sscMap: An extensible Java application for connecting small-molecule drugs using gene-expression signatures

Background: Connectivity mapping is a process to recognize novel pharmacological and toxicological properties in small molecules by comparing their gene expression signatures with others in a database. A simple and robust method for connectivity mapping with increased specificity and sensitivity was recently developed, and its utility demonstrated using experimentally derived gene signatures. Results: This paper introduces sscMap (statistically significant connections' map), a Java application designed to undertake connectivity mapping tasks using the recently published method. The software is bundled with a default collection of reference gene-expression profiles based on the publicly available dataset from the Broad Institute Connectivity Map 02, which includes data from over 7000 Affymetrix microarrays, for over 1000 small-molecule compounds, and 6100 treatment instances in 5 human cell lines. In addition, the application allows users to add their custom collections of reference profiles and is applicable to a wide range of other 'omics technologies. Conclusions: The utility of sscMap is two fold. First, it serves to make statistically significant connections between a user-supplied gene signature and the 6100 core reference profiles based on the Broad Institute expanded dataset. Second, it allows users to apply the same improved method to custom-built reference profiles which can be added to the database for future referencing. The software can be freely downloaded from http://purl.oclc.org/NET/sscMapComment: 3 pages, 1 table, 1 eps figur

Seeking Optimum System Settings for Physical Activity Recognition on Smartwatches

Physical activity recognition (PAR) using wearable devices can provide valued information regarding an individual's degree of functional ability and lifestyle. In this regards, smartphone-based physical activity recognition is a well-studied area. Research on smartwatch-based PAR, on the other hand, is still in its infancy. Through a large-scale exploratory study, this work aims to investigate the smartwatch-based PAR domain. A detailed analysis of various feature banks and classification methods are carried out to find the optimum system settings for the best performance of any smartwatch-based PAR system for both personal and impersonal models. To further validate our hypothesis for both personal (The classifier is built using the data only from one specific user) and impersonal (The classifier is built using the data from every user except the one under study) models, we tested single subject validation process for smartwatch-based activity recognition.Comment: 15 pages, 2 figures, Accepted in CVC'1

Deep Burst Denoising

Noise is an inherent issue of low-light image capture, one which is exacerbated on mobile devices due to their narrow apertures and small sensors. One strategy for mitigating noise in a low-light situation is to increase the shutter time of the camera, thus allowing each photosite to integrate more light and decrease noise variance. However, there are two downsides of long exposures: (a) bright regions can exceed the sensor range, and (b) camera and scene motion will result in blurred images. Another way of gathering more light is to capture multiple short (thus noisy) frames in a "burst" and intelligently integrate the content, thus avoiding the above downsides. In this paper, we use the burst-capture strategy and implement the intelligent integration via a recurrent fully convolutional deep neural net (CNN). We build our novel, multiframe architecture to be a simple addition to any single frame denoising model, and design to handle an arbitrary number of noisy input frames. We show that it achieves state of the art denoising results on our burst dataset, improving on the best published multi-frame techniques, such as VBM4D and FlexISP. Finally, we explore other applications of image enhancement by integrating content from multiple frames and demonstrate that our DNN architecture generalizes well to image super-resolution

PubChemSR: A search and retrieval tool for PubChem

<p>Abstract</p> <p>Background</p> <p>Recent years have seen an explosion in the amount of publicly available chemical and related biological information. A significant step has been the emergence of PubChem, which contains property information for millions of chemical structures, and acts as a repository of compounds and bioassay screening data for the NIH Roadmap. There is a strong need for tools designed for scientists that permit easy download and use of these data. We present one such tool, PubChemSR.</p> <p>Implementation</p> <p>PubChemSR (Search and Retrieve) is a freely available desktop application written for Windows using Microsoft <it>.NET </it>that is designed to assist scientists in search, retrieval and organization of chemical and biological data from the PubChem database. It employs SOAP web services made available by NCBI for extraction of information from PubChem.</p> <p>Results and Discussion</p> <p>The program supports a wide range of searching techniques, including queries based on assay or compound keywords and chemical substructures. Results can be examined individually or downloaded and exported in batch for use in other programs such as Microsoft Excel. We believe that PubChemSR makes it straightforward for researchers to utilize the chemical, biological and screening data available in PubChem. We present several examples of how it can be used.</p

