Overcomplete Independent Component Analysis via Linearly Constrained Minimum Variance Spatial Filtering

Independent Component Analysis (ICA) designed for complete bases is used in a variety of applications with great success, despite the often questionable assumption of having N sensors and M sources with N≥M. In this article, we assume a source model with more sources than sensors (M>N), only L<N of which are assumed to have a non-Gaussian distribution. We argue that this is a realistic source model for a variety of applications, and prove that for ICA algorithms designed for complete bases (i.e., algorithms assuming N=M) based on mutual information the mixture coefficients of the L non-Gaussian sources can be reconstructed in spite of the overcomplete mixture model. Further, it is shown that the reconstructed temporal activity of non-Gaussian sources is arbitrarily mixed with Gaussian sources. To obtain estimates of the temporal activity of the non-Gaussian sources, we use the correctly reconstructed mixture coefficients in conjunction with linearly constrained minimum variance spatial filtering. This results in estimates of the non-Gaussian sources minimizing the variance of the interference of other sources. The approach is applied to the denoising of Event Related Fields recorded by MEG, and it is shown that it performs superiorly to ordinary ICA.     

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     

Recognizing words and pictures in sentence contexts: A test of lexical modularity.

Words or pictures completed sentence fragments to form coherent or incoherent sentences. Ss made lexical decisions about words and object decisions about pictures. Modality was blocked in Exp 1 and mixed in Exp 2. In both experiments there were similar effects of context for words and pictures, contrary to the hypothesis that lexical priming produces the sentence context effect. Mixed conditions produced longer response latencies than blocked conditions but did not interact with the context effect. The finding of no interaction between the effect of context and the mixed-blocked manipulation supports a version of lexical modularity in which context effects arise as a function of post-access integration processing. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Sizzled: a secreted Xwnt8 antagonist expressed in the ventral marginal zone of Xenopus embryos

An expression cloning screen was used to isolate a novel gene homologous to the extracellular cysteine-rich domain of frizzled receptors. The gene (which we called sizzled for secreted frizzled) was shown to encode a soluble secreted protein, containing a functional signal sequence but no transmembrane domains. Sizzled (szl) is capable of inhibiting Xwnt8 as assayed by (1) dose-dependent inhibition of siamois induction by Xwnt8 in animal caps, (2) rescue of embryos ventralized by Xwnt8 DNA and (3) inhibition of XmyoD expression in the marginal zone. Szl can dorsalize Xenopus embryos if expressed after the midblastula transition, strengthening the idea that zygotic expression of wnts and in particular of Xwnt8 plays a role in antagonizing dorsal signals. It also suggests that inhibiting ventralizing wnts parallels the opposition of BMPs by noggin and chordin. szl expression is restricted to a narrow domain in the ventral marginal zone of gastrulating embryos. szl thus encodes a secreted antagonist of wnt signaling likely involved in inhibiting Xwnt8 and XmyoD ventrally and whose restricted expression represents a new element in the molecular pattern of the ventral marginal zone.