Development of Hydrologic Characterization Methodology of Faults: Outline of the Project in Berkeley, California

NASA Astrophysics Data System (ADS)

Goto, J.; Miwa, T.; Tsuchi, H.; Karasaki, K.

2009-12-01

The Nuclear Waste Management Organization of Japan (NUMO), after volunteering municipalities arise, will start a three-staged program for selecting a HLW and TRU waste repository site. It is recognized from experiences from various site characterization programs in the world that the hydrologic property of faults is one of the most important parameters in the early stage of the program. It is expected that numerous faults of interest exist in an investigation area of several tens of square kilometers. It is, however, impossible to characterize all these faults in a limited time and budget. This raises problems in the repository designing and safety assessment that we may have to accept unrealistic or over conservative results by using a single model or parameters for all the faults in the area. We, therefore, seek to develop an efficient and practical methodology to characterize hydrologic property of faults. This project is a five year program started in 2007, and comprises the basic methodology development through literature study and its verification through field investigations. The literature study tries to classify faults by correlating their geological features with hydraulic property, to search for the most efficient technology for fault characterization, and to develop a work flow diagram. The field investigation starts from selection of a site and fault(s), followed by existing site data analyses, surface geophysics, geological mapping, trenching, water sampling, a series of borehole investigations and modeling/analyses. Based on the results of the field investigations, we plan to develop a systematic hydrologic characterization methodology of faults. A classification method that correlates combinations of geological features (rock type, fault displacement, fault type, position in a fault zone, fracture zone width, damage zone width) with widths of high permeability zones around a fault zone was proposed through a survey on available documents of the site characterization programs. The field investigation started in 2008, by selecting the Wildcat Fault that cut across the Laurence Berkeley National Laboratory (LBNL) site as the target. Analyses on site-specific data, surface geophysics, geological mapping and trenching have confirmed the approximate location and characteristics of the fault (see Session H48, Onishi, et al). The plan for the remaining years includes borehole investigations at LBNL, and another series of investigations in the northern part of the Wildcat Fault.

The Battle of Bunker Hill: Now We Are at War. Revised. Teaching with Historic Places.

ERIC Educational Resources Information Center

Brue, Sandy

This lesson describes and discusses the Battle of Bunker Hill (Massachusetts), which took place during the Revolutionary War. The lesson plan contains eight sections: (1) "About this Lesson"; (2) "Getting Started: Inquiry Question"; (3) "Setting the Stage: Historical Context"; (4) "Locating the Site: Maps"…

Molecular Structure and Transformation of the Glucose Dehydrogenase Gene in Drosophila Melanogaster

PubMed Central

Whetten, R.; Organ, E.; Krasney, P.; Cox-Foster, D.; Cavener, D.

1988-01-01

We have precisely mapped and sequenced the three 5' exons of the Drosophila melanogaster Gld gene and have identified the start sites for transcription and translation. The first exon is composed of 335 nucleotides and does not contain any putative translation start codons. The second exon is separated from the first exon by 8 kb and contains the Gld translation start codon. The inferred amino acid sequence of the amino terminus contains two unusual features: three tandem repeats of serine-alanine, and a relatively high density of cysteine residues. P element-mediated transformation experiments demonstrated that a 17.5-kb genomic fragment contains the functional and regulatory components of the Gld gene. PMID:3143620

Aeromagnetic investigations of hazardous waste sites

USGS Publications Warehouse

,

1995-01-01

Aeromagnetic survey data collected by helicopter over hazardous waste sites can be used to map the distribution of buried metallic (ferrous) objects at these sites, including drums and scrap metal. Thorough knowledge of the locations and nature of hazardous waste containers and contaminated objects is needed prior to the start of remediation efforts. Non-invasive geophysical techniques such as the aeromagnetic method provide the best way to obtain this knowledge. The U.S. Geological Survey (USGS) not only has experience in processing and interpreting aeromagnetic surveys of this type but also offers aid in the design and monitoring of contracts for such surveys.

Identification and characterization of Kaposi's sarcoma-associated herpesvirus open reading frame 11 promotor activation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Lei

2008-01-01

Open reading frame 11 (ORF11) of Kaposi's sarcoma-associated herpesvirus belongs to a herpesviral homologous protein family shared by some members of the gamma- herpesvirus subfamily. Little is known about this ORF11 homologous protein family. We have characterized an unknown open reading frame, ORF11, located adjacent and in the opposite orientation to a well-characterized viral IL-6 gene. Northern blot analysis reveals that ORF11 is expressed during the KSHV lytic cycle with delayed-early transcription kinetics. We have determined the 5{prime} and 3{prime} untranslated region of the unspliced ORF11 transcript and identified both the transcription start site and the transcription termination site. Coremore » promoter region, representing ORF11 promoter activity, was mapped to a 159nt fragment 5{prime} most proximal to the transcription start site. A functional TATA box was identified in the core promoter region. Interestingly, we found that ORF11 transcriptional activation is not responsive to Rta, the KSHV lytic switch protein. We also discovered that part of the ORF11 promoter region, the 209nt fragment upstream of the transcription start site, was repressed by phorbol esters. Our data help to understand transcription regulation of ORF11 and to elucidate roles of ORF11 in KSHV pathogenesis and life cycle.« less

Systematic analysis of transcription start sites in avian development.

PubMed

Lizio, Marina; Deviatiiarov, Ruslan; Nagai, Hiroki; Galan, Laura; Arner, Erik; Itoh, Masayoshi; Lassmann, Timo; Kasukawa, Takeya; Hasegawa, Akira; Ros, Marian A; Hayashizaki, Yoshihide; Carninci, Piero; Forrest, Alistair R R; Kawaji, Hideya; Gusev, Oleg; Sheng, Guojun

2017-09-01

Cap Analysis of Gene Expression (CAGE) in combination with single-molecule sequencing technology allows precision mapping of transcription start sites (TSSs) and genome-wide capture of promoter activities in differentiated and steady state cell populations. Much less is known about whether TSS profiling can characterize diverse and non-steady state cell populations, such as the approximately 400 transitory and heterogeneous cell types that arise during ontogeny of vertebrate animals. To gain such insight, we used the chick model and performed CAGE-based TSS analysis on embryonic samples covering the full 3-week developmental period. In total, 31,863 robust TSS peaks (>1 tag per million [TPM]) were mapped to the latest chicken genome assembly, of which 34% to 46% were active in any given developmental stage. ZENBU, a web-based, open-source platform, was used for interactive data exploration. TSSs of genes critical for lineage differentiation could be precisely mapped and their activities tracked throughout development, suggesting that non-steady state and heterogeneous cell populations are amenable to CAGE-based transcriptional analysis. Our study also uncovered a large set of extremely stable housekeeping TSSs and many novel stage-specific ones. We furthermore demonstrated that TSS mapping could expedite motif-based promoter analysis for regulatory modules associated with stage-specific and housekeeping genes. Finally, using Brachyury as an example, we provide evidence that precise TSS mapping in combination with Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-on technology enables us, for the first time, to efficiently target endogenous avian genes for transcriptional activation. Taken together, our results represent the first report of genome-wide TSS mapping in birds and the first systematic developmental TSS analysis in any amniote species (birds and mammals). By facilitating promoter-based molecular analysis and genetic manipulation, our work also underscores the value of avian models in unravelling the complex regulatory mechanism of cell lineage specification during amniote development.

High-confidence coding and noncoding transcriptome maps

PubMed Central

2017-01-01

The advent of high-throughput RNA sequencing (RNA-seq) has led to the discovery of unprecedentedly immense transcriptomes encoded by eukaryotic genomes. However, the transcriptome maps are still incomplete partly because they were mostly reconstructed based on RNA-seq reads that lack their orientations (known as unstranded reads) and certain boundary information. Methods to expand the usability of unstranded RNA-seq data by predetermining the orientation of the reads and precisely determining the boundaries of assembled transcripts could significantly benefit the quality of the resulting transcriptome maps. Here, we present a high-performing transcriptome assembly pipeline, called CAFE, that significantly improves the original assemblies, respectively assembled with stranded and/or unstranded RNA-seq data, by orienting unstranded reads using the maximum likelihood estimation and by integrating information about transcription start sites and cleavage and polyadenylation sites. Applying large-scale transcriptomic data comprising 230 billion RNA-seq reads from the ENCODE, Human BodyMap 2.0, The Cancer Genome Atlas, and GTEx projects, CAFE enabled us to predict the directions of about 220 billion unstranded reads, which led to the construction of more accurate transcriptome maps, comparable to the manually curated map, and a comprehensive lncRNA catalog that includes thousands of novel lncRNAs. Our pipeline should not only help to build comprehensive, precise transcriptome maps from complex genomes but also to expand the universe of noncoding genomes. PMID:28396519

Fission yeast retrotransposon Tf1 integration is targeted to 5' ends of open reading frames.

