CoDoSA: A Lightweight, XML-Based Framework for Integrating Unstructured Textual Information

One of the most fundamental dimensions of information quality is access. For many organizations, a large part of their information assets is locked away in Unstructured Textual Information (UTI) in the form of email, letters, contracts, call notes, and spreadsheet. In addition to internal UTI, there is also a wealth of publicly available UTI on websites, in newspapers, courthouse records and other sources that can add value when combined with internally managed information. This paper describes a system called Compressed Document Set Architecture (CoDoSA) designed to facilitate the integration of UTI into a structured database environment where it can be more readily accessed and manipulated. The CoDoSA Framework comprises an XML-based metadata standard and an associated Application Program Interface (API). It further describes how CoDoSA can facilitate the storage and management of information during the ETL (Extract, Transform, and Load) process to integrate unstructured UTI information. It also explains how CoDoSA promotes higher information quality by providing several features that simplify the governance of metadata standards and enforcement of data quality constraints across different UTI applications and development teams. In addition, CoDoSA provides a mechanism for inserting semantic tags into captured UTI, tags that can be used in later steps to drive semantic-mediated queries and processes

A Mock Data and Science Challenge for Detecting an Astrophysical Stochastic Gravitational-Wave Background with Advanced LIGO and Advanced Virgo

The purpose of this mock data and science challenge is to prepare the data analysis and science interpretation for the second generation of gravitational-wave experiments Advanced LIGO-Virgo in the search for a stochastic gravitational-wave background signal of astrophysical origin. Here we present a series of signal and data challenges, with increasing complexity, whose aim is to test the ability of current data analysis pipelines at detecting an astrophysically produced gravitational-wave background, test parameter estimation methods and interpret the results. We introduce the production of these mock data sets that includes a realistic observing scenario data set where we account for different sensitivities of the advanced detectors as they are continuously upgraded toward their design sensitivity. After analysing these with the standard isotropic cross-correlation pipeline we find that we are able to recover the injected gravitational-wave background energy density to within $2\sigma$ for all of the data sets and present the results from the parameter estimation. The results from this mock data and science challenge show that advanced LIGO and Virgo will be ready and able to make a detection of an astrophysical gravitational-wave background within a few years of operations of the advanced detectors, given a high enough rate of compact binary coalescing events

Tail Wags the Dog? Functional Gene Classes Driving Genome-Wide GC Content in Plasmodium spp

Plasmodium parasites are valuable models to understand how nucleotide composition affects mutation, diversification, and adaptation. No other observed eukaryotes have undergone such large changes in genomic Guanine-Cytosine (GC) content as seen in the genus Plasmodium (approximate to 30% within 35-40 Myr). Although mutational biases are known to influence GC content in the human-infective Plasmodium vivax and Plasmodium falciparum; no study has addressed how different gene functional classes contribute to genus-wide compositional changes, or if Plasmodium GC content variation is driven by natural selection. Here, we tested the hypothesis that certain gene processes and functions drive variation in global GC content between Plasmodium species. We performed a large-scale comparative genomic analysis using the genomes and predicted genes of 17 Plasmodium species encompassing a wide genomic GC content range. Genic GC content was sorted and divided into ten equally sized quantiles that were then assessed for functional enrichment classes. In agreement that selection on gene classes may drive genomic GC content, trans-membrane proteins were enriched within extreme GC content quantiles (Q1 and Q10). Specifically, variant surface antigens, which primarily interact with vertebrate immune systems, showed skewed GC content distributions compared with other trans-membrane proteins. Although a definitive causation linking GC content, expression, and positive selection within variant surface antigens from Plasmodium vivax, Plasmodium berghei, and Plasmodium falciparum could not be established, we found that regardless of genomic nucleotide composition, genic GC content and expression were positively correlated during trophozoite stages. Overall, these data suggest that, alongside mutational biases, functional protein classes drive Plasmodium GC content change.National Science Foundation [NSF IOS-1339156, IOS-1444490]; CyVerse [NSF IOS-1339156, IOS-1444490, NSF DBI-0735191, DBI-1265383]Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Fluorescence in situ hybridization of YAC clones after Alu-PCR amplification

Alu-PCR protocols were optimized for the generation of human DNA probes from yeast strains containing yeast artificial chromosomes (YACs) with human inserts between 100 and 800 kb in size. The resulting DNA probes were used in chromosome in situ suppression (CISS) hybridization experiments. Strong fluorescent signals on both chromatids indicated the localization of specific YAC clones, while two clearly distinguishable signals were observed in ≥90% of diploid nuclei Signal intensities were generally comparable to those observed using chromosome-specific alphoid DNA probes. This approach will facilitate the rapid mapping of YAC clones and their use in chromosome analysis at all stages of the cell cycle

Fluorescence anisotropy of diphenylhexatriene and its cationic Trimethylamino derivative in liquid dipalmitoylphosphatidylcholine liposomes: opposing responses to isoflurane

<p>Abstract</p> <p>Background</p> <p>The mechanism of action of volatile general anesthetics has not yet been resolved. In order to identify the effects of isoflurane on the membrane, we measured the steady-state anisotropy of two fluorescent probes that reside at different depths. Incorporation of anesthetic was confirmed by shifting of the main phase transition temperature.</p> <p>Results</p> <p>In liquid crystalline dipalmitoylphosphatidylcholine liposomes, isoflurane (7-25 mM in the bath) increases trimethylammonium-diphenylhexatriene fluorescence anisotropy by ~0.02 units and decreases diphenylhexatriene anisotropy by the same amount.</p> <p>Conclusions</p> <p>The anisotropy data suggest that isoflurane decreases non-axial dye mobility in the headgroup region, while increasing it in the tail region. We propose that these results reflect changes in the lateral pressure profile of the membrane.</p

TREATMENT OF PARKINSON'S DISEASE USING THE CAYCE WET CELL BATTERY

Parkinson's disease, a condition involving progressive deterioration of the nervous system, is at present incurable by conventional medicine. Here we report on a study in which we have evidence of clinical improvement from using a treatment modality recommended by Edgar Cayce, a subtle energy device known as the wet cell battery. Cayce said that the wet cell would transfer vibratory energy into the body, and specifically recommended it for neurological disorders, but there have been no previous clinical studies of this modality. T en participants with Parkinson's disease used the wet cell, a chemical battery, with gold and silver solutions, for a four-month treatment period at home. Nine of the ten people followed the protocol consistently (but none completely or perfectly). They averaged slight to moderate improvement in Parkinson's disease symptoms over four months, based on observations by researchers and subjective questionnaires. Over the long term (three years), one participant obtained almost complete remission of his Parkinson's disease symptoms. Since there was no control group the placebo effect cannot be ruled out. However, many minor symptoms showed interesting improvement in several individuals. For example, two people reported regaining their sense of smell, and one had improved color vision. Several people had more facial emotional expressiveness, and reported reduced tremors