MPRAnalyze: statistical framework for massively parallel reporter assays.

Massively parallel reporter assays (MPRAs) can measure the regulatory function of thousands of DNA sequences in a single experiment. Despite growing popularity, MPRA studies are limited by a lack of a unified framework for analyzing the resulting data. Here we present MPRAnalyze: a statistical framework for analyzing MPRA count data. Our model leverages the unique structure of MPRA data to quantify the function of regulatory sequences, compare sequences' activity across different conditions, and provide necessary flexibility in an evolving field. We demonstrate the accuracy and applicability of MPRAnalyze on simulated and published data and compare it with existing methods

Three-dimensional elliptic grid generation technique with application to turbomachinery cascades

Described is a numerical method for generating 3-D grids for turbomachinery computational fluid dynamic codes. The basic method is general and involves the solution of a quasi-linear elliptic partial differential equation via pointwise relaxation with a local relaxation factor. It allows specification of the grid point distribution on the boundary surfaces, the grid spacing off the boundary surfaces, and the grid orthogonality at the boundary surfaces. A geometry preprocessor constructs the grid point distributions on the boundary surfaces for general turbomachinery cascades. Representative results are shown for a C-grid and an H-grid for a turbine rotor. Two appendices serve as user's manuals for the basic solver and the geometry preprocessor

Hybrid Beamforming via the Kronecker Decomposition for the Millimeter-Wave Massive MIMO Systems

Despite its promising performance gain, the realization of mmWave massive MIMO still faces several practical challenges. In particular, implementing massive MIMO in the digital domain requires hundreds of RF chains matching the number of antennas. Furthermore, designing these components to operate at the mmWave frequencies is challenging and costly. These motivated the recent development of hybrid-beamforming where MIMO processing is divided for separate implementation in the analog and digital domains, called the analog and digital beamforming, respectively. Analog beamforming using a phase array introduces uni-modulus constraints on the beamforming coefficients, rendering the conventional MIMO techniques unsuitable and call for new designs. In this paper, we present a systematic design framework for hybrid beamforming for multi-cell multiuser massive MIMO systems over mmWave channels characterized by sparse propagation paths. The framework relies on the decomposition of analog beamforming vectors and path observation vectors into Kronecker products of factors being uni-modulus vectors. Exploiting properties of Kronecker mixed products, different factors of the analog beamformer are designed for either nulling interference paths or coherently combining data paths. Furthermore, a channel estimation scheme is designed for enabling the proposed hybrid beamforming. The scheme estimates the AoA of data and interference paths by analog beam scanning and data-path gains by analog beam steering. The performance of the channel estimation scheme is analyzed. In particular, the AoA spectrum resulting from beam scanning, which displays the magnitude distribution of paths over the AoA range, is derived in closed-form. It is shown that the inter-cell interference level diminishes inversely with the array size, the square root of pilot sequence length and the spatial separation between paths.Comment: Submitted to IEEE JSAC Special Issue on Millimeter Wave Communications for Future Mobile Networks, minor revisio

DART-ID increases single-cell proteome coverage.

Analysis by liquid chromatography and tandem mass spectrometry (LC-MS/MS) can identify and quantify thousands of proteins in microgram-level samples, such as those comprised of thousands of cells. This process, however, remains challenging for smaller samples, such as the proteomes of single mammalian cells, because reduced protein levels reduce the number of confidently sequenced peptides. To alleviate this reduction, we developed Data-driven Alignment of Retention Times for IDentification (DART-ID). DART-ID implements principled Bayesian frameworks for global retention time (RT) alignment and for incorporating RT estimates towards improved confidence estimates of peptide-spectrum-matches. When applied to bulk or to single-cell samples, DART-ID increased the number of data points by 30-50% at 1% FDR, and thus decreased missing data. Benchmarks indicate excellent quantification of peptides upgraded by DART-ID and support their utility for quantitative analysis, such as identifying cell types and cell-type specific proteins. The additional datapoints provided by DART-ID boost the statistical power and double the number of proteins identified as differentially abundant in monocytes and T-cells. DART-ID can be applied to diverse experimental designs and is freely available at http://dart-id.slavovlab.net

Image processing for the extraction of nutritional information from food labels

Current techniques for tracking nutritional data require undesirable amounts of either time or man-power. People must choose between tediously recording and updating dietary information or depending on unreliable crowd-sourced or costly maintained databases. Our project looks to overcome these pitfalls by providing a programming interface for image analysis that will read and report the information present on a nutrition label directly. Our solution involves a C++ library that combines image pre-processing, optical character recognition, and post-processing techniques to pull the relevant information from an image of a nutrition label. We apply an understanding of a nutrition label\u27s content and data organization to approach the accuracy of traditional data-entry methods. Our system currently provides around 80% accuracy for most label images, and we will continue to work to improve our accuracy