A fast - Monte Carlo toolkit on GPU for treatment plan dose recalculation in proton therapy

In the context of the particle therapy a crucial role is played by Treatment Planning Systems (TPSs), tools aimed to compute and optimize the tratment plan. Nowadays one of the major issues related to the TPS in particle therapy is the large CPU time needed. We developed a software toolkit (FRED) for reducing dose recalculation time by exploiting Graphics Processing Units (GPU) hardware. Thanks to their high parallelization capability, GPUs significantly reduce the computation time, up to factor 100 respect to a standard CPU running software. The transport of proton beams in the patient is accurately described through Monte Carlo methods. Physical processes reproduced are: Multiple Coulomb Scattering, energy straggling and nuclear interactions of protons with the main nuclei composing the biological tissues. FRED toolkit does not rely on the water equivalent translation of tissues, but exploits the Computed Tomography anatomical information by reconstructing and simulating the atomic composition of each crossed tissue. FRED can be used as an efficient tool for dose recalculation, on the day of the treatment. In fact it can provide in about one minute on standard hardware the dose map obtained combining the treatment plan, earlier computed by the TPS, and the current patient anatomic arrangement

Exploratory analysis of transposable elements expression in the C. elegans early embryo

Background: Transposable Elements (TE) are mobile sequences that make up large portions of eukaryote genomes. The functions they play within the complex cellular architecture are still not clearly understood, but it is becoming evident that TE have a role in several physiological and pathological processes. In particular, it has been shown that TE transcription is necessary for the correct development of mice embryos and that their expression is able to finely modulate transcription of coding and non-coding genes. Moreover, their activity in the central nervous system (CNS) and other tissues has been correlated with the creation of somatic mosaicisms and with pathologies such as neurodevelopmental and neurodegenerative diseases as well as cancers. Results: We analyzed TE expression among different cell types of the Caenorhabditis elegans (C. elegans) early embryo asking if, where and when TE are expressed and whether their expression is correlated with genes playing a role in early embryo development. To answer these questions, we took advantage of a public C. elegans embryonic single-cell RNA-seq (sc-RNAseq) dataset and developed a bioinformatics pipeline able to quantify reads mapping specifically against TE, avoiding counting reads mapping on TE fragments embedded in coding/non-coding transcripts. Our results suggest that i) canonical TE expression analysis tools, which do not discard reads mapping on TE fragments embedded in annotated transcripts, may over-estimate TE expression levels, ii) Long Terminal Repeats (LTR) elements are mostly expressed in undifferentiated cells and might play a role in pluripotency maintenance and activation of the innate immune response, iii) non-LTR are expressed in differentiated cells, in particular in neurons and nervous system-Associated tissues, and iv) DNA TE are homogenously expressed throughout the C. elegans early embryo development. Conclusions: TE expression appears finely modulated in the C. elegans early embryo and different TE classes are expressed in different cell types and stages, suggesting that TE might play diverse functions during early embryo development

Hydrothermally-assisted recovery of Yttria- stabilized zirconia (YSZ) from end-of-life solid oxide cells

Effective and scalable recycling strategies for the recovery of critical raw materials are yet to be validated for solid oxide cells (SOCs) technologies. The current study aimed at filling this gap by developing optimized recycling processes for the recovery of Yttria-stabilized Zirconia (YSZ) from End-of-Life (EoL) SOC components, in view of using the recovered ceramic phase in cell re-manufacturing. A multi-step procedure, including milling, hydrothermal treatment (HT), and acidic-assisted leaching of nickel from composite Ni-YSZ materials, has been implemented to obtain recovered YSZ powders with defined specifications, in terms of particle size distribution, specific surface area, and chemical purity. The overall optimized procedure includes a pre-milling step (6 h) of the EoL composite materials, and a hydrothermal (HT) treatment at 200 °C for 4 h to further disaggregate the sintered composite, followed by selective oxidative leaching of Ni2+ by HNO3 solution at 80 °C for 2 h. In particular, the intermediate HT step was assessed to play an essential role in promoting the disaggregation of the sintered powders, with a related increase of specific surface area (up to 13 m2 g−1) and the overall reduction of the primary particle aggregates. The acid-assisted leaching allowed to fully extract Nickel from the composite Ni-YSZ powders, with retention of YSZ crystallinity and negligible loss of Zr and Y, as revealed by ICP analysis on the recovered supernatants. The developed multi-step pathway offers a promising strategy to recover valuable YSZ materials for the re-manufacturing of SOCs components, with the aim to boost a circular economy approach in the field of fuel-cell and hydrogen (FCH) technologies

