Trans-Proteomic Pipeline,a standardized data processing pipeline for large-scale reproducible proteomics informatics

Democratization of genomics technologies has enabled the rapid determination of genotypes. More recently the democratization of comprehensive proteomics technologies is enabling the determination of the cellular phenotype and the molecular events that define its dynamic state. Core proteomic technologies include MS to define protein sequence, protein:protein interactions, and protein PTMs. Key enabling technologies for proteomics are bioinformatic pipelines to identify, quantitate, and summarize these events. The Trans-Proteomics Pipeline (TPP) is a robust open-source standardized data processing pipeline for large-scale reproducible quantitative MS proteomics. It supports all major operating systems and instrument vendors via open data formats. Here, we provide a review of the overall proteomics workflow supported by the TPP, its major tools, and how it can be used in its various modes from desktop to cloud computing. We describe new features for the TPP, including data visualization functionality. We conclude by describing some common perils that affect the analysis of MS/MS datasets, as well as some major upcoming features.     

Quantum dots as versatile probes in medical sciences: Synthesis,modification and properties

Quantum dots (QDs) are semiconductor inorganic fluorescent nanocrystals in the size range between 1 and 20 nm. Due to their very small size, they possess unique properties and behave in different way than crystals in macro scale. The specificity of QDs makes them widespread in many branches of human life. The disciplines that took recently huge advantage from the development of nanotechnology are medicine and pharmacy. The creation of particles of very tiny sizes allowed these two sciences to develop or revolutionize the techniques of diagnosis or drug delivery. The most important feature for application of fluorescent nanocrystals in medical and pharmaceutical sciences is their high surface to volume ratio enabling QDs' conjugation to multiple ligands. Other properties of great importance are dispersibility and water stability, high and not easy quenched fluorescence, biocompatibility, and small and uniform sizes. In this review with ca. 200 references the recent developments in QD synthesis, surface modification, QD-based bioimaging, biotracking of drug molecules, biosensing and photodynamic therapy are summarized.     

On the communication of scientific data: The Full-Metadata Format

In this paper, we introduce a scientific format for text-based data files, which facilitates storing and communicating tabular data sets. The so-called Full-Metadata Format builds on the widely used INI-standard and is based on four principles: readable self-documentation, flexible structure, fail-safe compatibility, and searchability. As a consequence, all metadata required to interpret the tabular data are stored in the same file, allowing for the automated generation of publication-ready tables and graphs and the semantic searchability of data file collections. The Full-Metadata Format is introduced on the basis of three comprehensive examples. The complete format and syntax are given in the appendix.     

Nanocrystalline-diamond thin films with high pH and penicillin sensitivity prepared on a capacitive Si-SiO2 structure

A capacitive field-effect EDIS (electrolyte-diamond-insulator-semiconductor) sensor with improved pH and penicillin sensitivity has been realised using a nanocrystalline-diamond (NCD) film as sensitive gate material. The NCD growth process on SiO₂ as well as an additional surface treatment in oxidising medium have been optimised to provide high pH-sensitive, non-porous O-terminated films without damage of the underlying SiO₂ layer. The surface morphology of O-terminated NCD thin films and the layer structure of EDIS sensors have been studied by scanning electron microscopy (SEM) and transmission electron microscopy (TEM) methods. To establish the relative coverage of the surface functional groups generated by the oxidation of NCD surfaces, X-ray photoelectron spectroscopy analysis was carried out. The hydrophilicity of NCD thin films has been studied by water contact-angle measurements. A nearly Nernstian pH sensitivity of 54-57 mV/pH has been observed for O-terminated NCD films treated in an oxidising boiling mixture for 80 min and in oxygen plasma. The high pH-sensitive properties of O-terminated NCD have been used to develop an EDIS-based penicillin biosensor. A freshly prepared penicillin biosensor possesses a high sensitivity of 85 mV/decade in the concentration range of 0.1-2.5 mM penicillin G. The lower detection limit is 5 μM.     

