A comprehensive proteogenomic pipeline for neoantigen discovery to advance personalized cancer immunotherapy.

The accurate identification and prioritization of antigenic peptides is crucial for the development of personalized cancer immunotherapies. Publicly available pipelines to predict clinical neoantigens do not allow direct integration of mass spectrometry immunopeptidomics data, which can uncover antigenic peptides derived from various canonical and noncanonical sources. To address this, we present an end-to-end clinical proteogenomic pipeline, called NeoDisc, that combines state-of-the-art publicly available and in-house software for immunopeptidomics, genomics and transcriptomics with in silico tools for the identification, prediction and prioritization of tumor-specific and immunogenic antigens from multiple sources, including neoantigens, viral antigens, high-confidence tumor-specific antigens and tumor-specific noncanonical antigens.

Mass Transport via In-Plane Nanopores in Graphene Oxide Membranes.

Angstrom-confined solvents in 2D laminates can travel through interlayer spacings, through gaps between adjacent sheets, and via in-plane pores. Among these, experimental access to investigate the mass transport through in-plane pores is lacking. Our experiments allow an understanding of this mass transport via the controlled variation of oxygen functionalities, size and density of in-plane pores in graphene oxide membranes.

Charge Regulation at a Nanoporous Two-Dimensional Interface.

In this work, we have studied the pH-dependent surface charge nature of nanoporous graphene. This has been investigated by membrane potential and by streaming current measurements, both with varying pH. We observed a lowering of the membrane potential with decreasing pH for a fixed concentration gradient of potassium chloride (KCl) in the Donnan dominated regime.

Understanding Mono- and Bivalent Ion Selectivities of Nanoporous Graphene Using Ionic and Bi-ionic Potentials.

Nanoporous graphene displays salt-dependent ion permeation. In this work, we investigate the differences in Donnan potentials arising between reservoirs, separated by a perforated graphene membrane, containing different cations. We compare the case of monovalent cations interacting with nanoporous graphene with the case of bivalent cations.

Highly active single-layer MoS catalysts synthesized by swift heavy ion irradiation.

Two-dimensional molybdenum-disulfide (MoS2) catalysts can achieve high catalytic activity for the hydrogen evolution reaction upon appropriate modification of their surface. The intrinsic inertness of the compound's basal planes can be overcome by either increasing the number of catalytically active edge sites or by enhancing the activity of the basal planes via a controlled creation of sulfur vacancies. Here, we report a novel method of activating the MoS2 surface using swift heavy ion irradiation.

Sensitivity of Anatase and Rutile Phases of TiO to ion irradiation: Examination of the applicability of Coulomb Explosion and Thermal Spike Models.

Sensitivity of the anatase and rutile phases of titanium dioxide to Swift Heavy Ion (SHI) irradiation was experimentally probed and compared with the predictions of the Coulomb explosion, analytical and inelastic thermal spike models of ion-matter interaction. Conforming to the predictions of all these models, our study indicated higher sensitivity of anatase to these ions than the rutile phase. A detailed examination however revealed that Coulomb explosion model cannot explain either the nature of variation of the interaction cross section of SHI with the energy deposited by these ions, S to the target electrons, or the relative values of the threshold electronic energy loss, S of anatase and rutile.

High resolution AFM studies of irradiated mica-following the traces of swift heavy ions under grazing incidence.

High resolution AFM imaging of swift heavy ion irradiated muscovite mica under grazing incidence provides detailed insight into the created nanostructure features. Swift heavy ions under grazing incidence form a complex track structure along the surface, which consists of a double track of nanohillocks at the impact site accompanied by a single, several 100 nm long protrusion. Detailed track studies by varying the irradiation parameters, i.

A new setup for localized implantation and live-characterization of keV energy multiply charged ions at the nanoscale.

An innovative experimental setup, PELIICAEN, allowing the modification of materials and the study of the effects induced by multiply charged ion beams at the nanoscale is presented. This ultra-high vacuum (below 5 × 10 mbar) apparatus is equipped with a focused ion beam column using multiply charged ions and a scanning electron microscope developed by Orsay Physics, as well as a scanning probe microscope. The dual beam approach coupled to the scanning probe microscope achieves nanometer scale in situ topological analysis of the surface modifications induced by the ion beams.

Swift heavy ion irradiation of CaF2 - from grooves to hillocks in a single ion track.

A novel form of ion-tracks, namely nanogrooves and hillocks, are observed on CaF2 after irradiation with xenon and lead ions of about 100 MeV kinetic energy. The irradiation is performed under grazing incidence (0.3°-3°) which forces the track to a region in close vicinity to the surface.

An innovative experimental setup for the measurement of sputtering yield induced by keV energy ions.

An innovative experimental equipment allowing to study the sputtering induced by ion beam irradiation is presented. The sputtered particles are collected on a catcher which is analyzed in situ by Auger electron spectroscopy without breaking the ultra high vacuum (less than 10(-9) mbar), avoiding thus any problem linked to possible contamination. This method allows to measure the angular distribution of sputtering yield.

Superoleophobic behavior induced by nanofeatures on oleophilic surfaces.

The control of surface wetting properties to produce robust and strong hydrophobic and oleophobic effects on intrinsically oleophilic surfaces is at the heart of many technological applications. In this paper, we explore the conditions to observe such effects when the roughness of the substrate is of fractal nature and consists of nanofeatures obtained by the ion track etching technique. The wetting properties were investigated using eight different liquids with surface tensions gamma varying from 18 to 72 mN m(-1).

Wetting on nanorough surfaces.

We investigate the wetting properties of random nanostructured surfaces, with particular attention devoted to the phenomenon of contact angle hysteresis. For this purpose, solid substrates were initially tailored at a nanometric scale by using swift heavy ion irradiation which produced a random distribution of defects. We characterize the wetting properties of water on these heterogeneous surfaces by an average spreading parameter and by the contact angle hysteresis.