Planar channeling and quasichanneling oscillations in a bent crystal

Particles passing through a crystal under planar channeling experience transverse oscillations in their motion. As channeled particles approach the atomic planes of a crystal, they are likely to be dechanneled. This effect was used in ion-beam analysis with MeV energy. We studied this effect in a bent crystal for positive and negative particles within a wide range of energies in sight of application of such crystals at accelerators. We found the conditions for the appearance or not of channeling oscillations. Indeed a new kind of oscillations, strictly related to the motion of over-barrier particles, i.e. quasichanneling particles, has been predicted. Such oscillations, named planar quasichanneling oscillations, possess a different nature than channeling oscillations. Through computer simulation, we studied this effect and provided a theoretical interpretation for them. We show that channeling oscillations can be observed only for positive particles while quasichanneling oscillations can exist for particles with either sign. The conditions for experimental observation of channeling and quasichanneling oscillations at existing accelerators with available crystal has been found and optimized.Comment: 25 pages, 11 figure

Data from docking simulations to develop an efficient strategy able to evaluate the interactions between RAGE and MDA-induced albumin adducts

This data article contains the results of docking simulations performed in order to develop a suitable in silico strategy able to assess the stability of the putative complexes between RAGE and MDA induced adducts on human albumin as experimentally determined doi: 10.1016/j.redox.2016.12.017, (Degani et al., 2017) [1]. The docking simulations involved different approaches to give a simplified yet realistic representation of the protein adducts and their environment. With increasing complexity, simulations involved the corresponding albumin tripeptides and pentapeptides with the modified residue in the central position as well as pseudo-structures which were generated by collecting the albumin residues around the adducted residue within a sphere of 7.5 \uc5 and 5 \uc5 radius. The reliability of the tested approaches was assessed by monitoring the score differences between adducted and unmodified residues. The obtained results revealed the greater predictive power of the spherical pseudo-structures compared to the simple tri- or pentapeptidic sequences thus suggesting that RAGE recognition involves residues which are spatially close to the modified residue even though not necessarily adjacent in the primary sequence

Electromagnetic dipole moments of charged baryons with bent crystals at the LHC

We propose a unique program of measurements of electric and magnetic dipole moments of charm, beauty and strange charged baryons at the LHC, based on the phenomenon of spin precession of channeled particles in bent crystals. Studies of crystal channeling and spin precession of positively- and negatively-charged particles are presented, along with feasibility studies and expected sensitivities for the proposed experiment using a layout based on the LHCb detector.Comment: 19 pages, 13 figure

Experimental evidence of planar channeling in a periodically bent crystal

The usage of a Crystalline Undulator (CU) has been identified as a promising solution for generating powerful and monochromatic $\gamma$-rays. A CU was fabricated at SSL through the grooving method, i.e., by the manufacturing of a series of periodical grooves on the major surfaces of a crystal. The CU was extensively characterized both morphologically via optical interferometry at SSL and structurally via X-ray diffraction at ESRF. Then, it was finally tested for channeling with a 400 GeV/c proton beam at CERN. The experimental results were compared to Monte Carlo simulations. Evidence of planar channeling in the CU was firmly observed. Finally, the emission spectrum of the positron beam interacting with the CU was simulated for possible usage in currently existing facilities

Prediction of the Formation of Reactive Metabolites by A Novel Classifier Approach Based on Enrichment Factor Optimization (EFO) as Implemented in the VEGA Program.

The study is aimed at developing linear classifiers to predict the capacity of a given substrate to yield reactive metabolites. While most of the hitherto reported predictive models are based on the occurrence of known structural alerts (e.g., the presence of toxophoric groups), the present study is focused on the generation of predictive models involving linear combinations of physicochemical and stereo-electronic descriptors. The development of these models is carried out by using a novel classification approach based on enrichment factor optimization (EFO) as implemented in the VEGA suite of programs. The study took advantage of metabolic data as collected by manually curated analysis of the primary literature and published in the years 2004⁻2009. The learning set included 977 substrates among which 138 compounds yielded reactive first-generation metabolites, plus 212 substrates generating reactive metabolites in all generations (i.e., metabolic steps). The results emphasized the possibility of developing satisfactory predictive models especially when focusing on the first-generation reactive metabolites. The extensive comparison of the classifier approach presented here using a set of well-known algorithms implemented in Weka 3.8 revealed that the proposed EFO method compares with the best available approaches and offers two relevant benefits since it involves a limited number of descriptors and provides a score-based probability thus allowing a critical evaluation of the obtained results. The last analyses on non-cheminformatics UCI datasets emphasize the general applicability of the EFO approach, which conveniently performs using both balanced and unbalanced datasets

