic peptide with photoreactive 4-azidobenzoic acid. The photoreactive group was a critical component of the epitope recognized by CTL clones derived from mice immunized with such a peptide derivative. The majority of these clones expressed V beta 1-encoded beta chains that were paired with J alpha TA28-encoded alpha chains. For one of these TCR, the photoaffinity labeled sites were mapped on the alpha chain as a J alpha TA28-encoded tryptophan and on the beta chain as a residue of the C' strand of V beta 1. Molecular modeling of this TCR suggested the presence of a hydrophobic pocket that harbors this tryptophan as well as a tyrosine on the C' strand of V beta 1 between which the photoreactive side chain inserts. It is concluded that this avid binding principle may account for the preferential selection of V beta 1 and J alpha TA28-encoded TCR.

A Monte Carlo-Based Fiber Tracking Algorithm using Diffusion Tensor MRI

Diffusion tensor magnetic resonance imaging, which measures directional information of water diffusion in the brain, has emerged as a powerful tool for human brain studies. In this paper, we introduce a new Monte Carlo-based fiber tracking approach to estimate brain connectivity. One of the main characteristics of this approach is that all parameters of the algorithm are automatically determined at each point using the entropy of the eigenvalues of the diffusion tensor. Experimental results show the good performance of the proposed approach

Passive lipoidal diffusion and carrier-mediated cell uptake are both important mechanisms of membrane permeation in drug disposition.

Recently, it has been proposed that drug permeation is essentially carrier-mediated only and that passive lipoidal diffusion is negligible. This opposes the prevailing hypothesis of drug permeation through biological membranes, which integrates the contribution of multiple permeation mechanisms, including both carrier-mediated and passive lipoidal diffusion, depending on the compound's properties, membrane properties, and solution properties. The prevailing hypothesis of drug permeation continues to be successful for application and prediction in drug development. Proponents of the carrier-mediated only concept argue against passive lipoidal diffusion. However, the arguments are not supported by broad pharmaceutics literature. The carrier-mediated only concept lacks substantial supporting evidence and successful applications in drug development.

Imagerie de diffusion (DWI) dans la caractérisation de l'échinococcose alvéolaire hépatique.

Objectifs: Etudier l'utilité de DWI dans l'échinococcose alveolaire (EA) hépatique. Matériels et méthodes: Dix-sept patients (10 hommes, âge moyen 64.3) avec 55 lésions hépatiques ont été examinés par IRM. La sémiologie des lésions a été étudiée après classification selon Kodama. Les coefficients apparent de diffusion (ADCmax, ADCmin, ADCtot) ont été mesurés. Résultats: Trois lésions de Kodama de type 1, 13 de type 2, 15 de type 3, 3 de type 4, et 21 de type 5. L'ADCtot des lésions mesurait 1.23±0.18 x 10-3 mm2/s. L'ADCtot de Kodama type 1, 2, 3, 4 et 5 mesuraient 1.97±0.27, 1.66±0.13, 1.73±0.12, 1.15±0.27 et 1.76±0.10 x 10-3 mm2/s, respectivement. Il n'y avait pas de différence significative de l'ADCtot entre les types (p=0.25) hormis le type 4 qui représente une lésion solide (p=0.035). Conclusion: Les valeurs d'ADC des lésions d'EA ne se révèlent pas utiles pour différencier les différents types selon Kodama, hormis pour le type 4 ce qui suggère la présence d'une composante solide. Celles-ci sont relativement basses comparées à d'autres lésions kystiques hépatiques, ce qui peut aider à suggérer le diagnostic.

Identification of new MHC class I-restricted human tumor antigens for immunotherapy

