PeptideForest: Semisupervised Machine Learning Integrating Multiple Search Engines for Peptide Identification.

The first step in bottom-up proteomics is the assignment of measured fragmentation mass spectra to peptide sequences, also known as peptide spectrum matches. In recent years novel algorithms have pushed the assignment to new heights; unfortunately, different algorithms come with different strengths and weaknesses and choosing the appropriate algorithm poses a challenge for the user. Here we introduce PeptideForest, a semisupervised machine learning approach that integrates the assignments of multiple algorithms to train a random forest classifier to alleviate that issue.

Multi-scale high-performance computing in astrophysics: simulating clusters with stars, binaries and planets.

The demand on simulation software in astrophysics has dramatically increased over the last decades. This increase is driven by improvements in observational data and computer hardware. At the same time, computers have become more complicated to program due to the introduction of more parallelism and hybrid hardware.

A distributed ASTRA toolbox.

While iterative reconstruction algorithms for tomography have several advantages compared to standard backprojection methods, the adoption of such algorithms in large-scale imaging facilities is still limited, one of the key obstacles being their high computational load. Although GPU-enabled computing clusters are, in principle, powerful enough to carry out iterative reconstructions on large datasets in reasonable time, creating efficient distributed algorithms has so far remained a complex task, requiring low-level programming to deal with memory management and network communication. The ASTRA toolbox is a software toolbox that enables rapid development of GPU accelerated tomography algorithms.

ATZ11 recognizes not only Z-α1-antitrypsin-polymers and complexed forms of non-Z-α1-antitrypsin but also the von Willebrand factor.

Aims: The ATZ11 antibody has been well established for the identification of α1-anti-trypsin (AAT) molecule type PiZ (Z-AAT) in blood samples and liver tissue. In this study, we systematically analyzed the antibody for additional binding sites in human tissue.

Methods And Results: Ultrastructural ATZ11 binding was investigated immunoelectron microscopically in human umbilical vein endothelial cells (HUVECs) and in platelets of a healthy individual.

TLR2 down-regulates FcεRI and its transcription factor PU.1 in human Langerhans cells.

Background: Epidermal Langerhans cells (LC) expressing the high-affinity receptor for IgE (FcεRI) play a key role in atopic dermatitis (AD). AD skin is highly colonized with Staphylococcus aureus (S.a.

High glucose condition increases NADPH oxidase activity in endothelial microparticles that promote vascular inflammation.

Aims: Diabetes is a major risk factor for cardiovascular diseases. Circulating endothelial microparticles (EMP) are increased in diabetic patients, but their potential contribution in atherogenesis is unclear. We sought to determine the role of EMP derived under high glucose conditions in the development of atherosclerosis.

Endothelial microparticle uptake in target cells is annexin I/phosphatidylserine receptor dependent and prevents apoptosis.

Objective: Endothelial microparticles (EMP) are released from activated or apoptotic cells, but their effect on target cells and the exact way of incorporation are largely unknown. We sought to determine the uptake mechanism and the biological effect of EMP on endothelial and endothelial-regenerating cells.

Methods And Results: EMP were generated from starved endothelial cells and isolated by ultracentrifugation.