Prediction of cross-recognition of peptide-HLA A2 by Melan-A-specific cytotoxic T lymphocytes using three-dimensional quantitative structure-activity relationships.

The cross-recognition of peptides by cytotoxic T lymphocytes is a key element in immunology and in particular in peptide based immunotherapy. Here we develop three-dimensional (3D) quantitative structure-activity relationships (QSARs) to predict cross-recognition by Melan-A-specific cytotoxic T lymphocytes of peptides bound to HLA A*0201 (hereafter referred to as HLA A2). First, we predict the structure of a set of self- and pathogen-derived peptides bound to HLA A2 using a previously developed ab initio structure prediction approach [Fagerberg et al., J. Mol. Biol., 521-46 (2006)]. Second, shape and electrostatic energy calculations are performed on a 3D grid to produce similarity matrices which are combined with a genetic neural network method [So et al., J. Med. Chem., 4347-59 (1997)] to generate 3D-QSAR models. The models are extensively validated using several different approaches. During the model generation, the leave-one-out cross-validated correlation coefficient (q (2)) is used as the fitness criterion and all obtained models are evaluated based on their q (2) values. Moreover, the best model obtained for a partitioned data set is evaluated by its correlation coefficient (r = 0.92 for the external test set). The physical relevance of all models is tested using a functional dependence analysis and the robustness of the models obtained for the entire data set is confirmed using y-randomization. Finally, the validated models are tested for their utility in the setting of rational peptide design: their ability to discriminate between peptides that only contain side chain substitutions in a single secondary anchor position is evaluated. In addition, the predicted cross-recognition of the mono-substituted peptides is confirmed experimentally in chromium-release assays. These results underline the utility of 3D-QSARs in peptide mimetic design and suggest that the properties of the unbound epitope are sufficient to capture most of the information to determine the cross-recognition.

A critical evaluation of secondary cancer risk models applied to Monte Carlo dose distributions of 2-dimensional, 3-dimensional conformal and hybrid intensity-modulated radiation therapy for breast cancer.

The comparison of radiotherapy techniques regarding secondary cancer risk has yielded contradictory results possibly stemming from the many different approaches used to estimate risk. The purpose of this study was to make a comprehensive evaluation of different available risk models applied to detailed whole-body dose distributions computed by Monte Carlo for various breast radiotherapy techniques including conventional open tangents, 3D conformal wedged tangents and hybrid intensity modulated radiation therapy (IMRT). First, organ-specific linear risk models developed by the International Commission on Radiological Protection (ICRP) and the Biological Effects of Ionizing Radiation (BEIR) VII committee were applied to mean doses for remote organs only and all solid organs. Then, different general non-linear risk models were applied to the whole body dose distribution. Finally, organ-specific non-linear risk models for the lung and breast were used to assess the secondary cancer risk for these two specific organs. A total of 32 different calculated absolute risks resulted in a broad range of values (between 0.1% and 48.5%) underlying the large uncertainties in absolute risk calculation. The ratio of risk between two techniques has often been proposed as a more robust assessment of risk than the absolute risk. We found that the ratio of risk between two techniques could also vary substantially considering the different approaches to risk estimation. Sometimes the ratio of risk between two techniques would range between values smaller and larger than one, which then translates into inconsistent results on the potential higher risk of one technique compared to another. We found however that the hybrid IMRT technique resulted in a systematic reduction of risk compared to the other techniques investigated even though the magnitude of this reduction varied substantially with the different approaches investigated. Based on the epidemiological data available, a reasonable approach to risk estimation would be to use organ-specific non-linear risk models applied to the dose distributions of organs within or near the treatment fields (lungs and contralateral breast in the case of breast radiotherapy) as the majority of radiation-induced secondary cancers are found in the beam-bordering regions.

Lattices for 3-Dimensional Fuzzy Data generated by Fuzzy Galois Connections

Vagueness and high dimensional space data are usual features of current data. The paper is an approach to identify conceptual structures among fuzzy three dimensional data sets in order to get conceptual hierarchy. We propose a fuzzy extension of the Galois connections that allows to demonstrate an isomorphism theorem between fuzzy sets closures which is the basis for generating lattices ordered-sets

Study of the impact of tissue density heterogeneities on 3-dimensional abdominal dosimetry: comparison between dose kernel convolution and direct monte carlo methods.