Characterisation of the secondary-neutron production in particle therapy treatments with the MONDO tracking detector

Particle Therapy (PT) is a non-invasive technique that exploits charged light ions for the irradiation of tumours that cannot be effectively treated with surgery or conventional radiotherapy. While the largest dose fraction is released to the tumour volume by the primary beam, a non-negligible amount of additional dose is due to the beam fragmentation that occurs along the path towards the target volume. In particular, the produced neutrons are particularly dangerous as they can release their energy far away from the treated area, increasing the risk of developing a radiogenic secondary malignant neoplasm after undergoing a treatment. A precise measurement of the neutron flux, energy spectrum and angular distributions is eagerly needed in order to improve the treatment planning system software, so as to predict the normal tissue toxicity in the target region and the risk of late complications in the whole body. The MONDO (MOnitor for Neutron Dose in hadrOntherapy) project is dedicated to the characterisation of the secondary ultra-fast neutrons ([20-400] MeV energy range) produced in PT. The neutron tracking system exploits the reconstruction of the recoil protons produced in two consecutive (n, p) elastic scattering interactions to measure simultaneously the neutron incoming direction and energy. The tracker active media is a matrix of thin squared scintillating fibers arranged in orthogonally oriented layers that are read out by a sensor (SBAM) based on SPAD (Single-Photon Avalanche Diode) detectors developed in collaboration with the Fondazione Bruno Kessler (FBK)

In-room test results at CNAO of an innovative PT treatments online monitor (Dose Profiler)

The use of C, He and O ions as projectiles in Particle Therapy (PT) treatments is getting more and more widespread as a consequence of their enhanced relative biological effectiveness and oxygen enhancement ratio, when compared to the protons one. The advantages related to the incoming radiation improved efficacy are requiring an accurate online monitor of the dose release spatial distribution. Such monitor is necessary to prevent unwanted damage to the tissues surrounding the tumour that can arise, for example, due to morphological changes occurred in the patient during the treatment with respect to the initial CT scan. PT treatments with ions can be monitored by detecting the secondary radiation produced by the primary beam interactions with the patient body along the path towards the target volume. Charged fragments produced in the nuclear process of projectile fragmentation can be emitted at large angles with respect to the incoming beam direction and can be detected with high efficiency in a nearly background-free environment. The Dose Profiler (DP) detector, developed within the INSIDE project, is a scintillating fibre tracker that allows an online reconstruction and backtracking of such secondary charged fragments. The construction and preliminary in-room tests performed on the DP, carried out using the 12C ions beam of the CNAO treatment centre using an anthropomorphic phantom as a target, will be reviewed in this contribution. The impact of the secondary fragments interactions with the patient body will be discussed in view of a clinical application. Furthermore, the results implications for a pre-clinical trial on CNAO patients, foreseen in 2019, will be discussed

mRNA levels are buffered upon knockdown of RNA decay and translation factors via adjustment of transcription rates in human HepG2 cells

Evidence from yeast and mammals argues the existence of cross-talk between transcription and mRNA decay. Stabilization of transcripts upon depletion of mRNA decay factors generally leads to no changes in mRNA abundance, attributing this to decreased transcription rates. We show that knockdown of human XRN1, CNOT6 and ETF1 genes in HepG2 cells led to significant alteration in stability of specific mRNAs, alterations in half-life were inversely associated with transcription rates, mostly not resulting in changes in abundance. We demonstrate the existence of the gene expression buffering mechanism in human cells that responds to both transcript stabilization and destabilization to maintain mRNA abundance via altered transcription rates and may involve translation. We propose that this buffering may hold novel cancer therapeutic targets.</p