Summary Cancer is a leading cause of morbidity and mortality in Western countries (as an example, colorectal cancer accounts for about 300'000 new cases and 200'000 deaths each year in Europe and in the USA). Despite that many patients with cancer have complete macroscopic clearance of their disease after resection, radiotherapy and/or chemotherapy, many of these patients develop fatal recurrence. Vaccination with immunogenic peptide tumor antigens has shown encouraging progresses in the last decade; immunotherapy might therefore constitute a fourth therapeutic option in the future. We dissect here and critically evaluate the numerous steps of reverse immunology, a forecast procedure to identify antigenic peptides from the sequence of a gene of interest. Bioinformatic algorithms were applied to mine sequence databases for tumor-specific transcripts. A quality assessment of publicly available sequence databanks allowed defining strengths and weaknesses of bioinformatics-based prediction of colon cancer-specific alternative splicing: new splice variants could be identified, however cancer-restricted expression could not be significantly predicted. Other sources of target transcripts were quantitatively investigated by polymerase chain reactions, as cancer-testis genes or reported overexpressed transcripts. Based on the relative expression of a defined set of housekeeping genes in colon cancer tissues, we characterized a precise procedure for accurate normalization and determined a threshold for the definition of significant overexpression of genes in cancers versus normal tissues. Further steps of reverse immunology were applied on a splice variant of the Melan¬A gene. Since it is known that the C-termini of antigenic peptides are directly produced by the proteasome, longer precursor and overlapping peptides encoded by the target sequence were synthesized chemically and digested in vitro with purified proteasome. The resulting fragments were identified by mass spectroscopy to detect cleavage sites. Using this information and based on the available anchor motifs for defined HLA class I molecules, putative antigenic peptides could be predicted. Their relative affinity for HLA molecules was confirmed experimentally with functional competitive binding assays and they were used to search patients' peripheral blood lymphocytes for the presence of specific cytolytic T lymphocytes (CTL). CTL clones specific for a splice variant of Melan-A could be isolated; although they recognized peptide-pulsed cells, they failed to lyse melanoma cells in functional assays of antigen recognition. In the conclusion, we discuss advantages and bottlenecks of reverse immunology and compare the technical aspects of this approach with the more classical procedure of direct immunology, a technique introduced by Boon and colleagues more than 10 years ago to successfully clone tumor antigens.

Diffusion-weighted magnetic resonance imaging in metastatic gastrointestinal stromal tumor (GIST): a pilot study on the assessment of treatment response in comparison with 18F-FDG PET/CT.

BACKGROUND: Diffusion-weighted magnetic resonance imaging (MRI) is increasingly being used for assessing the treatment succes in oncology, but the real clinical value needs to evaluated by comparison with other, already established, metabolic imaging techniques. PURPOSE: To prospectively evaluate the clinical potential of diffusion-weighted MRI with apparent diffusion coefficient (ADC) mapping for gastrointestinal stromal tumor (GIST) response to targeted therapy compared with 18F-fluorodeoxyglucose positron emission tomography/computed tomography (18F-FDG PET/CT). MATERIAL AND METHODS: Eight patients (mean age, 56 ± 11 years) known to have metastatic GIST underwent 18F-FDG PET/CT and MRI (T1Gd, DWI [b = 50,300,600], ADC mapping) simultaneously, before and after change in targeted therapy. MR and PET/CT examinations were first analyzed blindly. Second, PET/CT images were co-registered with T1Gd-MR images for lesion detection. Only 18F-FDG avid lesions were considered. Maximum standardized uptake value (SUVmax) and the corresponding minimum ADCmin were measured for the six largest lesions per patient, if any, on baseline and follow-up examinations. The relationship between changes in SUVmax and ADCmin was analyzed (Spearman's correlation). RESULTS: Twenty-four metastases (12 hepatic, 12 extra-hepatic) were compared on PET/CT and MR images. SUVmax decreased from 7.7 ± 8.1 g/mL to 5.5 ± 5.4 g/mL (P = 0.20), while ADCmin increased from 1.2 ± 0.3 × 10(-3)mm(2)/s to 1.5 ± 0.3 × 10(-3)mm(2)/s (P = 0.0002). There was a significant association between changes in SUVmax and ADCmin (rho = - 0.62, P = 0.0014), but not between changes in lesions size (P = 0.40). CONCLUSION: Changes in ADCmin correlated with the response of 18F-FDG avid GIST to targeted therapy. Thus, diffusion-weighted MRI may represent a radiation-free alternative for follow-up treatment for metastatic GIST patients.