Dose kernel convolution (DK) methods have been proposed to speed up absorbed dose calculations in molecular radionuclide therapy. Our aim was to evaluate the impact of tissue density heterogeneities (TDH) on dosimetry when using a DK method and to propose a simple density-correction method. METHODS: This study has been conducted on 3 clinical cases: case 1, non-Hodgkin lymphoma treated with (131)I-tositumomab; case 2, a neuroendocrine tumor treatment simulated with (177)Lu-peptides; and case 3, hepatocellular carcinoma treated with (90)Y-microspheres. Absorbed dose calculations were performed using a direct Monte Carlo approach accounting for TDH (3D-RD), and a DK approach (VoxelDose, or VD). For each individual voxel, the VD absorbed dose, D(VD), calculated assuming uniform density, was corrected for density, giving D(VDd). The average 3D-RD absorbed dose values, D(3DRD), were compared with D(VD) and D(VDd), using the relative difference Δ(VD/3DRD). At the voxel level, density-binned Δ(VD/3DRD) and Δ(VDd/3DRD) were plotted against ρ and fitted with a linear regression. RESULTS: The D(VD) calculations showed a good agreement with D(3DRD). Δ(VD/3DRD) was less than 3.5%, except for the tumor of case 1 (5.9%) and the renal cortex of case 2 (5.6%). At the voxel level, the Δ(VD/3DRD) range was 0%-14% for cases 1 and 2, and -3% to 7% for case 3. All 3 cases showed a linear relationship between voxel bin-averaged Δ(VD/3DRD) and density, ρ: case 1 (Δ = -0.56ρ + 0.62, R(2) = 0.93), case 2 (Δ = -0.91ρ + 0.96, R(2) = 0.99), and case 3 (Δ = -0.69ρ + 0.72, R(2) = 0.91). The density correction improved the agreement of the DK method with the Monte Carlo approach (Δ(VDd/3DRD) < 1.1%), but with a lesser extent for the tumor of case 1 (3.1%). At the voxel level, the Δ(VDd/3DRD) range decreased for the 3 clinical cases (case 1, -1% to 4%; case 2, -0.5% to 1.5%, and -1.5% to 2%). No more linear regression existed for cases 2 and 3, contrary to case 1 (Δ = 0.41ρ - 0.38, R(2) = 0.88) although the slope in case 1 was less pronounced. CONCLUSION: This study shows a small influence of TDH in the abdominal region for 3 representative clinical cases. A simple density-correction method was proposed and improved the comparison in the absorbed dose calculations when using our voxel S value implementation.

Comparison between Radiographic (2-dimensional and 3-dimensional) and Histologic Findings of Periapical Lesions Treated with Apical Surgery.

INTRODUCTION: The aim of this study was to evaluate the concordance of 2- and 3-dimensional radiography and histopathology in the diagnosis of periapical lesions. METHODS: Patients were consecutively enrolled in this study provided that preoperative periapical radiography (PR) and cone-beam computed tomographic imaging of the tooth to be treated with apical surgery were performed. The periapical lesional tissue was histologically analyzed by 2 blinded examiners. The final histologic diagnosis was compared with the radiographic assessments of 4 blinded observers. The initial study material included 62 teeth in the same number of patients. RESULTS: Four lesions had to be excluded during processing, resulting in a final number of 58 evaluated cases (31 women and 27 men, mean age = 55 years). The final histologic diagnosis of the periapical lesions included 55 granulomas (94.8%) and 3 cysts (5.2%). Histologic analysis of the tissue samples from the apical lesions exhibited an almost perfect agreement between the 2 experienced investigators with an overall agreement of 94.83% (kappa = 0.8011). Radiographic assessment overestimated cysts by 28.4% (cone-beam computed tomographic imaging) and 20.7% (periapical radiography), respectively. Comparing the correlation of the radiographic diagnosis of 4 observers with the final histologic diagnosis, 2-dimensional (kappa = 0.104) and 3-dimensional imaging (kappa = 0.111) provided only minimum agreement. CONCLUSIONS: To establish a final diagnosis of an apical radiolucency, the tissue specimen should be evaluated histologically and specified as a granuloma (with/without epithelium) or a cyst. Analysis of 2-dimensional and 3-dimensional radiographic images alike results only in a tentative diagnosis that should be confirmed with biopsy.

3-D density structure and geological evolution of Stromboli volcano (Aeolian Islands, Italy) inferred from land-based and sea-surface gravity data

We present the first density model of Stromboli volcano (Aeolian Islands, Italy) obtained by simultaneously inverting land-based (543) and sea-surface (327) relative gravity data. Modern positioning technology, a 1 x 1 m digital elevation model, and a 15 x 15 m bathymetric model made it possible to obtain a detailed 3-D density model through an iteratively reweighted smoothness-constrained least-squares inversion that explained the land-based gravity data to 0.09 mGal and the sea-surface data to 5 mGal. Our inverse formulation avoids introducing any assumptions about density magnitudes. At 125 m depth from the land surface, the inferred mean density of the island is 2380 kg m(-3), with corresponding 2.5 and 97.5 percentiles of 2200 and 2530 kg m-3. This density range covers the rock densities of new and previously published samples of Paleostromboli I, Vancori, Neostromboli and San Bartolo lava flows. High-density anomalies in the central and southern part of the island can be related to two main degassing faults crossing the island (N41 and NM) that are interpreted as preferential regions of dyke intrusions. In addition, two low-density anomalies are found in the northeastern part and in the summit area of the island. These anomalies seem to be geographically related with past paroxysmal explosive phreato-magmatic events that have played important roles in the evolution of Stromboli Island by forming the Scari caldera and the Neostromboli crater, respectively. (C) 2014 Elsevier B.V. All rights reserved.