Association between two CHRNA3 variants and susceptibility of lung cancer: a meta-analysis

published_or_final_versio

Association between two CHRNA3 variants and susceptibility of lung cancer: a meta-analysis

published_or_final_versio

Localized-Surface-Plasmon Enhanced the 357 nm Forward Emission from ZnMgO Films Capped by Pt Nanoparticles

The Pt nanoparticles (NPs), which posses the wider tunable localized-surface-plasmon (LSP) energy varying from deep ultraviolet to visible region depending on their morphology, were prepared by annealing Pt thin films with different initial mass-thicknesses. A sixfold enhancement of the 357 nm forward emission of ZnMgO was observed after capping with Pt NPs, which is due to the resonance coupling between the LSP of Pt NPs and the band-gap emission of ZnMgO. The other factors affecting the ultraviolet emission of ZnMgO, such as emission from Pt itself and light multi-scattering at the interface, were also discussed. These results indicate that Pt NPs can be used to enhance the ultraviolet emission through the LSP coupling for various wide band-gap semiconductors

A simple and robust method for connecting small-molecule drugs using gene-expression signatures

Interaction of a drug or chemical with a biological system can result in a gene-expression profile or signature characteristic of the event. Using a suitably robust algorithm these signatures can potentially be used to connect molecules with similar pharmacological or toxicological properties. The Connectivity Map was a novel concept and innovative tool first introduced by Lamb et al to connect small molecules, genes, and diseases using genomic signatures [Lamb et al (2006), Science 313, 1929-1935]. However, the Connectivity Map had some limitations, particularly there was no effective safeguard against false connections if the observed connections were considered on an individual-by-individual basis. Further when several connections to the same small-molecule compound were viewed as a set, the implicit null hypothesis tested was not the most relevant one for the discovery of real connections. Here we propose a simple and robust method for constructing the reference gene-expression profiles and a new connection scoring scheme, which importantly allows the valuation of statistical significance of all the connections observed. We tested the new method with the two example gene-signatures (HDAC inhibitors and Estrogens) used by Lamb et al and also a new gene signature of immunosuppressive drugs. Our testing with this new method shows that it achieves a higher level of specificity and sensitivity than the original method. For example, our method successfully identified raloxifene and tamoxifen as having significant anti-estrogen effects, while Lamb et al's Connectivity Map failed to identify these. With these properties our new method has potential use in drug development for the recognition of pharmacological and toxicological properties in new drug candidates.Comment: 8 pages, 2 figures, and 2 tables; supplementary data supplied as a ZIP fil

Semimetallization of dielectrics in strong optical fields

At the heart of ever growing demands for faster signal processing is ultrafast charge transport and control by electromagnetic fields in semiconductors. Intense optical fields have opened fascinating avenues for new phenomena and applications in solids. Because the period of optical fields is on the order of a femtosecond, the current switching and its control by an optical field may pave a way to petahertz optoelectronic devices. Lately, a reversible semimetallization in fused silica on a femtosecond time scale by using a few-cycle strong field (similar to 1 V/angstrom) is manifested. The strong Wannier-Stark localization and Zener-type tunneling were expected to drive this ultrafast semimetallization. Wider spread of this technology demands better understanding of whether the strong field behavior is universally similar for different dielectrics. Here we employ a carrier-envelope-phase stabilized, few-cycle strong optical field to drive the semimetallization in sapphire, calcium fluoride and quartz and to compare this phenomenon and show its remarkable similarity between them. The similarity in response of these materials, despite the distinguishable differences in their physical properties, suggests the universality of the physical picture explained by the localization of Wannier-Stark states. Our results may blaze a trail to PHz-rate optoelectronics.open11178sciescopu