A Probabilistic Environmental Decision Support Framework for Managing Risk and Resources

The ability to make cost effective, timely decisions associated with waste management and environmental remediation problems has been the subject of considerable debate in recent years. On one hand, environmental decision makers do not have unlimited resources that they can apply to come to resolution on outstanding and uncertain technical issues. On the other hand, because of the possible impending consequences associated with these types of systems, avoiding making a decision is usually not an alternative either. Therefore, a structured, quantitative process is necessary that will facilitate technically defensible decision making in light of both uncertainty and resource constraints. An environmental decision support framework has been developed to provide a logical structure that defines a cost-effective, traceable, and defensible path to closure on decision regarding compliance and resource allocation. The methodology has been applied effectively to waste disposal problems and is being adapted and implemented in subsurface environmental remediation problems

The Cost of Treating Chronic Non-Communicable Diseases: Does it Matter?

Heart disease and Type 2 diabetes mellitus are among the two leading causes of death in the CARICOM member states with HIV/AIDS a distant sixth. Attention is now being paid to non-communicable diseases which have outpaced communicable diseases as the major cause of death. This paper investigated the link between the public medical cost of treating chronic non-communicable diseases, namely heart disease and diabetes, on national output in Barbados, Guyana, Jamaica, and Trinidad and Tobago. The results provide evidence that the public medical cost of treating chronic non-communicable diseases does have a statistically significant negative impact on national output

Ground-Water Quality in Kentucky: Fluoride

Fluoride (F-) is an ion of the element fluorine, and is a natural component in most water resources. According to Hem (1989), fluoride concentrations in fresh water are generally less than 1 mg/L (milligrams per liter), and the concentration of fluoride in the world\u27s oceans is about 1.3 mg/L. The source of most fluoride in natural fresh-water resources is various rocks and minerals in bedrock and sediments

ROCker Models for Reliable Detection and Typing of Short-Read Sequences Carrying beta-Lactamase Genes

Identification of genes encoding beta-lactamases (BLs) from short-read sequences remains challenging due to the high frequency of shared amino acid functional domains and motifs in proteins encoded by BL genes and related non-BL gene sequences. Divergent BL homologs can be frequently missed during similarity searches, which has important practical consequences for monitoring antibiotic resistance. To address this limitation, we built ROCker models that targeted broad classes (e.g., class A, B, C, and D) and individual families (e.g., TEM) of BLs and challenged them with mock 150-bp- and 250-bp-read data sets of known composition. ROCker identifies most-discriminant bit score thresholds in sliding windows along the sequence of the target protein sequence and hence can account for nondiscriminative domains shared by unrelated proteins. BL ROCker models showed a 0% false-positive rate (FPR), a 0% to 4% false-negative rate (FNR), and an up-to-50-fold-higher F1 score [2 x precision x recall/(precision + recall)] compared to alternative methods, such as similarity searches using BLASTx with various e-value thresholds and BL hidden Markov models, or tools like DeepARG, ShortBRED, and AMRFinder. The ROCker models and the underlying protein sequence reference data sets and phylogenetic trees for read placement are freely available through http://enve-omics.ce.gatech.edu/data/rocker-bla. Application of these BL ROCker models to metagenomics, metatranscriptomics, and high-throughput PCR gene amplicon data should facilitate the reliable detection and quantification of BL variants encoded by environmental or clinical isolates and microbiomes and more accurate assessment of the associated public health risk, compared to the current practice. IMPORTANCE Resistance genes encoding beta-lactamases (BLs) confer resistance to the widely prescribed antibiotic class beta-lactams. Therefore, it is important to assess the prevalence of BL genes in clinical or environmental samples for monitoring the spreading of these genes into pathogens and estimating public health risk. However, detecting BLs in short-read sequence data is technically challenging. Our ROCker model-based bioinformatics approach showcases the reliable detection and typing of BLs in complex data sets and thus contributes toward solving an important problem in antibiotic resistance surveillance. The ROCker models developed substantially expand the toolbox for monitoring antibiotic resistance in clinical or environmental settings

Systematic searching for theory to inform systematic reviews: is it feasible? Is it desirable?

Background In recognising the potential value of theory in understanding how interventions work comes a challenge – how to make identification of theory less haphazard? Objectives To explore the feasibility of systematic identification of theory. Method We searched PubMed for published reviews (1998–2012) that had explicitly sought to identify theory. Systematic searching may be characterised by a structured question, methodological filters and an itemised search procedure. We constructed a template (BeHEMoTh – Behaviour of interest; Health context; Exclusions; Models or Theories) for use when systematically identifying theory. The authors tested the template within two systematic reviews. Results Of 34 systematic reviews, only 12 reviews (35%) reported a method for identifying theory. Nineteen did not specify how they identified studies containing theory. Data were unavailable for three reviews. Candidate terms include concept(s)/conceptual, framework(s), model(s), and theory/theories/theoretical. Information professionals must overcome inadequate reporting and the use of theory out of context. The review team faces an additional concern in lack of ‘theory fidelity’. Conclusions Based on experience with two systematic reviews, the BeHEMoTh template and procedure offers a feasible and useful approach for identification of theory. Applications include realist synthesis, framework synthesis or review of complex interventions. The procedure requires rigorous evaluation

A population of gamma-ray emitting globular clusters seen with the Fermi Large Area Telescope