An??lisis del aprendizaje de geometr??a espacial en un entorno de geometr??a din??mica 3-dimensional

Resumen tomado de la publicaci??n

Topotactic oxidation of TiGaPO-1, a pyridine-templated titanium gallophosphate with a new octahedral-tetrahedral 3-D framework structure containing Ti-III/Ti-IV

The first 3-D open-framework TiGaPO complex, constructed from (TiO6)-O-III, (TiO6)-O-IV, GaO4, and PO4 polyhedra, contains pyridinium cations in a 1-D pore network and can be oxidized in air at 543 K with retention of the original framework structure.

First results from a 3-dimensional middle atmosphere model

Initial results are presented from a middle atmosphere extension to a version of the European Centre For Medium Range Weather Forecasting tropospheric model. The extended version of the model has been developed as part of the UK Universities Global Atmospheric Modelling Project and extends from the ground to approximately 90 km. A comprehensive solar radiation scheme is included which uses monthly averaged climatological ozone values. A linearised infrared cooling scheme is employed. The basic climatology of the model is described; the parametrization of drag due to orographically forced gravity waves is shown to have a dramatic effect on the simulations of the winter hemisphere.

Three-dimensional quantitative structure-activity relationships for a large series of potent antitubercular agents

Comparative molecular field analysis (CoMFA) studies were conducted on a series of 100 isoniazid derivatives as anti-tuberculosis agents using two receptor-independent structural data set alignment strategies: (1) rigid-body fit, and (2) pharmacophore-based. Significant cross-validated correlation coefficients were obtained (CoMFA(1), q(2) = 0,75 and CoMFA(2), q(2) = 0.74), indicating the potential of the models for untested compounds. The models were then used to predict the inhibitory potency of 20 test set compounds that were not included in the training set, and the predicted values were in good agreement with the experimental results.

Stress Analysis in Platform-Switching Implants: A 3-Dimensional Finite Element Study

The aim of this study was to evaluate the influence of the platform-switching technique on stress distribution in implant, abutment, and pen-implant tissues, through a 3-dimensional finite element study. Three 3-dimensional mandibular models were fabricated using the Solid Works 2006 and InVesalius software. Each model was composed of a bone block with one implant 10 mm long and of different diameters (3.75 and 5.00 mm). The UCLA abutments also ranged in diameter from 5.00 mm to 4.1 mm. After obtaining the geometries, the models were transferred to the software FEMAP 10.0 for pre- and postprocessing of finite elements to generate the mesh, loading, and boundary conditions. A total load of 200 N was applied in axial (0 degrees), oblique (45 degrees), and lateral (90) directions. The models were solved by the software NeiNastran 9.0 and transferred to the software FEMAP 10.0 to obtain the results that were visualized through von Mises and maximum principal stress maps. Model A (implants with 3.75 mm/abutment with 4.1 mm) exhibited the highest area of stress concentration with all loadings (axial, oblique, and lateral) for the implant and the abutment. All models presented the stress areas at the abutment level and at the implant/abutment interface. Models B (implant with 5.0 mm/abutment with 5.0 mm) and C (implant with 5.0 mm/abutment with 4.1 mm) presented minor areas of stress concentration and similar distribution pattern. For the cortical bone, low stress concentration was observed in the pen-implant region for models B and C in comparison to model A. The trabecular bone exhibited low stress that was well distributed in models B and C. Model A presented the highest stress concentration. Model B exhibited better stress distribution. There was no significant difference between the large-diameter implants (models B and C).

Mechanical behavior of ceramic veneer in zirconia-based restorations: a 3-dimensional finite element analysis using microcomputed tomography data

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Placental Volumes Measured by 3-Dimensional Ultrasonography in Normal Pregnancies From 12 to 40 Weeks' Gestation

Objective. The purpose of this study was to construct nomograms of placental volumes according to gestational age and estimated fetal weight. Methods. From March to November 2007, placental volumes were prospectively measured by ultrasonography in 295 normal pregnancies from 12 to 40 weeks' gestation and correlated with gestational age and estimated fetal weight. Inclusion criteria were healthy women, singleton pregnancies with normal fetal morphologic characteristics on ultrasonography, and confirmed gestational age by first-trimester ultrasonography. Results. The mean placental volume ranged from 83 cm(3) at 12 weeks to 427.7 cm(3) at 40 weeks. Linear regression yielded the following formula for the expected placental volumes (ePV) according to gestational age (GA): ePV` (cm(3)) = -64.68 + 12.31 x GA (r = 0.572; P < .001). Placental volumes also varied according to estimated fetal weight (EFW), and the following mathematical equation was also obtained by linear regression: ePV = 94.19 + 0.09 x EFW (r = 0.505; P < 0.001). Conclusions. Nomograms of placental volumes according to gestational age and estimated fetal weight were constructed, generating reference values.

VACUUM POLARIZATION TENSOR IN 3-DIMENSIONAL QUANTUM ELECTRODYNAMICS

We evaluate the one-loop vacuum polarization tensor for three-dimensional quantum electrodynamics (QED), using an analytic regularization technique, implemented in a gauge-invariant way. We show thus that a gauge boson mass is generated at this level of radiative correction to the photon propagator. We also point out in our conclusions that the generalization for the non Abelian case is straightforward.