PubMed

Behrens, R; Hayles, J; Nurse, P

2000-12-01

Target site selection of transposable elements is usually not random but involves some specificity for a DNA sequence or a DNA binding host factor. We have investigated the target site selection of the long terminal repeat-containing retrotransposon Tf1 from the fission yeast Schizosaccharomyces pombe. By monitoring induced transposition events we found that Tf1 integration sites were distributed throughout the genome. Mapping these insertions revealed that Tf1 did not integrate into open reading frames, but occurred preferentially in longer intergenic regions with integration biased towards a region 100-420 bp upstream of the translation start site. Northern blot analysis showed that transcription of genes adjacent to Tf1 insertions was not significantly changed.

Fission yeast retrotransposon Tf1 integration is targeted to 5′ ends of open reading frames

PubMed Central

Behrens, Ralf; Hayles, Jacky; Nurse, Paul

2000-01-01

Target site selection of transposable elements is usually not random but involves some specificity for a DNA sequence or a DNA binding host factor. We have investigated the target site selection of the long terminal repeat-containing retrotransposon Tf1 from the fission yeast Schizosaccharomyces pombe. By monitoring induced transposition events we found that Tf1 integration sites were distributed throughout the genome. Mapping these insertions revealed that Tf1 did not integrate into open reading frames, but occurred preferentially in longer intergenic regions with integration biased towards a region 100–420 bp upstream of the translation start site. Northern blot analysis showed that transcription of genes adjacent to Tf1 insertions was not significantly changed. PMID:11095681

International Map Year: Results and Implications

NASA Astrophysics Data System (ADS)

Rystedt, Bengt; Ormeling, Ferjan; Buckley, Aileen; Coetzee, Serena; Voženilek, Vit; Fairbairn, David; Kagawa, Ayako

2018-05-01

IMY was a worldwide celebration of maps and their unique role in our world. Supported by the United Nations, IMY provides opportunities to demonstrate, follow, and get involved in the art, science, and technology of making and using maps and geographic information. International Map Year (IMY) started in Paris 2011 when the General Assembly of the International Cartographic Association (ICA) asked the ICA Executive Committee (EC) to follow up on the proposal given in a motion from the Swedish Cartographic Society. An IMY Working Group (WG) was constituted - it defined the IMY goals and the activities required to reach them, and it proposed a suitable time period for the IMY to the ICA EC. IMY commenced in August 2015 and ended in December 2016. The success of IMY was dependent on all member nations of the ICA participating in an effort to broaden the knowledge of cartography and geographic information in society in general, especially among citizens and school children. Member nations of the ICA were responsible for organizing IMY activities, such as a national Map Day, through national IMY committees tasked to engage national organizations and spearheading collaboration. The IMY WG set up an IMY web site with general information on IMY, guidelines for how to organize Map Days, suggestions relating to activities aimed at general map awareness, and more. The web site also provides access to the electronic book The World of Maps, which has been translated from English into five other languages.

Structure of the human gene encoding the protein repair L-isoaspartyl (D-aspartyl) O-methyltransferase.

PubMed

DeVry, C G; Tsai, W; Clarke, S

1996-11-15

The protein L-isoaspartyl/D-aspartyl O-methyltransferase (EC 2.1.1.77) catalyzes the first step in the repair of proteins damaged in the aging process by isomerization or racemization reactions at aspartyl and asparaginyl residues. A single gene has been localized to human chromosome 6 and multiple transcripts arising through alternative splicing have been identified. Restriction enzyme mapping, subcloning, and DNA sequence analysis of three overlapping clones from a human genomic library in bacteriophage P1 indicate that the gene spans approximately 60 kb and is composed of 8 exons interrupted by 7 introns. Analysis of intron/exon splice junctions reveals that all of the donor and acceptor splice sites are in agreement with the mammalian consensus splicing sequence. Determination of transcription initiation sites by primer extension analysis of poly(A)+ mRNA from human brain identifies multiple start sites, with a major site 159 nucleotides upstream from the ATG start codon. Sequence analysis of the 5'-untranslated region demonstrates several potential cis-acting DNA elements including SP1, ETF, AP1, AP2, ARE, XRE, CREB, MED-1, and half-palindromic ERE motifs. The promoter of this methyltransferase gene lacks an identifiable TATA box but is characterized by a CpG island which begins approximately 723 nucleotides upstream of the major transcriptional start site and extends through exon 1 and into the first intron. These features are characteristic of housekeeping genes and are consistent with the wide tissue distribution observed for this methyltransferase activity.

Topography of eye-position sensitivity of saccades evoked electrically from the cat's superior colliculus.

PubMed

McIlwain, J T

1990-03-01

Saccades evoked electrically from the deep layers of the superior colliculus have been examined in the alert cat with its head fixed. Amplitudes of the vertical and horizontal components varied linearly with the starting position of the eye. The slopes of the linear-regression lines provided an estimate of the sensitivity of these components to initial eye position. In observations on 29 sites in nine cats, the vertical and horizontal components of saccades evoked from a given site were rarely influenced to the same degree by initial eye position. For most sites, the horizontal component was more sensitive than the vertical component. Sensitivities of vertical and horizontal components were lowest near the representations of the horizontal and vertical meridians, respectively, of the collicular retinotopic map, but otherwise exhibited no systematic retinotopic dependence. Estimates of component amplitudes for saccades evoked from the center of the oculomotor range also diverged significantly from those predicted from the retinotopic map. The results of this and previous studies indicate that electrical stimulation of the cat's superior colliculus cannot yield a unique oculomotor map or one that is in register everywhere with the sensory retinotopic map. Several features of these observations suggest that electrical stimulation of the colliculus produces faulty activation of a saccadic control system that computes target position with respect to the head and that small and large saccades are controlled differently.

GC-Rich DNA Elements Enable Replication Origin Activity in the Methylotrophic Yeast Pichia pastoris

PubMed Central

Liachko, Ivan; Youngblood, Rachel A.; Tsui, Kyle; Bubb, Kerry L.; Queitsch, Christine; Raghuraman, M. K.; Nislow, Corey; Brewer, Bonita J.; Dunham, Maitreya J.

2014-01-01

The well-studied DNA replication origins of the model budding and fission yeasts are A/T-rich elements. However, unlike their yeast counterparts, both plant and metazoan origins are G/C-rich and are associated with transcription start sites. Here we show that an industrially important methylotrophic budding yeast, Pichia pastoris, simultaneously employs at least two types of replication origins—a G/C-rich type associated with transcription start sites and an A/T-rich type more reminiscent of typical budding and fission yeast origins. We used a suite of massively parallel sequencing tools to map and dissect P. pastoris origins comprehensively, to measure their replication dynamics, and to assay the global positioning of nucleosomes across the genome. Our results suggest that some functional overlap exists between promoter sequences and G/C-rich replication origins in P. pastoris and imply an evolutionary bifurcation of the modes of replication initiation. PMID:24603708

GC-rich DNA elements enable replication origin activity in the methylotrophic yeast Pichia pastoris.

PubMed

Liachko, Ivan; Youngblood, Rachel A; Tsui, Kyle; Bubb, Kerry L; Queitsch, Christine; Raghuraman, M K; Nislow, Corey; Brewer, Bonita J; Dunham, Maitreya J

2014-03-01

The well-studied DNA replication origins of the model budding and fission yeasts are A/T-rich elements. However, unlike their yeast counterparts, both plant and metazoan origins are G/C-rich and are associated with transcription start sites. Here we show that an industrially important methylotrophic budding yeast, Pichia pastoris, simultaneously employs at least two types of replication origins--a G/C-rich type associated with transcription start sites and an A/T-rich type more reminiscent of typical budding and fission yeast origins. We used a suite of massively parallel sequencing tools to map and dissect P. pastoris origins comprehensively, to measure their replication dynamics, and to assay the global positioning of nucleosomes across the genome. Our results suggest that some functional overlap exists between promoter sequences and G/C-rich replication origins in P. pastoris and imply an evolutionary bifurcation of the modes of replication initiation.

Data Delivery and Mapping Over the Web: National Water-Quality Assessment Data Warehouse

USGS Publications Warehouse

Bell, Richard W.; Williamson, Alex K.

2006-01-01

The U.S. Geological Survey began its National Water-Quality Assessment (NAWQA) Program in 1991, systematically collecting chemical, biological, and physical water-quality data from study units (basins) across the Nation. In 1999, the NAWQA Program developed a data warehouse to better facilitate national and regional analysis of data from 36 study units started in 1991 and 1994. Data from 15 study units started in 1997 were added to the warehouse in 2001. The warehouse currently contains and links the following data: -- Chemical concentrations in water, sediment, and aquatic-organism tissues and related quality-control data from the USGS National Water Information System (NWIS), -- Biological data for stream-habitat and ecological-community data on fish, algae, and benthic invertebrates, -- Site, well, and basin information associated with thousands of descriptive variables derived from spatial analysis, like land use, soil, and population density, and -- Daily streamflow and temperature information from NWIS for selected sampling sites.