Rescoring and Linearly Combining: a Highly Effective Consensus Strategy for Virtual Screening Campaigns

The study proposes a novel consensus strategy based on linear combinations of different docking scores to be used in the evaluation of virtual screening campaigns. The consensus models are generated by applying the recently proposed Enrichment Factor Optimization (EFO) method, which develops the linear equations by exhaustively combining the available docking scores and by optimizing the resulting enrichment factors. The performances of such a consensus strategy were evaluated by simulating the entire Directory of Useful Decoys (DUD datasets). In detail, the poses were initially generated by the PLANTS docking program and then rescored by ReScore+ with and without the minimization of the complexes. The so calculated scores were then used to generate the mentioned consensus models including two or three different scoring functions. The reliability of the generated models was assessed by a per target validation as performed by default by the EFO approach. The encouraging performances of the here proposed consensus strategy are emphasized by the average increase of the 17% in the Top 1% enrichment factor (EF) values when comparing the single best score with the linear combination of three scores. Specifically, kinases offer a truly convincing demonstration of the efficacy of the here proposed consensus strategy since their Top 1% EF average ranges from 6.4 when using the single best performing primary score to 23.5 when linearly combining scoring functions. The beneficial effects of this consensus approach are clearly noticeable even when considering the entire DUD datasets as evidenced by the area under the curve (AUC) averages revealing a 14% increase when combining three scores. The reached AUC values compare very well with those reported in literature by an extended set of recent benchmarking studies and the three-variable models afford the highest AUC average

ITGB2 mutation combined with deleted ring 21 chromosome in a child with leukocyte adhesion deficiency

Leukocyte adhesion deficiency type 1(LAD-1) is a rare autosomal recessive primary immunodeficiency caused by defects in the ITGB2 gene located on chromosome 21q22. Clinically, LAD-1 patients are characterized by recurrent infections, slow wound healing and dystrophic scars after skin injuries, associated with persistent neutrophilia. The severity of symptoms is related to the level of CD11/CD18 expression on patients’ leucocytes and those with less than 1% expression treated with hematopoietic stem cell transplant (HSCT). We present a child affected by LAD-1 who received HSCT from a matched unrelated donor. Molecular analysis revealed apparent homozygosis for a point mutation in the ITGB2 gene, only the mother however was carrier of the mutation. Cytogenetic and FISH analysis showed the presence of a de-novo ring chromosome 21. Whole Genome Analysis with the Affymetrix GeneChip Human Mapping 250K NspI array confirmed in the child the presence of a de novo deletion of the chromosomal region 21q22.3-qter, where the ITGB2 gene maps. While HSCT resulted in successful engraftment and correction of the immunodeficiency, all the phenotypic features of ring (21) syndrome with a deletion of a 4.6Mb (including 69 genes) clearly remained unchange

Enhancement of the Inelastic Nuclear Interaction Rate in Crystals via Antichanneling

The interaction rate of a charged particle beam with the atomic nuclei of a target varies significantly if the target has a crystalline structure. In particular, under specific orientations of the target with respect to the incident beam, the probability of inelastic interaction with nuclei can be enhanced with respect to the unaligned case. This effect, which can be named antichanneling, can be advantageously used in the cases where the interaction between beam and target has to be maximized. Here we propose to use antichanneling to increase the radioisotope production yield via cyclotron. A dedicated set of experimental measurements was carried out at the INFN Legnaro Laboratories with the AN2000 and CN accelerators to prove the existence of the antichanneling effect. The variation of the interaction yield at hundreds of keV to MeV energies was observed by means of sapphire and indium phosphide crystals, achieving an enhancement of the interaction rate up to 73% and 25%, respectively. Such a result may pave the way to the development of a novel type of nozzle for the existing cyclotrons, which can exploit crystalline materials as targets for radioisotope production, especially to enhance the production rate for expensive prime materials with minor upgrades of the current instrumentation