Tuning of leapfrog multiple loop feedback bandpass filters

Off-line tuning of leapfrog multiple loop feedback bandpass filters is demonstrated using a modification of Dishal's method. The proposed method has advantages including simplified tuning circuits and algorithms, minimal additional circuit parasitics and suitability for high frequency applications     

Construction features and environmental factors influencingcorrosion on a self-contained fluid-filled submarine cable circuit inLong Island Sound

A 345 kV self-contained fluid-filled cable circuit was installed in an environment where corrosion of the armor may occur. To better understand the conditions that may result in corrosion, stray currents in the cable end zones and in the middle (submarine) of the circuit were measured, and cable samples were analyzed to determine the electrochemical activity of the cable's outer layers. The results of the project revealed that electrolytic corrosion would affect the semiconductive polyethylene if sufficient stray current density (greater than 0.15 A/m²) was induced by stray currents which were present in Long Island Sound where the cables are installed. Measurements revealed stray current densities in excess of this level towards one end of the cable route. Various other considerations for corrosion are also discussed     

Propagation and structure of streamers in liquid dielectrics

Our purpose is to present a critical review of the current understanding of streamer propagation in dielectric liquids in order to help define the direction of future research. We show that the molecular structure has a significant effect on streamer propagation. The main parameter affecting propagation is the electronic affinity of the liquid molecules     

Active Site Mapping of Human Cathepsin F with Dipeptide Nitrile Inhibitors

Cleavage of the invariant chain is the key event in the trafficking pathway of major histocompatibility complex class II. Cathepsin S is the major processing enzyme of the invariant chain, but cathepsin F acts in macrophages as its functional synergist which is as potent as cathepsin S in invariant chain cleavage. Dedicated low‐molecular‐weight inhibitors for cathepsin F have not yet been developed. An active site mapping with 52 dipeptide nitriles, reacting as covalent–reversible inhibitors, was performed to draw structure–activity relationships for the non‐primed binding region of human cathepsin F. In a stepwise process, new compounds with optimized fragment combinations were designed and synthesized. These dipeptide nitriles were evaluated on human cysteine cathepsins F, B, L, K and S. Compounds 10 (N‐(4‐phenylbenzoyl)‐leucylglycine nitrile) and 12 (N‐(4‐phenylbenzoyl)leucylmethionine nitrile) were found to be potent inhibitors of human cathepsin F, with K_i values <10 nM . With all dipeptide nitriles from our study, a 3D activity landscape was generated to visualize structure–activity relationships for this series of cathepsin F inhibitors.     

Process design and modelling methods for automated handling and draping strategies for composite components

Fibre-reinforced-thermoplastics (FRT) have excellent weight-specific properties compared to conventional engineering materials. However, a wider dissemination of this technology into existing plant technologies is restrained by the low degree of automation. Complex FRT component geometries pose special challenges to gripper design and handling strategies in automated preform processes regarding limp material behaviour and fast cooling time. The preform quality is influenced by the component geometry, reinforcing fabric, and preform process. This paper presents the development of an automated handling and draping strategy, which is validated by finite-element-analysis and experimental testing to meet the requirements of large-scale preforming processes for complex geometries.     

Trimming of Graphs, with Application to Point Labeling

For t>0 and g≥0, a vertex-weighted graph of total weight W is (t,g)-trimmable if it contains a vertex-induced subgraph of total weight at least (1−1/t)W and with no simple path of more than g edges. A family of graphs is trimmable if for every constant t>0, there is a constant g≥0 such that every vertex-weighted graph in the family is (t,g)-trimmable. We show that every family of graphs of bounded domino treewidth is trimmable. This implies that every family of graphs of bounded degree is trimmable if the graphs in the family have bounded treewidth or are planar. We also show that every family of directed graphs of bounded layer bandwidth (a less restrictive condition than bounded directed bandwidth) is trimmable. As an application of these results, we derive polynomial-time approximation schemes for various forms of the problem of labeling a subset of given weighted point features with nonoverlapping sliding axes-parallel rectangular labels so as to maximize the total weight of the labeled features, provided that the ratios of label heights or the ratios of label lengths are bounded by a constant. This settles one of the last major open questions in the theory of map labeling.