Systematic data ingratiation of clinical trial recruitment locations for geographic-based query and visualization

PubMed Central

Luo, Jake; Chen, Weiheng; Wu, Min; Weng, Chunhua

2018-01-01

Background Prior studies of clinical trial planning indicate that it is crucial to search and screen recruitment sites before starting to enroll participants. However, currently there is no systematic method developed to support clinical investigators to search candidate recruitment sites according to their interested clinical trial factors. Objective In this study, we aim at developing a new approach to integrating the location data of over one million heterogeneous recruitment sites that are stored in clinical trial documents. The integrated recruitment location data can be searched and visualized using a map-based information retrieval method. The method enables systematic search and analysis of recruitment sites across a large amount of clinical trials. Methods The location data of more than 1.4 million recruitment sites of over 183,000 clinical trials was normalized and integrated using a geocoding method. The integrated data can be used to support geographic information retrieval of recruitment sites. Additionally, the information of over 6000 clinical trial target disease conditions and close to 4000 interventions was also integrated into the system and linked to the recruitment locations. Such data integration enabled the construction of a novel map-based query system. The system will allow clinical investigators to search and visualize candidate recruitment sites for clinical trials based on target conditions and interventions. Results The evaluation results showed that the coverage of the geographic location mapping for the 1.4 million recruitment sites was 99.8%. The evaluation of 200 randomly retrieved recruitment sites showed that the correctness of geographic information mapping was 96.5%. The recruitment intensities of the top 30 countries were also retrieved and analyzed. The data analysis results indicated that the recruitment intensity varied significantly across different countries and geographic areas. Conclusion This study contributed a new data processing framework to extract and integrate the location data of heterogeneous recruitment sites from clinical trial documents. The developed system can support effective retrieval and analysis of potential recruitment sites using target clinical trial factors. PMID:29132636

Systematic data ingratiation of clinical trial recruitment locations for geographic-based query and visualization.

PubMed

Luo, Jake; Chen, Weiheng; Wu, Min; Weng, Chunhua

2017-12-01

Prior studies of clinical trial planning indicate that it is crucial to search and screen recruitment sites before starting to enroll participants. However, currently there is no systematic method developed to support clinical investigators to search candidate recruitment sites according to their interested clinical trial factors. In this study, we aim at developing a new approach to integrating the location data of over one million heterogeneous recruitment sites that are stored in clinical trial documents. The integrated recruitment location data can be searched and visualized using a map-based information retrieval method. The method enables systematic search and analysis of recruitment sites across a large amount of clinical trials. The location data of more than 1.4 million recruitment sites of over 183,000 clinical trials was normalized and integrated using a geocoding method. The integrated data can be used to support geographic information retrieval of recruitment sites. Additionally, the information of over 6000 clinical trial target disease conditions and close to 4000 interventions was also integrated into the system and linked to the recruitment locations. Such data integration enabled the construction of a novel map-based query system. The system will allow clinical investigators to search and visualize candidate recruitment sites for clinical trials based on target conditions and interventions. The evaluation results showed that the coverage of the geographic location mapping for the 1.4 million recruitment sites was 99.8%. The evaluation of 200 randomly retrieved recruitment sites showed that the correctness of geographic information mapping was 96.5%. The recruitment intensities of the top 30 countries were also retrieved and analyzed. The data analysis results indicated that the recruitment intensity varied significantly across different countries and geographic areas. This study contributed a new data processing framework to extract and integrate the location data of heterogeneous recruitment sites from clinical trial documents. The developed system can support effective retrieval and analysis of potential recruitment sites using target clinical trial factors. Copyright © 2017 Elsevier B.V. All rights reserved.

The nucleotide sequence of the putative transcription initiation site of a cloned ribosomal RNA gene of the mouse.

PubMed Central

Urano, Y; Kominami, R; Mishima, Y; Muramatsu, M

1980-01-01

Approximately one kilobase pairs surrounding and upstream the transcription initiation site of a cloned ribosomal DNA (rDNA) of the mouse were sequenced. The putative transcription initiation site was determined by two independent methods: one nuclease S1 protection and the other reverse transcriptase elongation mapping using isolated 45S ribosomal RNA precursor (45S RNA) and appropriate restriction fragments of rDNA. Both methods gave an identical result; 45S RNA had a structure starting from ACTCTTAG---. Characteristically, mouse rDNA had many T clusters (greater than or equal to 5) upstream the initiation site, the longest being 21 consecutive T's. A pentadecanucleotide, TGCCTCCCGAGTGCA, appeared twice within 260 nucleotides upstream the putative initiation site. No such characteristic sequences were found downstream this site. Little similarity was found in the upstream of the transcription initiation site between the mouse, Xenopus laevis and Saccharomyces cerevisiae rDNA. Images PMID:6162156

The DNA-encoded nucleosome organization of a eukaryotic genome.

PubMed

Kaplan, Noam; Moore, Irene K; Fondufe-Mittendorf, Yvonne; Gossett, Andrea J; Tillo, Desiree; Field, Yair; LeProust, Emily M; Hughes, Timothy R; Lieb, Jason D; Widom, Jonathan; Segal, Eran

2009-03-19

Nucleosome organization is critical for gene regulation. In living cells this organization is determined by multiple factors, including the action of chromatin remodellers, competition with site-specific DNA-binding proteins, and the DNA sequence preferences of the nucleosomes themselves. However, it has been difficult to estimate the relative importance of each of these mechanisms in vivo, because in vivo nucleosome maps reflect the combined action of all influencing factors. Here we determine the importance of nucleosome DNA sequence preferences experimentally by measuring the genome-wide occupancy of nucleosomes assembled on purified yeast genomic DNA. The resulting map, in which nucleosome occupancy is governed only by the intrinsic sequence preferences of nucleosomes, is similar to in vivo nucleosome maps generated in three different growth conditions. In vitro, nucleosome depletion is evident at many transcription factor binding sites and around gene start and end sites, indicating that nucleosome depletion at these sites in vivo is partly encoded in the genome. We confirm these results with a micrococcal nuclease-independent experiment that measures the relative affinity of nucleosomes for approximately 40,000 double-stranded 150-base-pair oligonucleotides. Using our in vitro data, we devise a computational model of nucleosome sequence preferences that is significantly correlated with in vivo nucleosome occupancy in Caenorhabditis elegans. Our results indicate that the intrinsic DNA sequence preferences of nucleosomes have a central role in determining the organization of nucleosomes in vivo.

Implementation of the NMR CHEmical Shift Covariance Analysis (CHESCA): A Chemical Biologist's Approach to Allostery.

PubMed

Boulton, Stephen; Selvaratnam, Rajeevan; Ahmed, Rashik; Melacini, Giuseppe

2018-01-01

Mapping allosteric sites is emerging as one of the central challenges in physiology, pathology, and pharmacology. Nuclear Magnetic Resonance (NMR) spectroscopy is ideally suited to map allosteric sites, given its ability to sense at atomic resolution the dynamics underlying allostery. Here, we focus specifically on the NMR CHEmical Shift Covariance Analysis (CHESCA), in which allosteric systems are interrogated through a targeted library of perturbations (e.g., mutations and/or analogs of the allosteric effector ligand). The atomic resolution readout for the response to such perturbation library is provided by NMR chemical shifts. These are then subject to statistical correlation and covariance analyses resulting in clusters of allosterically coupled residues that exhibit concerted responses to the common set of perturbations. This chapter provides a description of how each step in the CHESCA is implemented, starting from the selection of the perturbation library and ending with an overview of different clustering options.

The Wnt-1 (int-1) oncogene promoter and its mechanism of activation by insertion of proviral DNA of the mouse mammary tumor virus.

PubMed Central

Nusse, R; Theunissen, H; Wagenaar, E; Rijsewijk, F; Gennissen, A; Otte, A; Schuuring, E; van Ooyen, A

1990-01-01

Wnt-1 (int-1) is a cellular oncogene often activated by insertion of proviral DNA of the mouse mammary tumor virus. We have mapped the 5' end and the promoter area of the Wnt-1 gene by nuclease protection and primer extension assays. In differentiating P19 embryonal carcinoma cells, in which Wnt-1 is naturally expressed, two start sites of transcription were found, one preceded by two TATA boxes and one preceded by several GC boxes. In P19 cells, a 1-kilobase upstream sequence of Wnt-1 was able to confer differentiation-specific expression on a heterologous gene. We have investigated how Wnt-1 transcription was affected by mouse mammary tumor virus proviral integrations in various configurations near the promoters of the gene. One provirus has been inserted in the 5' nontranslated part of Wnt-1, in the same transcriptional orientation, and has functionally replaced the Wnt-1 promoters. Wnt-1 transcription in this tumor starts in the right long terminal repeat of the provirus, with considerable readthrough transcription from the left long terminal repeat. Another provirus has been inserted in the orientation opposite that of Wnt-1 into a GC box, disrupting the first Wnt-1 transcription start site but not the downstream start site. Most insertions have not structurally altered the Wnt-1 transcripts and have enhanced the activity of the normal two promoters. Images PMID:1695322

Intramural activation and repolarization sequences in canine ventricles. Experimental and simulation studies.

