Interface Engineering to Create a Strong Spin Filter Contact to Silicon

Integrating epitaxial and ferromagnetic Europium Oxide (EuO) directly on silicon is a perfect route to enrich silicon nanotechnology with spin filter functionality. To date, the inherent chemical reactivity between EuO and Si has prevented a heteroepitaxial integration without significant contaminations of the interface with Eu silicides and Si oxides. We present a solution to this long-standing problem by applying two complementary passivation techniques for the reactive EuO/Si interface: ($i$) an $in\:situ$ hydrogen-Si $(001)$ passivation and ($ii$) the application of oxygen-protective Eu monolayers --- without using any additional buffer layers. By careful chemical depth profiling of the oxide-semiconductor interface via hard x-ray photoemission spectroscopy, we show how to systematically minimize both Eu silicide and Si oxide formation to the sub-monolayer regime --- and how to ultimately interface-engineer chemically clean, heteroepitaxial and ferromagnetic EuO/Si $(001)$ in order to create a strong spin filter contact to silicon.Comment: 11 pages of scientific paper, 10 high-resolution color figures. Supplemental information on the thermodynamic problem available (PDF). High-resolution abstract graphic available (PNG). Original research (2016

sORFs.org : a repository of small ORFs identified by ribosome profiling

With the advent of ribosome profiling, a next generation sequencing technique providing a ‘snap-shot’ of translated mRNA in a cell, many short open reading frames (sORFs) with were identified. Follow-up studies revealed the existence of functional peptides, so-called micropeptides, translated from these ‘sORFs’, indicating a new class of bio-active peptides. Over the last few years, several micropeptides exhibiting important cellular functions were discovered. However, ribosome occupancy does not necessarily imply an actual function of the translated peptide, leading to the development of various tools assessing the coding potential of sORFs. Here, we introduce sORFs.org (http://www.sorfs.org), a novel database for sORFs identified using ribosome profiling. Starting from ribosome profiling, sORFs.org identifies sORFs, incorporates state-of-the-art tools and metrics and stores results in a public database. Two query interfaces are provided, a default one enabling quick lookup of sORFs and a BioMart interface providing advanced query and export possibilities. At present, sORFs.org harbors 263 354 sORFs that demonstrate ribosome occupancy, originating from three different cell lines: HCT116 (human), E14_mESC (mouse) and S2 (fruit fly). sORFs.org aims to provide an extensive sORFs database accessible to researchers with limited bioinformatics knowledge, thus enabling easy integration into personal projects

PeptiCKDdb-peptide- and protein-centric database for the investigation of genesis and progression of chronic kidney disease

The peptiCKDdb is a publicly available database platform dedicated to support research in the field of chronic kidney disease (CKD) through identification of novel biomarkers and molecular features of this complex pathology. PeptiCKDdb collects peptidomics and proteomics datasets manually extracted from published studies related to CKD. Datasets from peptidomics or proteomics, human case/control studies on CKD and kidney or urine profiling were included. Data from 114 publications (studies of body fluids and kidney tissue: 26 peptidomics and 76 proteomics manuscripts on human CKD, and 12 focusing on healthy proteome profiling) are currently deposited and the content is quarterly updated. Extracted datasets include information about the experimental setup, clinical study design, discovery-validation sample sizes and list of differentially expressed proteins (P-value < 0.05). A dedicated interactive web interface, equipped with multiparametric search engine, data export and visualization tools, enables easy browsing of the data and comprehensive analysis. In conclusion, this repository might serve as a source of data for integrative analysis or a knowledgebase for scientists seeking confirmation of their findings and as such, is expected to facilitate the modeling of molecular mechanisms underlying CKD and identification of biologically relevant biomarkers.Database URL: www.peptickddb.com

Scanning Auger microscopy as applied to the analysis of highly textured YBaCu3Ox thin films

Scanning Auger electron spectroscopy and scanning electron microscopy have been used to investigate the local composition and structure of highly textured axis oriented YBaCuO films with thicknesses in the range 0.4–1 μm. The cuprate films were sputtered on MgO and sapphire (100)-oriented single-crystal substrates at room temperature followed by several anneal stages below or at 920°C in pure oxygen. The YBaCuO/sapphire sample was examined again after an additional 750°C air anneal for 24 h. By applying Auger line profiling on a freshly prepared cross-sectional surface of a thin cuprate film deposited on a sapphire substrate we have been able to show that barium aluminate segregation at grain boundaries is the main cause of the higher electrical resistance usually observed for cuprate films on Al2O3. The (drastic) reduction in Tc can be attributed to the substitution of aluminium in the cuprate at copper sites. Severe interdiffusion has been observed for the epitaxial c axis oriented YBaCu oxide films grown on an MgO substrate, which leads to a deterioration in the superconductivity. The main reason for reduced Tc and quality of cuprate films on MgO is the copper loss into the substrate, the depth of penetration of copper extending more than 400 nm below the YBaCuO---MgO interface. From our experimental results it is evident that Auger line profiling is an important tool in the analysis of high Tc superconducting thin films