Dynamics of charge-displacement channeling in intense laser-plasma interactions

The dynamics of transient electric fields generated by the interaction of high intensity laser pulses with underdense plasmas has been studied experimentally with the proton projection imaging technique. The formation of a charged channel, the propagation of its front edge and the late electric field evolution have been characterised with high temporal and spatial resolution. Particle-in-cell simulations and an electrostatic, ponderomotive model reproduce the experimental features and trace them back to the ponderomotive expulsion of electrons and the subsequent ion acceleration.Comment: 5 figures, accepted for publication in New Journal of Physic

The major allergen of the Parietaria pollen contains an LPS-binding region with immuno-modulatory activity

Background: The major allergens in Parietaria pollen, Par j 1 and Par j 2, have been identified as lipid transfer proteins. The family of the Par j 1 allergens is composed of two isoforms, which differ by the presence of a 37 amino acid peptide (Par37) exclusive to the Par j 1.0101 isoform. The goal of this study was to elucidate the biological properties of the Par37 peptide. Methods: In silico analysis, spectrofluorimetric experiments and in vitro cell culture assays were used to identify the biological properties of Par37. In addition, a mouse model of sensitization was used to study the influence of Par37 in the murine immune response. Results: In silico analysis predicted that Par37 displays characteristics of a host defence peptide. Spectrofluorimetric analysis, real-time PCR and ELISA assays demonstrated that Par37 possesses an LPS-binding activity influencing cell signalling in vitro. In RAW264.7 cells, LPS-induced IL-6 and TNF-a transcription and translation were inhibited after preincubation with Par37. Consistent with these data, inhibition of IFN-c secretion was observed in murine spleen cells and in human PBMC. Finally, mice immunized with the two Par j 1 isoforms differing in the presence or absence of the Par37 peptide showed different immunological behaviours in vivo. Conclusions: This study demonstrates that the Par j 1.0101 allergen displays LPSbinding activity due to the presence of a 37 amino acid COOH-terminal region and that this region is capable of influencing cytokine and antibody responses in vitro and in vivo

Trigger Selection Software for Beauty Physics in ATLAS

The unprecedented rate of beauty production at the LHC will yield high statistics for measurements such as CP violation and Bs oscillation and will provide the opportunity to search for and study very rare decays, such as Bâ ï­ï­ .The trigger is a vital component for this work and must select events containing the channels of interest from a huge background in order to reduce the 40 MHz bunch crossing rate down to 100-200 Hz for recording, of which only a part will be assigned to B-physics. Requiring a single or di-muon trigger provides the first stage of the B-trigger selection. Track reconstruction is then performed in the Inner Detector, either using the full detector, at initial luminosity, or within Regions of Interest identified by the first level trigger at higher luminosities. Based on invariant mass, combinations of tracks are selected as likely decay products of the channel of interest and secondary vertex fits are performed. Events are selected based on properties such as fit quality and invariant mass. We present fast vertex reconstruction algorithms suitable for use in the second level trigger and event filter (level three). We discuss the selection software and the flexible trigger strategies that will enable ATLAS to pursue a B-physics programme from the first running at a luminosity of about 1031 cm-2s-1 through to the design luminosity running at 1034 cm-2s-1

EXAFS and XANES structural characterization of bimetallic AuPd vapor derived catalysts

Using an innovative procedure known as metal vapor synthesis (MVS) to prepare bimetallic catalysts, starting from Au and Pd vapors, [AuPd] co-evaporated and [Au][Pd] separately evaporated bimetallic catalysts were achieved. After being tested, the catalytic activity and selectivity of the [AuPd] catalyst turned out to be higher than the [Au][Pd] ones. Using EXAFS spectroscopy it was shown that, in the [AuPd] samples, small bimetallic AuPd nanoparticles were present, having an Au rich core surrounded by an AuPd alloyed shell while in the [Au][Pd] sample there was the presence of monometallic Au and Pd nanoparticles showing some alloying only in the boundary regions. The EXAFS results were also qualitatively conrmed by the XANES spectra