PubMed

Taccardi, Bruno; Punske, Bonnie B; Sachse, Frank; Tricoche, Xavier; Colli-Franzone, Piero; Pavarino, Luca F; Zabawa, Christine

2005-10-01

There are no published data showing the three-dimensional sequence of repolarization and the associated potential fields in the ventricles. Knowledge of the sequence of repolarization has medical relevance because high spatial dispersion of recovery times and action potential durations favors cardiac arrhythmias. In this study we describe measured and simulated 3-D excitation and recovery sequences and activation-recovery intervals (ARIs) (measured) or action potential durations (APDs) (simulated) in the ventricular walls. We recorded from 600 to 1400 unipolar electrograms from canine ventricular walls during atrial and ventricular pacing at 350-450 ms cycle length. Measured excitation and recovery times and ARIs were displayed as 2-D maps in transmural planes or 3-D maps in the volume explored, using specially developed software. Excitation and recovery sequences and APD distributions were also simulated in parallelepipedal slabs using anisotropic monodomain or bidomain models based on the Lou-Rudy version 1 model with homogeneous membrane properties. Simulations showed that in the presence of homogeneous membrane properties, the sequence of repolarization was similar but not identical to the excitation sequence. In a transmural plane perpendicular to epicardial fiber direction, both activation and recovery pathways starting from an epicardial pacing site returned toward the epicardium at a few cm distance from the pacing site. However, APDs were not constant, but had a dispersion of approximately 14 ms in the simulated domain. The maximum APD value was near the pacing site and two minima appeared along a line perpendicular to fiber directions, passing through the pacing site. Electrical measurements in dog ventricles showed that, for short cycle lengths, both excitation and recovery pathways, starting from an epicardial pacing site, returned toward the epicardium. For slower pacing rates, pathways of recovery departed from the pathway of excitation. Highest ARI values were observed near the pacing site in part of the experiments. In addition, maps of activation-recovery intervals showed mid-myocardial clusters with activation-recovery intervals that were slightly longer than ARIs closer to the epi- or endocardium, suggesting the presence of M cells in those areas. Transmural dispersion of measured ARIs was on the order of 20-25 ms. Potential distributions during recovery were less affected by myocardial anisotropy than were excitation potentials.

ACTG: novel peptide mapping onto gene models.

PubMed

Choi, Seunghyuk; Kim, Hyunwoo; Paek, Eunok

2017-04-15

In many proteogenomic applications, mapping peptide sequences onto genome sequences can be very useful, because it allows us to understand origins of the gene products. Existing software tools either take the genomic position of a peptide start site as an input or assume that the peptide sequence exactly matches the coding sequence of a given gene model. In case of novel peptides resulting from genomic variations, especially structural variations such as alternative splicing, these existing tools cannot be directly applied unless users supply information about the variant, either its genomic position or its transcription model. Mapping potentially novel peptides to genome sequences, while allowing certain genomic variations, requires introducing novel gene models when aligning peptide sequences to gene structures. We have developed a new tool called ACTG (Amino aCids To Genome), which maps peptides to genome, assuming all possible single exon skipping, junction variation allowing three edit distances from the original splice sites, exon extension and frame shift. In addition, it can also consider SNVs (single nucleotide variations) during mapping phase if a user provides the VCF (variant call format) file as an input. Available at http://prix.hanyang.ac.kr/ACTG/search.jsp . eunokpaek@hanyang.ac.kr. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Fish assemblage composition and mapped mesohabitat features over a range of streamflows in the Middle Rio Grande, New Mexico, winter 2011-12, summer 2012

USGS Publications Warehouse

Pearson, Daniel K.; Braun, Christopher L.; Moring, J. Bruce

2016-01-21

This report documents differences in the mapped spatial extents and physical characteristics of in-channel fish habitat evaluated at the mesohabitat scale during winter 2011–12 (moderate streamflow) and summer 2012 (low streamflow) at 15 sites on the Middle Rio Grande in New Mexico starting about 3 kilometers downstream from Cochiti Dam and ending about 40 kilometers upstream from Elephant Butte Reservoir. The results of mesohabitat mapping, physical characterization, and fish assemblage surveys are summarized from the data that were collected. The report also presents general comparisons of physical mesohabitat data, such as wetted area and substrate type, and biological mesohabitat data, which included fish assemblage composition, species richness, Rio Grande silvery minnow relative abundance, and Rio Grande silvery minnow catch per unit effort.

Molecular Targeting of Prostate Cancer During Androgen Ablation: Inhibition of CHES1/FOXN3

DTIC Science & Technology

2013-05-01

the DNA sequences (~25^6 reads/sample) were mapped to the human genome reference sequence (hg19...tumor the AR has a genomic abnormality, placing the novel sequence 3’ of the transcriptional start site. However, it is unclear if a genomic alteration...exon/intron organization of the CHES1 gene was determined by BLAST analysis of the human genome using the 1,473-bp CHES1 cDNA sequence

Coherent exciton transport in dendrimers and continuous-time quantum walks

NASA Astrophysics Data System (ADS)

Mülken, Oliver; Bierbaum, Veronika; Blumen, Alexander

2006-03-01

We model coherent exciton transport in dendrimers by continuous-time quantum walks. For dendrimers up to the second generation the coherent transport shows perfect recurrences when the initial excitation starts at the central node. For larger dendrimers, the recurrence ceases to be perfect, a fact which resembles results for discrete quantum carpets. Moreover, depending on the initial excitation site, we find that the coherent transport to certain nodes of the dendrimer has a very low probability. When the initial excitation starts from the central node, the problem can be mapped onto a line which simplifies the computational effort. Furthermore, the long time average of the quantum mechanical transition probabilities between pairs of nodes shows characteristic patterns and allows us to classify the nodes into clusters with identical limiting probabilities. For the (space) average of the quantum mechanical probability to be still or to be again at the initial site, we obtain, based on the Cauchy-Schwarz inequality, a simple lower bound which depends only on the eigenvalue spectrum of the Hamiltonian.

Ub-ISAP: a streamlined UNIX pipeline for mining unique viral vector integration sites from next generation sequencing data.

PubMed

Kamboj, Atul; Hallwirth, Claus V; Alexander, Ian E; McCowage, Geoffrey B; Kramer, Belinda

2017-06-17

The analysis of viral vector genomic integration sites is an important component in assessing the safety and efficiency of patient treatment using gene therapy. Alongside this clinical application, integration site identification is a key step in the genetic mapping of viral elements in mutagenesis screens that aim to elucidate gene function. We have developed a UNIX-based vector integration site analysis pipeline (Ub-ISAP) that utilises a UNIX-based workflow for automated integration site identification and annotation of both single and paired-end sequencing reads. Reads that contain viral sequences of interest are selected and aligned to the host genome, and unique integration sites are then classified as transcription start site-proximal, intragenic or intergenic. Ub-ISAP provides a reliable and efficient pipeline to generate large datasets for assessing the safety and efficiency of integrating vectors in clinical settings, with broader applications in cancer research. Ub-ISAP is available as an open source software package at https://sourceforge.net/projects/ub-isap/ .

A novel intra-operative, high-resolution atrial mapping approach.

PubMed

Yaksh, Ameeta; van der Does, Lisette J M E; Kik, Charles; Knops, Paul; Oei, Frans B S; van de Woestijne, Pieter C; Bekkers, Jos A; Bogers, Ad J J C; Allessie, Maurits A; de Groot, Natasja M S

2015-12-01

A new technique is demonstrated for extensive high-resolution intra-operative atrial mapping that will facilitate the localization of atrial fibrillation (AF) sources and identification of the substrate perpetuating AF. Prior to the start of extra-corporal circulation, a 8 × 24-electrode array (2-mm inter-electrode distance) is placed subsequently on all the right and left epicardial atrial sites, including Bachmann's bundle, for recording of unipolar electrograms during sinus rhythm and (induced) AF. AF is induced by high-frequency pacing at the right atrial free wall. A pacemaker wire stitched to the right atrium serves as a reference signal. The indifferent pole is connected to a steal wire fixed to subcutaneous tissue. Electrograms are recorded by a computerized mapping system and, after amplification (gain 1000), filtering (bandwidth 0.5-400 Hz), sampling (1 kHz) and analogue to digital conversion (16 bits), automatically stored on hard disk. During the mapping procedure, real-time visualization secures electrogram quality. Analysis will be performed offline. This technique was performed in 168 patients of 18 years and older, with coronary and/or structural heart disease, with or without AF, electively scheduled for cardiac surgery and a ventricular ejection fraction above 40 %. The mean duration of the entire mapping procedure including preparation time was 9 ± 2 min. Complications related to the mapping procedure during or after cardiac surgery were not observed. We introduce the first epicardial atrial mapping approach with a high resolution of ≥1728 recording sites which can be performed in a procedure time of only 9±2 mins. This mapping technique can potentially identify areas responsible for initiation and persistence of AF and hopefully can individualize both diagnosis and therapy of AF.

Nucleotide sequence and transcriptional start site of the Methylobacterium organophilum XX methanol dehydrogenase structural gene

DOE Office of Scientific and Technical Information (OSTI.GOV)

Machlin, S.M.; Hanson, R.S.

