Analyzing chemical data in more than two dimensions: A tutorial on factor and cluster analysis

This tutorial is intended to introduce factor and cluster analysis at a level that will afford a senior student-and the practicing chemist, for that matter-some insights into the workings of the computer packages employing these methods, without overwhelming him or her with mathematical detail in the process

Strain evolution in GaN Nanowires: from free-surface objects to coalesced templates

Top-down fabricated GaN nanowires, 250 nm in diameter and with various heights, have been used to experimentally determine the evolution of strain along the vertical direction of 1-dimensional objects. X-ray diffraction and photoluminescence techniques have been used to obtain the strain profile inside the nanowires from their base to their top facet for both initial compressive and tensile strains. The relaxation behaviors derived from optical and structural characterizations perfectly match the numerical results of calculations based on a continuous media approach. By monitoring the elastic relaxation enabled by the lateral free-surfaces, the height from which the nanowires can be considered strain-free has been estimated. Based on this result, NWs sufficiently high to be strain-free have been coalesced to form a continuous GaN layer. X-ray diffraction, photoluminescence and cathodoluminescence clearly show that despite the initial strain-free nanowires template, the final GaN layer is strained

Molecular dynamics simulations of liquid crystals and photoresponsive systems

Neisseria gonorrhoeae (Ngo) expressing the outer membrane protein OpaHSPG can adhere to and invade epithelial cells via binding to heparan sulphate proteoglycan (HSPG) receptors. In this study, we have investigated the role of syndecan-1 and syndecan-4, two members of the HSPG family, in the uptake of Ngo by epithelial cells. When overexpressed in HeLa cells, both syndecans co-localize with adherent Ngo on the host cell surface. This overexpression of syndecan-1 and syndecan-4 leads to a three- and sevenfold increase in Ngo invasion respectively. In contrast, transfection with the syndecan-1 and syndecan-4 mutant constructs lacking the intracellular domain results in an abrogation of the invasion process, characteristic of a dominant-negative mode of action. A concomitant loss of the capacity to mediate Ngo uptake was also observed with syndecan-4 mutant constructs carrying lesions in the dimerization motif necessary for the binding of protein kinase C (PKC) and phosphatidylinositol 4,5-bisphosphate (PIP2), and mutants that are deficient in a C-terminal EFYA amino acid motif responsible for binding to syntenin or CASK. We conclude that syndecan-1 and syndecan-4 can both mediate Ngo uptake into epithelial cells, and that their intracellular domains play a crucial role in this process, perhaps by mediating signal transduction or anchorage to the cytoskeleton

Geometric conductive filament confinement by nanotips for resistive switching of HfO2-RRAM devices with high performance

Filament-type HfO2-based RRAM has been considered as one of the most promising candidates for future non-volatile memories. Further improvement of the stability, particularly at the "OFF" state, of such devices is mainly hindered by resistance variation induced by the uncontrolled oxygen vacancies distribution and filament growth in HfO2 films. We report highly stable endurance of TiN/Ti/HfO2/Si-tip RRAM devices using a CMOS compatible nanotip method. Simulations indicate that the nanotip bottom electrode provides a local confinement for the electrical field and ionic current density; thus a nano-confinement for the oxygen vacancy distribution and nano-filament location is created by this approach. Conductive atomic force microscopy measurements confirm that the filaments form only on the nanotip region. Resistance switching by using pulses shows highly stable endurance for both ON and OFF modes, thanks to the geometric confinement of the conductive path and filament only above the nanotip. This nano-engineering approach opens a new pathway to realize forming-free RRAM devices with improved stability and reliability

Spiranthes vernalis Engelm. & A. Gray

https://thekeep.eiu.edu/herbarium_specimens_byname/21408/thumbnail.jp

Comprehensive analysis of the base composition around the transcription start site in Metazoa

BACKGROUND: The transcription start site of a metazoan gene remains poorly understood, mostly because there is no clear signal present in all genes. Now that several sequenced metazoan genomes have been annotated, we have been able to compare the base composition around the transcription start site for all annotated genes across multiple genomes. RESULTS: The most prominent feature in the base compositions is a significant local variation in G+C content over a large region around the transcription start site. The change is present in all animal phyla but the extent of variation is different between distinct classes of vertebrates, and the shape of the variation is completely different between vertebrates and arthropods. Furthermore, the height of the variation correlates with CpG frequencies in vertebrates but not in invertebrates and it also correlates with gene expression, especially in mammals. We also detect GC and AT skews in all clades (where %G is not equal to %C or %A is not equal to %T respectively) but these occur in a more confined region around the transcription start site and in the coding region. CONCLUSIONS: The dramatic changes in nucleotide composition in humans are a consequence of CpG nucleotide frequencies and of gene expression, the changes in Fugu could point to primordial CpG islands, and the changes in the fly are of a totally different kind and unrelated to dinucleotide frequencies

CP-31398, a putative p53-stabilizing molecule tested in mammalian cells and in yeast for its effects on p53 transcriptional activity

BACKGROUND: CP-31398 is a small molecule that has been reported to stabilize the DNA-binding core domain of the human tumor suppressor protein p53 in vitro. The compound was also reported to function as a potential anti-cancer drug by rescuing the DNA-binding activity and, consequently, the transcription activation function of mutant p53 protein in mammalian tissue culture cells and in mice. RESULTS: We performed a series of gene expression experiments to test the activity of CP-31398 in yeast and in human cell cultures. With these cell-based assays, we were unable to detect any specific stimulation of mutant p53 activity by this compound. Concentrations of CP-31398 that were reported to be active in the published work were highly toxic to the human H1299 lung carcinoma and Saos-2 cell lines in our experiments. CONCLUSION: In our experiments, the small molecule CP-31398 was unable to reactivate mutant p53 protein. The results of our in vivo experiments are in agreement with the recently published biochemical analysis of CP-31398 showing that this molecule does not bind p53 as previously claimed, but intercalates into DNA