RNA-based liquid biopsies for better clinical management of Barrett’s esophagus and esophageal adenocarcinoma

In the past decades the incidence of esophageal adenocarcinoma (EAC) has increased dramatically in most Western populations. Due to the lack of symptoms EAC is often detected in a late stage, contributing to a poor 5-year survival rate. The potential of RNA (coding and miRNA) as circulating biomarker in blood has already been shown for many cancer entities but requires further investigation for EAC. In this study we will explore several RNA types in blood, including microRNA, messenger RNA, long non-coding RNA and circular RNA as a potential liquid biomarker to facilitate early diagnosis, prognosis and monitoring of esophageal adenocarcinoma We have been collecting blood and tissue samples from patients with non-dysplastic Barrett’s esophagus (NDBE), high-grade dysplasia (HGD) and EAC. Currently, our biobank includes >5000 samples from 120 patients. A proof-of-concept study was conducted including 17 patients from three groups (EAC, HGD and NDBE). For each patient, biopsies from diseased tissue and healthy tissue as well as blood were collected and analyzed using small RNA and total RNA sequencing. Gene expression analysis was performed to identify differentially expressed genes across the three groups. The highest number of significantly differentially expressed m(i)RNAs were present in the tissues of EAC versus NDBE patients, while these differences were much lower or even absent in the plasma samples. Moreover, we have identified between 1500 and 7500 unique circular RNAs in individual EAC cancer patients’ plasma, indicating promising opportunities for a blood-based liquid biomarker for BE and EAC. Currently, we are collecting additional samples to significantly increase the power of the differential expression study as well as to verify the results of our proof-of-concept study

Monte Carlo Modeling of Crystal Channeling at High Energies

Charged particles entering a crystal close to some preferred direction can be trapped in the electromagnetic potential well existing between consecutive planes or strings of atoms. This channeling effect can be used to extract beam particles if the crystal is bent beforehand. Crystal channeling is becoming a reliable and efficient technique for collimating beams and removing halo particles. At the European Organization for Nuclear Research (CERN), the installation of silicon crystals in the Large Hadron Collider (LHC) is under scrutiny by the UA9 collaboration with the goal of investigating if they are a viable option for the collimation system upgrade. This thesis describes a new Monte Carlo model of planar channeling which has been developed from scratch in order to be implemented in the FLUKA code simulating particle transport and interactions. Crystal channels are described through the concept of continuous potential taking into account thermal motion of the lattice atoms and using Moliere screening function. The energy of the particle transverse motion determines whether or not it is trapped between the crystal planes while single Coulomb scattering on lattice atoms can lead to dechanneling. The volume capture and reflection applying to quasi-channeled particles are also modeled. Analogously to dechanneling, single scattering is used to determine the occurrence of volume capture. The parameters of the crystals, such as torsion or miscut, are described as well. For channeled particles, the suppression of electromagnetic and nuclear collisions is implemented. It is stronger for particles oscillating close to the center of the channel and is crucial for a correct evaluation of the rate of dechanneling without having recourse to the use of a macroscopic dechanneling length. The UA9-H8 experiment conducted at CERN aims at investigating new crystal physics as well as characterizing crystals that can be of interest in view of the implementation of crystal collimation at CERN, including in the LHC. This experiment uses silicon strip detectors situated on both sides of the crystal. Putting together upstream and downstream tracks in coincidence and matching at an identical fitted location on the crystal, it yields information about the deflections given to the beam population. Several runs from the UA9-H8 experiment are analyzed and compared to the model results. Channeling and dechanneling rates, as well as angular distributions at crystal exit are shown to be in a very encouraging agreement both for strip and quasi-mosaic crystals

Observation of channeling for 6500 GeV/c protons in the crystal assisted collimation setup for LHC

Two high-accuracy goniometers equipped with two bent silicon crystals were installed in the betatron cleaning insertion of the CERN Large Hadron Collider (LHC) during its long shutdown. First beam tests were recently performed at the LHC with 450 GeV/c and 6500 GeV/c stored proton beams to investigate the feasibility of beam halo collimation assisted by bent crystals. For the first time channeling of 6500 GeV/c protons was observed in a particle accelerator. A strong reduction of beam losses due to nuclear inelastic interactions in the aligned crystal in comparison with its amorphous orientation was detected. The loss reduction value was about 24. Thus, the results show that deflection of particles by a bent crystal due to channeling is effective for this record particle energy.peer-reviewe

Strong reduction of the off-momentum halo in crystal assisted collimation of the SPS beam