The nucleotide sequence of a cloned 2.5-kilobase-pair SmaI fragment containing the methanol dehydrogenase (MDH) structural gene from Methylobacterium organophilum XX was determined. A single open reading frame with a coding capacity of 626 amino acids (molecular weight, 66,000) was identified on one stand, and N-terminal sequencing of purified MDH revealed that 27 of these residues constituted a putative signal peptide. Primer extension mapping of in vivo transcripts indicated that the start of mRNA synthesis was 160 to 170 base pairs upstream of the ATG codon. Northern (RNA) blot analysis further demonstrated that the transcript was 2.1 kilobase pairs in lengthmore » and therefore appeared to encode only MDH.« less

Genome-wide identification and characterisation of human DNA replication origins by initiation site sequencing (ini-seq)

PubMed Central

Langley, Alexander R.; Gräf, Stefan; Smith, James C.; Krude, Torsten

2016-01-01

Next-generation sequencing has enabled the genome-wide identification of human DNA replication origins. However, different approaches to mapping replication origins, namely (i) sequencing isolated small nascent DNA strands (SNS-seq); (ii) sequencing replication bubbles (bubble-seq) and (iii) sequencing Okazaki fragments (OK-seq), show only limited concordance. To address this controversy, we describe here an independent high-resolution origin mapping technique that we call initiation site sequencing (ini-seq). In this approach, newly replicated DNA is directly labelled with digoxigenin-dUTP near the sites of its initiation in a cell-free system. The labelled DNA is then immunoprecipitated and genomic locations are determined by DNA sequencing. Using this technique we identify >25,000 discrete origin sites at sub-kilobase resolution on the human genome, with high concordance between biological replicates. Most activated origins identified by ini-seq are found at transcriptional start sites and contain G-quadruplex (G4) motifs. They tend to cluster in early-replicating domains, providing a correlation between early replication timing and local density of activated origins. Origins identified by ini-seq show highest concordance with sites identified by SNS-seq, followed by OK-seq and bubble-seq. Furthermore, germline origins identified by positive nucleotide distribution skew jumps overlap with origins identified by ini-seq and OK-seq more frequently and more specifically than do sites identified by either SNS-seq or bubble-seq. PMID:27587586

Genome-wide identification and characterisation of human DNA replication origins by initiation site sequencing (ini-seq).

PubMed

Langley, Alexander R; Gräf, Stefan; Smith, James C; Krude, Torsten

2016-12-01

Next-generation sequencing has enabled the genome-wide identification of human DNA replication origins. However, different approaches to mapping replication origins, namely (i) sequencing isolated small nascent DNA strands (SNS-seq); (ii) sequencing replication bubbles (bubble-seq) and (iii) sequencing Okazaki fragments (OK-seq), show only limited concordance. To address this controversy, we describe here an independent high-resolution origin mapping technique that we call initiation site sequencing (ini-seq). In this approach, newly replicated DNA is directly labelled with digoxigenin-dUTP near the sites of its initiation in a cell-free system. The labelled DNA is then immunoprecipitated and genomic locations are determined by DNA sequencing. Using this technique we identify >25,000 discrete origin sites at sub-kilobase resolution on the human genome, with high concordance between biological replicates. Most activated origins identified by ini-seq are found at transcriptional start sites and contain G-quadruplex (G4) motifs. They tend to cluster in early-replicating domains, providing a correlation between early replication timing and local density of activated origins. Origins identified by ini-seq show highest concordance with sites identified by SNS-seq, followed by OK-seq and bubble-seq. Furthermore, germline origins identified by positive nucleotide distribution skew jumps overlap with origins identified by ini-seq and OK-seq more frequently and more specifically than do sites identified by either SNS-seq or bubble-seq. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

The Tianlai 21cm intensity mapping experiment

NASA Astrophysics Data System (ADS)

Chen, Xuelei

2015-08-01

The Tianlai 21cm intensity mapping experiment is aimed at surveying the northern sky 21cm intensity at mid-redshifts, thus map out the neutral hydrogen distribution. The experiment is named "Tianlai" which means "heavenly sound" in classic Chinese, because its ultimate goal is to use the baryon acoustic oscillation (BAO) feature in the correlation function or power spectrum of large scale structure to constrain the cosmic expansion rate, and determine the nature of dark energy.The pathfinder experiment consists three cylinder reflectors of 15m wide x 40m long, and 16 dishes of 6 meter aperture, for testing the basic principle and key technologies. A radio-quiet site in Hongliuxia, Xinjiang of north-west China is selected, currently the facilities are under construction, and the prototype is expected to start commissioning later this year. The experiment is run by NAOC, with members from France, USA and Canada.

Recent Advancements in DNA Damage-Transcription Crosstalk and High-Resolution Mapping of DNA Breaks.

PubMed

Vitelli, Valerio; Galbiati, Alessandro; Iannelli, Fabio; Pessina, Fabio; Sharma, Sheetal; d'Adda di Fagagna, Fabrizio

2017-08-31

Until recently, DNA damage arising from physiological DNA metabolism was considered a detrimental by-product for cells. However, an increasing amount of evidence has shown that DNA damage could have a positive role in transcription activation. In particular, DNA damage has been detected in transcriptional elements following different stimuli. These physiological DNA breaks are thought to be instrumental for the correct expression of genomic loci through different mechanisms. In this regard, although a plethora of methods are available to precisely map transcribed regions and transcription start sites, commonly used techniques for mapping DNA breaks lack sufficient resolution and sensitivity to draw a robust correlation between DNA damage generation and transcription. Recently, however, several methods have been developed to map DNA damage at single-nucleotide resolution, thus providing a new set of tools to correlate DNA damage and transcription. Here, we review how DNA damage can positively regulate transcription initiation, the current techniques for mapping DNA breaks at high resolution, and how these techniques can benefit future studies of DNA damage and transcription.

Emergence of dominant initiation sites for interictal spikes in rat neocortex

PubMed Central

Vitantonio, Daniel; Xu, Weifeng; Geng, Xinling; Wolff, Brian S.; Takagaki, Kentaroh; Motamedi, Gholam K.

2015-01-01

Neuronal populations with unbalanced inhibition can generate interictal spikes (ISs), where each IS starts from a small initiation site and then spreads activation across a larger area. We used in vivo voltage-sensitive dye imaging to map the initiation site of ISs in rat visual cortex disinhibited by epidural application of bicuculline methiodide. Immediately after the application of bicuculline, the IS initiation sites were widely distributed over the entire disinhibited area. After ∼10 min, a small number of sites became “dominant” and initiated the majority of the ISs throughout the course of imaging. Such domination also occurred in cortical slices, which lack long-range connections between the cortex and subcortical structures. This domination of IS initiation sites may allow timing-related plasticity mechanisms to provide a spatial organization where connections projecting outward from the dominant initiation site become strengthened. Understanding the spatiotemporal organization of IS initiation sites may contribute to our understanding of epileptogenesis in its very early stages, because a dominant IS initiation site with strengthened outward connectivity may ultimately develop into a seizure focus. PMID:26445866

The chicken skeletal alpha-actin gene promoter region exhibits partial dyad symmetry and a capacity to drive bidirectional transcription.

PubMed Central

Grichnik, J M; French, B A; Schwartz, R J

1988-01-01

The chicken skeletal alpha-actin gene promoter region (-202 to -12) provides myogenic transcriptional specificity. This promoter contains partial dyad symmetry about an axis at nucleotide -108 and in transfection experiments is capable of directing transcription in a bidirectional manner. At least three different transcription initiation start sites, oriented toward upstream sequences, were mapped 25 to 30 base pairs from TATA-like regions. The opposing transcriptional activity was potentiated upon the deletion of sequences proximal to the alpha-actin transcription start site. Thus, sequences which serve to position RNA polymerase for alpha-actin transcription may allow, in their absence, the selection of alternative and reverse-oriented start sites. Nuclear runoff transcription assays of embryonic muscle indicated that divergent transcription may occur in vivo but with rapid turnover of nuclear transcripts. Divergent transcriptional activity enabled us to define the 3' regulatory boundary of the skeletal alpha-actin promoter which retains a high level of myogenic transcriptional activity. The 3' regulatory border was detected when serial 3' deletions bisected the element (-91 CCAAA TATGG -82) which reduced transcriptional activity by 80%. Previously we showed that disruption of its upstream counterpart (-127 CCAAAGAAGG -136) resulted in about a 90% decrease in activity. These element pairs, which we describe as CCAAT box-associated repeats, are conserved in all sequenced vertebrate sarcomeric actin genes and may act in a cooperative manner to facilitate transcription in myogenic cells. Images PMID:3211124

In vitro transcription of a cloned mouse ribosomal RNA gene.

PubMed Central

Mishima, Y; Yamamoto, O; Kominami, R; Muramatsu, M

1981-01-01

An in vitro transcription system which utilizes cloned mouse ribosomal RNA gene (rDNA) fragments and a mouse cell extract has been developed. RNA polymerases I is apparently responsible for this transcription as evidenced by the complete resistance to a high concentration (200 micrograms/ml) of alpha-amanitin. Run-off products obtained with three different truncated rDNA fragments indicated that RNA was transcribed from a unique site of rDNA. The S1 nuclease protection mapping of the in vitro product and of in vivo 45S RNA confirmed this site, indicating that, in this in vitro system, transcription of rDNA started from the same site as in vivo. This site is located at several hundred nucleotides upstream from the putative initiation site reported by us (1) and by others (2). Some sequence homology surrounding this region was noted among mouse, Xenopus laevis and Drosophila melanogaster. The data also suggest that some processing of the primary transcript occurs in this in vitro system. Images PMID:6278446

X-Linked Syndrome of Polyendocrinopathy, Immune Dysfunction, and Diarrhea Maps to Xp11.23-Xq13.3

PubMed Central

Bennett, Craig L.; Yoshioka, Ritsuko; Kiyosawa, Hidenori; Barker, David F.; Fain, Pamela R.; Shigeoka, Ann O.; Chance, Phillip F.