Do labour mobility and networks foster geographical knowledge diffusion? The case of European regions

The goal of this paper is twofold: first, we aim to assess the role played by inventors’ cross-regional mobility and networks of collaboration in fostering knowledge diffusion across regions and subsequent innovation. Second, we intend to evaluate the feasibility of using mobility and networks information to build cross-regional interaction matrices to be used within the spatial econometrics toolbox. To do so, we depart from a knowledge production function where regional innovation intensity is a function not only of the own regional innovation inputs but also external accessible R&D gained through interregional interactions. Differently from much of the previous literature, cross-section gravity models of mobility and networks are estimated to use the fitted values to build our ‘spatial’ weights matrices, which characterize the intensity of knowledge interactions across a panel of 269 regions covering most European countries over 6 years.

Neurofilament triplet proteins are restricted to a subset of neurons in the rat neocortex.

The cellular localisation of neurofilament triplet subunits was investigated in the rat neocortex. A subset of mainly pyramidal neurons showed colocalisation of subunit immunolabelling throughout the neocortex, including labelling with the antibody SMI32, which has been used extensively in other studies of the primate cortex as a selective cellular marker. Neurofilament-labelled neurons were principally localised to two or three cell layers in most cortical regions, but dramatically reduced labelling was present in areas such as the perirhinal cortex, anterior cingulate and a strip of cortex extending from caudal motor regions through the medial parietal region to secondary visual areas. However, quantitative analysis demonstrated a similar proportion (10-20%) of cells with neurofilament triplet labelling in regions of high or low labelling. Combining retrograde tracing with immunolabelling showed that cellular content of the neurofilament proteins was not correlated with the length of projection. Double labelling immunohistochemistry demonstrated that neurofilament content in axons was closely associated with myelination. Analysis of SMI32 labelling in development indicated that content of this epitope within cell bodies was associated with relatively late maturation, between postnatal days 14 and 21. This study is further evidence of a cell type-specific regulation of neurofilament proteins within neocortical neurons. Neurofilament triplet content may be more closely related to the degree of myelination, rather than the absolute length, of the projecting axon.

The connectome mapper: an open-source processing pipeline to map connectomes with MRI.

Researchers working in the field of global connectivity analysis using diffusion magnetic resonance imaging (MRI) can count on a wide selection of software packages for processing their data, with methods ranging from the reconstruction of the local intra-voxel axonal structure to the estimation of the trajectories of the underlying fibre tracts. However, each package is generally task-specific and uses its own conventions and file formats. In this article we present the Connectome Mapper, a software pipeline aimed at helping researchers through the tedious process of organising, processing and analysing diffusion MRI data to perform global brain connectivity analyses. Our pipeline is written in Python and is freely available as open-source at www.cmtk.org.

Mapping complex tissue architecture with diffusion spectrum magnetic resonance imaging.

Methods are presented to map complex fiber architectures in tissues by imaging the 3D spectra of tissue water diffusion with MR. First, theoretical considerations show why and under what conditions diffusion contrast is positive. Using this result, spin displacement spectra that are conventionally phase-encoded can be accurately reconstructed by a Fourier transform of the measured signal's modulus. Second, studies of in vitro and in vivo samples demonstrate correspondence between the orientational maxima of the diffusion spectrum and those of the fiber orientation density at each location. In specimens with complex muscular tissue, such as the tongue, diffusion spectrum images show characteristic local heterogeneities of fiber architectures, including angular dispersion and intersection. Cerebral diffusion spectra acquired in normal human subjects resolve known white matter tracts and tract intersections. Finally, the relation between the presented model-free imaging technique and other available diffusion MRI schemes is discussed.

3-d residual eddy current field characterisation: applied to diffusion weighted magnetic resonance imaging.

Clinical use of the Stejskal-Tanner diffusion weighted images is hampered by the geometric distortions that result from the large residual 3-D eddy current field induced. In this work, we aimed to predict, using linear response theory, the residual 3-D eddy current field required for geometric distortion correction based on phantom eddy current field measurements. The predicted 3-D eddy current field induced by the diffusion-weighting gradients was able to reduce the root mean square error of the residual eddy current field to ~1 Hz. The model's performance was tested on diffusion weighted images of four normal volunteers, following distortion correction, the quality of the Stejskal-Tanner diffusion-weighted images was found to have comparable quality to image registration based corrections (FSL) at low b-values. Unlike registration techniques the correction was not hindered by low SNR at high b-values, and results in improved image quality relative to FSL. Characterization of the 3-D eddy current field with linear response theory enables the prediction of the 3-D eddy current field required to correct eddy current induced geometric distortions for a wide range of clinical and high b-value protocols.