Globular clusters with their large populations of millisecond pulsars (MSPs) are believed to be potential emitters of high-energy gamma-ray emission. Our goal is to constrain the millisecond pulsar populations in globular clusters from analysis of gamma-ray observations. We use 546 days of continuous sky-survey observations obtained with the Large Area Telescope aboard the Fermi Gamma-ray Space Telescope to study the gamma-ray emission towards 13 globular clusters. Steady point-like high-energy gamma-ray emission has been significantly detected towards 8 globular clusters. Five of them (47 Tucanae, Omega Cen, NGC 6388, Terzan 5, and M 28) show hard spectral power indices $(0.7 < \Gamma <1.4)$ and clear evidence for an exponential cut-off in the range 1.0-2.6 GeV, which is the characteristic signature of magnetospheric emission from MSPs. Three of them (M 62, NGC 6440 and NGC 6652) also show hard spectral indices $(1.0 < \Gamma < 1.7)$, however the presence of an exponential cut-off can not be unambiguously established. Three of them (Omega Cen, NGC 6388, NGC 6652) have no known radio or X-ray MSPs yet still exhibit MSP spectral properties. From the observed gamma-ray luminosities, we estimate the total number of MSPs that is expected to be present in these globular clusters. We show that our estimates of the MSP population correlate with the stellar encounter rate and we estimate 2600-4700 MSPs in Galactic globular clusters, commensurate with previous estimates. The observation of high-energy gamma-ray emission from a globular cluster thus provides a reliable independent method to assess their millisecond pulsar populations that can be used to make constraints on the original neutron star X-ray binary population, essential for understanding the importance of binary systems in slowing the inevitable core collapse of globular clusters.Comment: Accepted for publication in A&A. Corresponding authors: J. Kn\"odlseder, N. Webb, B. Pancraz

PKS 1502+106: a new and distant gamma-ray blazar in outburst discovered by the Fermi Large Area Telescope

The Large Area Telescope (LAT) on board the Fermi Gamma-ray Space Telescope discovered a rapid (about 5 days duration), high-energy (E >100 MeV) gamma-ray outburst from a source identified with the blazar PKS 1502+106 (OR 103, S3 1502+10, z=1.839) starting on August 05, 2008 and followed by bright and variable flux over the next few months. Results on the gamma-ray localization and identification, as well as spectral and temporal behavior during the first months of the Fermi all-sky survey are reported here in conjunction with a multi-waveband characterization as a result of one of the first Fermi multi-frequency campaigns. The campaign included a Swift ToO (followed up by 16-day observations on August 07-22, MJD 54685-54700), VLBA (within the MOJAVE program), Owens Valley (OVRO) 40m, Effelsberg-100m, Metsahovi-14m, RATAN-600 and Kanata-Hiroshima radio/optical observations. Results from the analysis of archival observations by INTEGRAL, XMM-Newton and Spitzer space telescopes are reported for a more complete picture of this new gamma-ray blazar.Comment: 17 pages, 11 figures, accepted for The Astrophysical Journa

Functional studies on transfected cell microarray analysed by linear regression modelling

Transfected cell microarray is a promising method for accelerating the functional exploration of the genome, giving information about protein function in the living cell. The microarrays consist of clusters of cells (spots) overexpressing or silencing a particular gene product. The subsequent analysis of the phenotypic consequences of such perturbations can then be detected using cell-based assays. The focus in the present study was to establish an experimental design and a robust analysis approach for fluorescence intensity data, and to address the use of replicates for studying regulation of gene expression with varying complexity and effect size. Our analysis pipeline includes measurement of fluorescence intensities, normalization strategies using negative control spots and internal control plasmids, and linear regression (ANOVA) modelling for estimating biological effects and calculating P-values for comparisons of interests. Our results show the potential of transfected cell microarrays in studying complex regulation of gene expression by enabling measurement of biological responses in cells with overexpression and downregulation of specific gene products, combined with the possibility of assaying the effects of external stimuli. Simulation experiments show that transfected cell microarrays can be used to reliably detect even quantitatively minor biological effects by including several technical and experimental replicates

Mitochondria of the Yeasts Saccharomyces cerevisiae and Kluyveromyces lactis Contain Nuclear rDNA-Encoded Proteins

In eukaryotes, the nuclear ribosomal DNA (rDNA) is the source of the structural 18S, 5.8S and 25S rRNAs. In hemiascomycetous yeasts, the 25S rDNA sequence was described to lodge an antisense open reading frame (ORF) named TAR1 for Transcript Antisense to Ribosomal RNA. Here, we present the first immuno-detection and sub-cellular localization of the authentic product of this atypical yeast gene. Using specific antibodies against the predicted amino-acid sequence of the Saccharomyces cerevisiae TAR1 product, we detected the endogenous Tar1p polypeptides in S. cerevisiae (Sc) and Kluyveromyces lactis (Kl) species and found that both proteins localize to mitochondria. Protease and carbonate treatments of purified mitochondria further revealed that endogenous Sc Tar1p protein sub-localizes in the inner membrane in a Nin-Cout topology. Plasmid-versions of 5′ end or 3′ end truncated TAR1 ORF were used to demonstrate that neither the N-terminus nor the C-terminus of Sc Tar1p were required for its localization. Also, Tar1p is a presequence-less protein. Endogenous Sc Tar1p was found to be a low abundant protein, which is expressed in fermentable and non-fermentable growth conditions. Endogenous Sc TAR1 transcripts were also found low abundant and consistently 5′ flanking regions of TAR1 ORF exhibit modest promoter activity when assayed in a luciferase-reporter system. Using rapid amplification of cDNA ends (RACE) PCR, we also determined that endogenous Sc TAR1 transcripts possess heterogeneous 5′ and 3′ ends probably reflecting the complex expression of a gene embedded in actively transcribed rDNA sequence. Altogether, our results definitively ascertain that the antisense yeast gene TAR1 constitutes a functional transcription unit within the nuclear rDNA repeats