2000-01-01

Summary We describe genetic analysis of a large pedigree with an X-linked syndrome of polyendocrinopathy, immune dysfunction, and diarrhea (XPID), which frequently results in death during infancy or childhood. Linkage analysis mapped the XPID gene to a 17-cM interval defined by markers DXS8083 and DXS8107 on the X chromosome, at Xp11.23-Xq13.3. The maximum LOD score was 3.99 (recombination fraction0) at DXS1235. Because this interval also harbors the gene for Wiskott-Aldrich syndrome (WAS), we investigated mutations in the WASP gene, as the molecular basis of XPID. Northern blot analysis detected the same relative amount and the same-sized WASP message in patients with XPID and in a control. Analysis of the WASP coding sequence, an alternate promoter, and an untranslated upstream first exon was carried out, and no mutations were found in patients with XPID. A C→T transition within the alternate translation start site cosegregated with the XPID phenotype in this family; however, the same transition site was detected in a normal control male. We conclude that XPID maps to Xp11.23-Xq13.3 and that mutations of WASP are not associated with XPID. PMID:10677306

FEM: Feature-enhanced map

DOE Office of Scientific and Technical Information (OSTI.GOV)

Afonine, Pavel V.; Moriarty, Nigel W.; Mustyakimov, Marat

A method is presented that modifies a 2 m F obs- D F modelσ A-weighted map such that the resulting map can strengthen a weak signal, if present, and can reduce model bias and noise. The method consists of first randomizing the starting map and filling in missing reflections using multiple methods. This is followed by restricting the map to regions with convincing density and the application of sharpening. The final map is then created by combining a series of histogram-equalized intermediate maps. In the test cases shown, the maps produced in this way are found to have increased interpretabilitymore » and decreased model bias compared with the starting 2 m F obs- D F modelσ A-weighted map.« less

FEM: feature-enhanced map

PubMed Central

Afonine, Pavel V.; Moriarty, Nigel W.; Mustyakimov, Marat; Sobolev, Oleg V.; Terwilliger, Thomas C.; Turk, Dusan; Urzhumtsev, Alexandre; Adams, Paul D.

2015-01-01

A method is presented that modifies a 2m F obs − D F model σA-weighted map such that the resulting map can strengthen a weak signal, if present, and can reduce model bias and noise. The method consists of first randomizing the starting map and filling in missing reflections using multiple methods. This is followed by restricting the map to regions with convincing density and the application of sharpening. The final map is then created by combining a series of histogram-equalized intermediate maps. In the test cases shown, the maps produced in this way are found to have increased interpretability and decreased model bias compared with the starting 2m F obs − D F model σA-weighted map. PMID:25760612

FEM: Feature-enhanced map

DOE PAGES

Afonine, Pavel V.; Moriarty, Nigel W.; Mustyakimov, Marat; ...

2015-02-26

A method is presented that modifies a 2 m F obs- D F modelσ A-weighted map such that the resulting map can strengthen a weak signal, if present, and can reduce model bias and noise. The method consists of first randomizing the starting map and filling in missing reflections using multiple methods. This is followed by restricting the map to regions with convincing density and the application of sharpening. The final map is then created by combining a series of histogram-equalized intermediate maps. In the test cases shown, the maps produced in this way are found to have increased interpretabilitymore » and decreased model bias compared with the starting 2 m F obs- D F modelσ A-weighted map.« less

Intraoperative language localization in multilingual patients with gliomas.

PubMed

Bello, Lorenzo; Acerbi, Francesco; Giussani, Carlo; Baratta, Pietro; Taccone, Paolo; Songa, Valeria; Fava, Marica; Stocchetti, Nino; Papagno, Costanza; Gaini, Sergio M

2006-07-01

Intraoperative localization of speech is problematic in patients who are fluent in different languages. Previous studies have generated various results depending on the series of patients studied, the type of language, and the sensitivity of the tasks applied. It is not clear whether languages are mediated by multiple and separate cortical areas or shared by common areas. Globally considered, previous studies recommended performing a multiple intraoperative mapping for all the languages in which the patient is fluent. The aim of this work was to study the feasibility of performing an intraoperative multiple language mapping in a group of multilingual patients with a glioma undergoing awake craniotomy for tumor removal and to describe the intraoperative cortical and subcortical findings in the area of craniotomy, with the final goal to maximally preserve patients' functional language. Seven late, highly proficient multilingual patients with a left frontal glioma were submitted preoperatively to a battery of tests to evaluate oral language production, comprehension, and repetition. Each language was tested serially starting from the first acquired language. Items that were correctly named during these tests were used to build personalized blocks to be used intraoperatively. Language mapping was undertaken during awake craniotomies by the use of an Ojemann cortical stimulator during counting and oral naming tasks. Subcortical stimulation by using the same current threshold was applied during tumor resection, in a back and forth fashion, and the same tests. Cortical sites essential for oral naming were found in 87.5% of patients, those for the first acquired language in one to four sites, those for the other languages in one to three sites. Sites for each language were distinct and separate. Number and location of sites were not predictable, being randomly and widely distributed in the cortex around or less frequently over the tumor area. Subcortical stimulations found tracts for the first acquired language in four patients and for the other languages in three patients. Three of these patients decreased their fluency immediately after surgery, affecting the first acquired language, which fully recovered in two patients and partially in one. The procedure was agile and well tolerated by the patients. These findings show that multiple cortical and subcortical language mapping during awake craniotomy for tumor removal is a feasible procedure. They support the concept that intraoperative mapping should be performed for all the languages in which the patient is fluent in to preserve functional integrity.

Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer.

PubMed

Kim, Jung H; Dhanasekaran, Saravana M; Prensner, John R; Cao, Xuhong; Robinson, Daniel; Kalyana-Sundaram, Shanker; Huang, Christina; Shankar, Sunita; Jing, Xiaojun; Iyer, Matthew; Hu, Ming; Sam, Lee; Grasso, Catherine; Maher, Christopher A; Palanisamy, Nallasivam; Mehra, Rohit; Kominsky, Hal D; Siddiqui, Javed; Yu, Jindan; Qin, Zhaohui S; Chinnaiyan, Arul M

2011-07-01

Beginning with precursor lesions, aberrant DNA methylation marks the entire spectrum of prostate cancer progression. We mapped the global DNA methylation patterns in select prostate tissues and cell lines using MethylPlex-next-generation sequencing (M-NGS). Hidden Markov model-based next-generation sequence analysis identified ∼68,000 methylated regions per sample. While global CpG island (CGI) methylation was not differential between benign adjacent and cancer samples, overall promoter CGI methylation significantly increased from ~12.6% in benign samples to 19.3% and 21.8% in localized and metastatic cancer tissues, respectively (P-value < 2 × 10(-16)). We found distinct patterns of promoter methylation around transcription start sites, where methylation occurred not only on the CGIs, but also on flanking regions and CGI sparse promoters. Among the 6691 methylated promoters in prostate tissues, 2481 differentially methylated regions (DMRs) are cancer-specific, including numerous novel DMRs. A novel cancer-specific DMR in the WFDC2 promoter showed frequent methylation in cancer (17/22 tissues, 6/6 cell lines), but not in the benign tissues (0/10) and normal PrEC cells. Integration of LNCaP DNA methylation and H3K4me3 data suggested an epigenetic mechanism for alternate transcription start site utilization, and these modifications segregated into distinct regions when present on the same promoter. Finally, we observed differences in repeat element methylation, particularly LINE-1, between ERG gene fusion-positive and -negative cancers, and we confirmed this observation using pyrosequencing on a tissue panel. This comprehensive methylome map will further our understanding of epigenetic regulation in prostate cancer progression.

Mapped Landmark Algorithm for Precision Landing

NASA Technical Reports Server (NTRS)

Johnson, Andrew; Ansar, Adnan; Matthies, Larry

2007-01-01

A report discusses a computer vision algorithm for position estimation to enable precision landing during planetary descent. The Descent Image Motion Estimation System for the Mars Exploration Rovers has been used as a starting point for creating code for precision, terrain-relative navigation during planetary landing. The algorithm is designed to be general because it handles images taken at different scales and resolutions relative to the map, and can produce mapped landmark matches for any planetary terrain of sufficient texture. These matches provide a measurement of horizontal position relative to a known landing site specified on the surface map. Multiple mapped landmarks generated per image allow for automatic detection and elimination of bad matches. Attitude and position can be generated from each image; this image-based attitude measurement can be used by the onboard navigation filter to improve the attitude estimate, which will improve the position estimates. The algorithm uses normalized correlation of grayscale images, producing precise, sub-pixel images. The algorithm has been broken into two sub-algorithms: (1) FFT Map Matching (see figure), which matches a single large template by correlation in the frequency domain, and (2) Mapped Landmark Refinement, which matches many small templates by correlation in the spatial domain. Each relies on feature selection, the homography transform, and 3D image correlation. The algorithm is implemented in C++ and is rated at Technology Readiness Level (TRL) 4.

