Bioinformatics process management: information flow via a computational journal

This paper presents the Bioinformatics Computational Journal (BCJ), a framework for conducting and managing computational experiments in bioinformatics and computational biology. These experiments often involve series of computations, data searches, filters, and annotations which can benefit from a structured environment. Systems to manage computational experiments exist, ranging from libraries with standard data models to elaborate schemes to chain together input and output between applications. Yet, although such frameworks are available, their use is not widespread–ad hoc scripts are often required to bind applications together. The BCJ explores another solution to this problem through a computer based environment suitable for on-site use, which builds on the traditional laboratory notebook paradigm. It provides an intuitive, extensible paradigm designed for expressive composition of applications. Extensive features facilitate sharing data, computational methods, and entire experiments. By focusing on the bioinformatics and computational biology domain, the scope of the computational framework was narrowed, permitting us to implement a capable set of features for this domain. This report discusses the features determined critical by our system and other projects, along with design issues. We illustrate the use of our implementation of the BCJ on two domain-specific examples

The Pilatus unmanned aircraft system for lower atmospheric research

This paper presents details of the University of Colorado (CU) “Pilatus” unmanned research aircraft, assembled to provide measurements of aerosols, radiation and thermodynamics in the lower troposphere. This aircraft has a wingspan of 3.2 m and a maximum take-off weight of 25 kg, and it is powered by an electric motor to reduce engine exhaust and concerns about carburetor icing. It carries instrumentation to make measurements of broadband up- and downwelling shortwave and longwave radiation, aerosol particle size distribution, atmospheric temperature, relative humidity and pressure and to collect video of flights for subsequent analysis of atmospheric conditions during flight. In order to make the shortwave radiation measurements, care was taken to carefully position a high-quality compact inertial measurement unit (IMU) and characterize the attitude of the aircraft and its orientation to the upward-looking radiation sensor. Using measurements from both of these sensors, a correction is applied to the raw radiometer measurements to correct for aircraft attitude and sensor tilt relative to the sun. The data acquisition system was designed from scratch based on a set of key driving requirements to accommodate the variety of sensors deployed. Initial test flights completed in Colorado provide promising results with measurements from the radiation sensors agreeing with those from a nearby surface site. Additionally, estimates of surface albedo from onboard sensors were consistent with local surface conditions, including melting snow and bright runway surface. Aerosol size distributions collected are internally consistent and have previously been shown to agree well with larger, surface-based instrumentation. Finally the atmospheric state measurements evolve as expected, with the near-surface atmosphere warming over time as the day goes on, and the atmospheric relative humidity decreasing with increased temperature. No directional bias on measured temperature, as might be expected due to uneven heating of the sensor housing over the course of a racetrack pattern, was detected. The results from these flights indicate that the CU Pilatus platform is capable of performing research-grade lower tropospheric measurement missions

Nuclear Pore Complex Protein Mediated Nuclear Localization of Dicer Protein in Human Cells

Human DICER1 protein cleaves double-stranded RNA into small sizes, a crucial step in production of single-stranded RNAs which are mediating factors of cytoplasmic RNA interference. Here, we clearly demonstrate that human DICER1 protein localizes not only to the cytoplasm but also to the nucleoplasm. We also find that human DICER1 protein associates with the NUP153 protein, one component of the nuclear pore complex. This association is detected predominantly in the cytoplasm but is also clearly distinguishable at the nuclear periphery. Additional characterization of the NUP153-DICER1 association suggests NUP153 plays a crucial role in the nuclear localization of the DICER1 protein

Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data.

Telomere length is a risk factor in disease and the dynamics of telomere length are crucial to our understanding of cell replication and vitality. The proliferation of whole genome sequencing represents an unprecedented opportunity to glean new insights into telomere biology on a previously unimaginable scale. To this end, a number of approaches for estimating telomere length from whole-genome sequencing data have been proposed. Here we present Telomerecat, a novel approach to the estimation of telomere length. Previous methods have been dependent on the number of telomeres present in a cell being known, which may be problematic when analysing aneuploid cancer data and non-human samples. Telomerecat is designed to be agnostic to the number of telomeres present, making it suited for the purpose of estimating telomere length in cancer studies. Telomerecat also accounts for interstitial telomeric reads and presents a novel approach to dealing with sequencing errors. We show that Telomerecat performs well at telomere length estimation when compared to leading experimental and computational methods. Furthermore, we show that it detects expected patterns in longitudinal data, repeated measurements, and cross-species comparisons. We also apply the method to a cancer cell data, uncovering an interesting relationship with the underlying telomerase genotype

GWAS meta-analysis of intrahepatic cholestasis of pregnancy implicates multiple hepatic genes and regulatory elements

Intrahepatic cholestasis of pregnancy (ICP) is a pregnancy-specific liver disorder affecting 0.5–2% of pregnancies. The majority of cases present in the third trimester with pruritus, elevated serum bile acids and abnormal serum liver tests. ICP is associated with an increased risk of adverse outcomes, including spontaneous preterm birth and stillbirth. Whilst rare mutations affecting hepatobiliary transporters contribute to the aetiology of ICP, the role of common genetic variation in ICP has not been systematically characterised to date. Here, we perform genome-wide association studies (GWAS) and meta-analyses for ICP across three studies including 1138 cases and 153,642 controls. Eleven loci achieve genome-wide significance and have been further investigated and fine-mapped using functional genomics approaches. Our results pinpoint common sequence variation in liver-enriched genes and liver-specific cis-regulatory elements as contributing mechanisms to ICP susceptibility

Publisher Correction: Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data.

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CAN bus interfacing and PID control for mobile robot navigation under Linux OS

This report covers how the Segway RMP was developed into a stable platform under Linux OS for the future development of more complex algorithms. It reviews how the CAN bus interfacing of the Segway RMP was achieved and then moved on into the development of a navigation system using PID controllers in order to achieve fast and precise turning and movement maneuvers.Bachelor of Engineerin

The Hong Kong government's role in the SAR's future after China's WTO accession.

This study starts with a question: "How may the special administrative region (SAR) government play a role in preventing Hong Kong from losing her economic significance following China's recession to the WTO?" and proceeds with a quanlitative case study approach, focusing on the broad macro strategic issues to the Hong Kong economy.Master of Business Administration (Business Law

A Long-Term, High-Quality, High-Vertical-Resolution GPS Dropsonde Dataset for Hurricane and Other Studies

The article of record as published may be found at http://dx.doi.org/10.1175/BAMS-D-13-00203.1A long-term, high-quality, high-vertical-resolution GPS dropsonde dataset is created by NOAA hurricane flights and consists of 13,681 atmospheric profiles for 120 tropical cyclones.Funding support from the National Science Foundation Grant AGS1132576. Support for P. Black is gratefully acknowledged through Naval Research Laboratory Contract N00173-10-C-6019