A study of crystal assisted collimation has been continued at the CERN SPS for different energies of stored beams using 120 GeV/. c and 270 GeV/. c protons and Pb ions with 270 GeV/. c per charge. A bent silicon crystal used as a primary collimator deflected halo particles using channeling and directing them into the tungsten absorber. A strong correlation of the beam losses in the crystal and off-momentum halo intensity measured in the first high dispersion (HD) area downstream was observed. In channeling conditions, the beam loss rate induced by inelastic interactions of particles with nuclei is significantly reduced in comparison with the non-oriented crystal. A maximal reduction of beam losses in the crystal larger than 20 was observed with 270 GeV/. c protons. The off-momentum halo intensity measured in the HD area was also strongly reduced in channeling conditions. The reduction coefficient was larger than 7 for the case of Pb ions. A strong loss reduction was also detected in regions of the SPS ring far from the collimation area. It was shown by simulations that the miscut angle between the crystal surface and its crystallographic planes doubled the beam losses in the aligned crystal.peer-reviewe

Comparative results on collimation of the SPS beam of protons and Pb ions with bent crystals

New experiments on crystal assisted collimation have been carried out at the CERN SPS with stored beams of 120 GeV/. c protons and Pb ions. Bent silicon crystals of 2 mm long with about 170 μrad bend angle and a small residual torsion were used as primary collimators. In channeling conditions, the beam loss rate induced by inelastic interactions of particles with the crystal nuclei is minimal. The loss reduction was about 6 for protons and about 3 for Pb ions. Lower reduction value for Pb ions can be explained by their considerably larger ionization losses in the crystal. In one of the crystals, the measured fraction of the Pb ion beam halo deflected in channeling conditions was 74%, a value very close to that for protons. The intensity of the off-momentum halo leaking out from the collimation station was measured in the first high dispersion area downstream. The particle population in the shadow of the secondary collimator-absorber was considerably smaller in channeling conditions than for amorphous orientations of the crystal. The corresponding reduction was in the range of 2-5 for both protons and Pb ions.peer-reviewe

Observation of parametric X-rays produced by 400 GeV/c protons in bent crystals

Spectral maxima of parametric X-ray radiation (PXR) produced by 400 GeV/c protons in bent silicon crystals aligned with the beam have been observed in an experiment at the H8 external beam of the CERN SPS. The total yield of PXR photons was about 10-6 per proton. Agreement between calculations and the experimental data shows that the PXR kinematic theory is valid for bent crystals with sufficiently small curvature as used in the experiment. The intensity of PXR emitted from halo protons in a bent crystal used as a primary collimator in a circular accelerator may be considered as a possible tool to control its crystal structure, which is slowly damaged because of irradiation. The intensity distribution of PXR peaks depends on the crystal thickness intersected by the beam, which changes for different orientations of a crystal collimator. This dependence may be used to control crystal collimator alignment by analyzing PXR spectra produced by halo protons.peer-reviewe

Genome sequence of the tsetse fly (Glossina morsitans):Vector of African trypanosomiasis

Tsetse flies are the sole vectors of human African trypanosomiasis throughout sub-Saharan Africa. Both sexes of adult tsetse feed exclusively on blood and contribute to disease transmission. Notable differences between tsetse and other disease vectors include obligate microbial symbioses, viviparous reproduction, and lactation. Here, we describe the sequence and annotation of the 366-megabase Glossina morsitans morsitans genome. Analysis of the genome and the 12,308 predicted protein-encoding genes led to multiple discoveries, including chromosomal integrations of bacterial (Wolbachia) genome sequences, a family of lactation-specific proteins, reduced complement of host pathogen recognition proteins, and reduced olfaction/chemosensory associated genes. These genome data provide a foundation for research into trypanosomiasis prevention and yield important insights with broad implications for multiple aspects of tsetse biology.IS

Modelling human choices: MADeM and decision‑making

Research supported by FAPESP 2015/50122-0 and DFG-GRTK 1740/2. RP and AR are also part of the Research, Innovation and Dissemination Center for Neuromathematics FAPESP grant (2013/07699-0). RP is supported by a FAPESP scholarship (2013/25667-8). ACR is partially supported by a CNPq fellowship (grant 306251/2014-0)

Improving the spatial resolution of intravascular ultrasound imaging with synthetic aperture Fourier-based methods

International audienc

Structure changes along the lowest rotational band of the antiprotonic helium atom

Along its lowest rotational band, the antiprotonic helium atom undergoes several changes of structure. It evolves from an hydrogenlike atom with broader and broader resonant states, to a quasistable molecularlike structure with narrow resonances, and then to a quasistable Rydberg pseudoatom. The antiprotonic helium atom is studied with high accuracy as a nonrelativistic three-body Coulomb system in the framework of the Lagrange-mesh method. Its metastable states are first determined from L=0 to L=80 by searching conditions of calculation for which energies are stationary. Mean values of distances between the particles are then easily deduced. They show the evolution of the structure of the system. Broad resonances are also analyzed with the complex scaling method. Physical interpretations are provided.SCOPUS: ar.jinfo:eu-repo/semantics/publishe