The Siná river delta on the northwestern Caribbean coast of Colombia: Bay infilling associated with delta development

NASA Astrophysics Data System (ADS)

Suarez, Beatriz Elena Serrano

2004-04-01

Between 1938 and 1945, the Sinú River changed its course and started a new delta at a site known as Tinajones. The change took place after the infilling of Cispata Bay, the site of the previous delta. The infilling is studied with two isopach maps made from bathymetric charts from 1762, 1849, and 1938. The isopachs help show the distribution of the sediments inside the bay and provide estimations of sedimentation rates. The results are compared with the sediment distribution and estimated sedimentation rate found for the delta at Tinajones. The results suggest that the infilling of the Cispata Bay produced the river avulsion and the change to Tinajones and probably was accelerated by sediments that came from outside the bay.

Unmanned Aerial Vehicle (UAV) Data Acquisition for Archaeological Site Identification and Mapping

NASA Astrophysics Data System (ADS)

Handayani, W.; Ayuningtyas, E. A.; Candra R, F. S.; Arif S, B.; Argadyanto, B.

2017-12-01

Archaeological sites as part of human history and located around community are important to be preserved for connecting historical information from generation to generation. Mapping of archaeological sites can be done as one of preservation efforts. Yogyakarta has several archaeological sites such as Pleret Palace, the former royal palace of Mataram Islam in the 16th Century. Data limitations and the difficulty of reconstructing the site sketches into a map become obstacles in archaeological sites mapping. Unmanned Aerial Vehicle (UAV) can be an alternative of high-resolution spatial data acquisition for detail mapping, including archaeological sites mapping. This study aims to see how far the UAV acquisition results can be used for Archaeological Site mapping in Pleret Palace. Data acquisition using UAV generated to mosaic orthophoto, Digital Surface Model (DSM), and Digital Terrain Model (DTM). Archaeological sites identified using DTM and matched with site sketch made by Cultural Agency. From these data, it can be recognized some relics form, such as palace fortress, moats and canals, and also dikes of Segarayasa. This research is expected to be a reference in archaeological site mapping using detailed spatial data, especially UAV. Furthermore, it can be obtained archaeological site map close to real condition; as well as archaeological sites preservation in Indonesia.

Spirit's Course

NASA Technical Reports Server (NTRS)

2004-01-01

[figure removed for brevity, see original site] [figure removed for brevity, see original site] Figure 1Figure 2

This digital elevation map shows the topography of the 'Columbia Hills,' just in front of the Mars Exploration Rover Spirit's current position. Rover planners have plotted the safest route for Spirit to climb to the front hill, called 'West Spur.' The black line in the middle of the image represents the rover's traverse path, which starts at 'Hank's Hollow' and ends at the top of 'West Spur.' Scientists are sending Spirit up the hill to investigate the interesting rock outcrops visible in images taken by the rover. Data from the Mars Orbital Camera on the orbiting Mars Global Surveyor were used to create this 3-D map.

In figure 1, the digital map shows the slopes of the 'Columbia Hills,' just in front of the Mars Exploration Rover Spirit's current position. Colors indicate the slopes of the hills, with red areas being the gentlest and blue the steepest. Rover planners have plotted the safest route for Spirit to climb the front hill, called 'West Spur.' The path is indicated here with a curved black line. Stereo images from the Mars Orbital Camera on the orbiting Mars Global Surveyor were used to create this 3-D map.

In figure 2, the map shows the north-facing slopes of the 'Columbia Hills,' just in front of the Mars Exploration Rover Spirit's current position. Bright areas indicate surfaces sloping more toward the north than dark areas. To reach the rock outcrop at the top of the hill, engineers will aim to drive the rover around the dark areas, which would yield less solar power. The curved black line in the middle represents the rover's planned traverse path.

Structural analysis of the 5{prime} region of mouse and human Huntington disease genes reveals conservation of putative promoter region and Di- and trinucleotide polymorphisms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lin, Biaoyang; Nasir, J.; Kalchman, M.A.

1995-02-10

We have previously cloned and characterized the murine homologue of the Huntington disease (HD) gene and shown that it maps to mouse chromosome 5 within a region of conserved synteny with human chromosome 4p16.3. Here we present a detailed comparison of the sequence of the putative promoter and the organization of the 5{prime} genomic region of the murine (Hdh) and human HD genes encompassing the first five exons. We show that in this region these two genes share identical exon boundaries, but have different-size introns. Two dinucleotide (CT) and one trinucleotide intronic polymorphism in Hdh and an intronic CA polymorphismmore » in the HD gene were identified. Comparison of 940-bp sequence 5{prime} to the putative translation start site reveals a highly conserved region (78.8% nucleotide identity) between Hdh and the HD gene from nucleotide -56 to -206 (of Hdh). Neither Hdh nor the HD gene have typical TATA or CCAAT elements, but both show one putative AP2 binding site and numerous potential Sp1 binding sites. The high sequence identity between Hdh and the HD gene for approximately 200 bp 5{prime} to the putative translation start site indicates that these sequences may play a role in regulating expression of the Huntington disease gene. 30 refs., 4 figs., 2 tabs.« less

PreTIS: A Tool to Predict Non-canonical 5’ UTR Translational Initiation Sites in Human and Mouse

PubMed Central

Reuter, Kerstin; Helms, Volkhard

2016-01-01

Translation of mRNA sequences into proteins typically starts at an AUG triplet. In rare cases, translation may also start at alternative non–AUG codons located in the annotated 5’ UTR which leads to an increased regulatory complexity. Since ribosome profiling detects translational start sites at the nucleotide level, the properties of these start sites can then be used for the statistical evaluation of functional open reading frames. We developed a linear regression approach to predict in–frame and out–of–frame translational start sites within the 5’ UTR from mRNA sequence information together with their translation initiation confidence. Predicted start codons comprise AUG as well as near–cognate codons. The underlying datasets are based on published translational start sites for human HEK293 and mouse embryonic stem cells that were derived by the original authors from ribosome profiling data. The average prediction accuracy of true vs. false start sites for HEK293 cells was 80%. When applied to mouse mRNA sequences, the same model predicted translation initiation sites observed in mouse ES cells with an accuracy of 76%. Moreover, we illustrate the effect of in silico mutations in the flanking sequence context of a start site on the predicted initiation confidence. Our new webservice PreTIS visualizes alternative start sites and their respective ORFs and predicts their ability to initiate translation. Solely, the mRNA sequence is required as input. PreTIS is accessible at http://service.bioinformatik.uni-saarland.de/pretis. PMID:27768687

Precise assignment of the heavy-strand promoter of mouse mitochondrial DNA: cognate start sites are not required for transcriptional initiation.

PubMed Central

Chang, D D; Clayton, D A

1986-01-01

Transcription of the heavy strand of mouse mitochondrial DNA starts from two closely spaced, distinct sites located in the displacement loop region of the genome. We report here an analysis of regulatory sequences required for faithful transcription from these two sites. Data obtained from in vitro assays demonstrated that a 51-base-pair region, encompassing nucleotides -40 to +11 of the downstream start site, contains sufficient information for accurate transcription from both start sites. Deletion of the 3' flanking sequences, including one or both start sites to -17, resulted in the initiation of transcription by the mitochondrial RNA polymerase from alternative sites within vector DNA sequences. This feature places the mouse heavy-strand promoter uniquely among other known mitochondrial promoters, all of which absolutely require cognate start sites for transcription. Comparison of the heavy-strand promoter with those of other vertebrate mitochondrial DNAs revealed a remarkably high rate of sequence divergence among species. Images PMID:3785226

Story Map Instruction: A Road Map for Reading Comprehension.

ERIC Educational Resources Information Center

Davis, Zephaniah, T.; McPherson, Michael D.

1989-01-01

Introduces teachers to the development and use of story maps as a tool for promoting reading comprehension. Presents a definition and review of story map research. Explains how to construct story maps, and offers suggestions for starting story map instruction. Provides variations on the use of story maps. (MG)

Regulation of transcription of the cell division gene ftsA during sporulation of Bacillus subtilis.

PubMed Central

Gholamhoseinian, A; Shen, Z; Wu, J J; Piggot, P

1992-01-01

Three distinct 5' ends of ftsA mRNA were identified by S1 mapping and by primer extension analysis. These are thought to represent three transcription start sites. The transcripts from the downstream and upstream sites were detected throughout growth. The transcript from the middle site was not detected during exponential growth but was detected within 30 min of the start of sporulation, when it was the predominant transcript. Insertion of a cat cassette in the middle promoter, ftsAp2 (p2), did not affect vegetative growth but prevented postexponential symmetrical division and spore formation. Transcription from p2 was dependent on RNA polymerase containing sigma H, and promoter p2 resembled the consensus sigma H promoter. Transcription from p2 did not require expression of the spo0A, spo0B, spo0E, spo0F, or spo0K loci. Northern (RNA) blot analysis indicated that ftsA is cotranscribed with the adjacent ftsZ gene. Multiple promoters provide a mechanism by which essential vegetative genes can be subjected to sporulation control independent of control during vegetative growth. In the case of ftsA,Z, the promoters provide a mechanism to permit septum formation in conditions of nutrient depletion that might be expected to shut down the vegetative division machinery. Images PMID:1624452

Plans for a sensitivity analysis of bridge-scour computations

USGS Publications Warehouse

Dunn, David D.; Smith, Peter N.

1993-01-01

Plans for an analysis of the sensitivity of Level 2 bridge-scour computations are described. Cross-section data from 15 bridge sites in Texas are modified to reflect four levels of field effort ranging from no field surveys to complete surveys. Data from United States Geological Survey (USGS) topographic maps will be used to supplement incomplete field surveys. The cross sections are used to compute the water-surface profile through each bridge for several T-year recurrence-interval design discharges. The effect of determining the downstream energy grade-line slope from topographic maps is investigated by systematically varying the starting slope of each profile. The water-surface profile analyses are then used to compute potential scour resulting from each of the design discharges. The planned results will be presented in the form of exceedance-probability versus scour-depth plots with the maximum and minimum scour depths at each T-year discharge presented as error bars.

New Explorer-class AUV Ready for Deep-water, High-resolution Habitat Mapping Studies

NASA Astrophysics Data System (ADS)

Potts, T. A.; Shepard, A.

2006-12-01

In 2002, a partnership was formed to design, construct, field test, and operate an Autonomous Underwater Vehicle (AUV) equipped to provide high-resolution (<1 m) maps of offshore seafloor habitats down to 2200 meters depth. An ISE Explorer-class AUV was constructed and equipped to conduct seafloor characterization via multi-beam EM2000 providing both bathymetry and backscatter. Three 10-day cruises will be conducted between August and November 2006 to put the vehicle through its paces and refine operating protocols. It is anticipated that the vehicle will log over 200 hours of bottom time and acquire over 30 GB of data at proposed marine protected area sites off North and South Carolina, Gray's Reef National Marine Sanctuary off Georgia, and at the Oculina Habitat Area of Particular Concern off the east coast of Florida. The AUV will begin supporting competitively reviewed science projects starting in 2007.

Methotrexate, Doxorubicin, and Cisplatin (MAP) Plus Maintenance Pegylated Interferon Alfa-2b Versus MAP Alone in Patients With Resectable High-Grade Osteosarcoma and Good Histologic Response to Preoperative MAP: First Results of the EURAMOS-1 Good Response Randomized Controlled Trial

PubMed Central

Bielack, Stefan S.; Smeland, Sigbjørn; Whelan, Jeremy S.; Marina, Neyssa; Jovic, Gordana; Hook, Jane M.; Krailo, Mark D.; Gebhardt, Mark; Pápai, Zsuzsanna; Meyer, James; Nadel, Helen; Randall, R. Lor; Deffenbaugh, Claudia; Nagarajan, Rajaram; Brennan, Bernadette; Letson, G. Douglas; Teot, Lisa A.; Goorin, Allen; Baumhoer, Daniel; Kager, Leo; Werner, Mathias; Lau, Ching C.; Sundby Hall, Kirsten; Gelderblom, Hans; Meyers, Paul; Gorlick, Richard; Windhager, Reinhard; Helmke, Knut; Eriksson, Mikael; Hoogerbrugge, Peter M.; Schomberg, Paula; Tunn, Per-Ulf; Kühne, Thomas; Jürgens, Heribert; van den Berg, Henk; Böhling, Tom; Picton, Susan; Renard, Marleen; Reichardt, Peter; Gerss, Joachim; Butterfass-Bahloul, Trude; Morris, Carol; Hogendoorn, Pancras C.W.; Seddon, Beatrice; Calaminus, Gabriele; Michelagnoli, Maria; Dhooge, Catharina; Sydes, Matthew R.; Bernstein, Mark

2015-01-01

Purpose EURAMOS-1, an international randomized controlled trial, investigated maintenance therapy with pegylated interferon alfa-2b (IFN-α-2b) in patients whose osteosarcoma showed good histologic response (good response) to induction chemotherapy. Patients and Methods At diagnosis, patients age ≤ 40 years with resectable high-grade osteosarcoma were registered. Eligibility after surgery for good response random assignment included ≥ two cycles of preoperative MAP (methotrexate, doxorubicin, and cisplatin), macroscopically complete surgery of primary tumor, < 10% viable tumor, and no disease progression. These patients were randomly assigned to four additional cycles MAP with or without IFN-α-2b (0.5 to 1.0 μg/kg per week subcutaneously, after chemotherapy until 2 years postregistration). Outcome measures were event-free survival (EFS; primary) and overall survival and toxicity (secondary). Results Good response was reported in 1,041 of 2,260 registered patients; 716 consented to random assignment (MAP, n = 359; MAP plus IFN-α-2b, n = 357), with baseline characteristics balanced by arm. A total of 271 of 357 started IFN-α-2b; 105 stopped early, and 38 continued to receive treatment at data freeze. Refusal and toxicity were the main reasons for never starting IFN-α-2b and for stopping prematurely, respectively. Median IFN-α-2b duration, if started, was 67 weeks. A total of 133 of 268 patients who started IFN-α-2b and provided toxicity information reported grade ≥ 3 toxicity during IFN-α-2b treatment. With median follow-up of 44 months, 3-year EFS for all 716 randomly assigned patients was 76% (95% CI, 72% to 79%); 174 EFS events were reported (MAP, n = 93; MAP plus IFN-α-2b, n = 81). Hazard ratio was 0.83 (95% CI, 0.61 to 1.12; P = .214) from an adjusted Cox model. Conclusion At the preplanned analysis time, MAP plus IFN-α-2b was not statistically different from MAP alone. A considerable proportion of patients never started IFN-α-2b or stopped prematurely. Long-term follow-up for events and survival continues. PMID:26033801

Expression of the Caulobacter heat shock gene dnaK is developmentally controlled during growth at normal temperatures.

PubMed Central

Gomes, S L; Gober, J W; Shapiro, L

1990-01-01

Caulobacter crescentus has a single dnaK gene that is highly homologous to the hsp70 family of heat shock genes. Analysis of the cloned and sequenced dnaK gene has shown that the deduced amino acid sequence could encode a protein of 67.6 kilodaltons that is 68% identical to the DnaK protein of Escherichia coli and 49% identical to the Drosophila and human hsp70 protein family. A partial open reading frame 165 base pairs 3' to the end of dnaK encodes a peptide of 190 amino acids that is 59% identical to DnaJ of E. coli. Northern blot analysis revealed a single 4.0-kilobase mRNA homologous to the cloned fragment. Since the dnaK coding region is 1.89 kilobases, dnaK and dnaJ may be transcribed as a polycistronic message. S1 mapping and primer extension experiments showed that transcription initiated at two sites 5' to the dnaK coding sequence. A single start site of transcription was identified during heat shock at 42 degrees C, and the predicted promoter sequence conformed to the consensus heat shock promoters of E. coli. At normal growth temperature (30 degrees C), a different start site was identified 3' to the heat shock start site that conformed to the E. coli sigma 70 promoter consensus sequence. S1 protection assays and analysis of expression of the dnaK gene fused to the lux transcription reporter gene showed that expression of dnaK is temporally controlled under normal physiological conditions and that transcription occurs just before the initiation of DNA replication. Thus, in both human cells (I. K. L. Milarski and R. I. Morimoto, Proc. Natl. Acad. Sci. USA 83:9517-9521, 1986) and in a simple bacterium, the transcription of a hsp70 gene is temporally controlled as a function of the cell cycle under normal growth conditions. Images PMID:2345134

Advance Inspection of NASA Next Mars Landing Site

NASA Image and Video Library

2017-03-29

This map shows footprints of images taken from Mars orbit by the High Resolution Imaging Science Experiment (HiRISE) camera as part of advance analysis of the area where NASA's InSight mission will land in 2018. The final planned image of the set is targeted to fill in the yellow-outlined rectangle on March 30, 2017. HiRISE is one of six science instruments on NASA's Mars Reconnaissance Orbiter, which reached Mars in 2006 and surpassed 50,000 orbits on March 27, 2017. The map covers an area about 100 miles (160 kilometers) across. HiRISE has been used since 2006 to inspect dozens of candidate landing sites on Mars, including the sites where the Phoenix and Curiosity missions landed in 2008 and 2012. The site selected for InSight's Nov. 26, 2018, landing is on a flat plain in the Elysium Planitia region of Mars, between 4 and 5 degrees north of the equator. HiRISE images are detailed enough to reveal individual boulders big enough to be a landing hazard. The March 30 observation that completes the planned advance imaging of this landing area brings the number of HiRISE images of the area to 73. Some are pairs covering the same ground. Overlapping observations provide stereoscopic, 3-D information for evaluating characteristics such as slopes. On this map, coverage by stereo pairs is coded in pale blue, compared to the gray-green of single HiRISE image footprints. The ellipses on the map are about 81 miles (130 kilometers) west-to-east by about 17 miles (27 kilometers) north-to-south. InSight has about 99 percent odds of landing within the ellipse for which it is targeted. The three ellipses indicate landing expectations for three of the possible InSight launch dates: white outline for launch at the start of the launch period, on May 5, 2018; blue for launch on May 26, 2018; orange for launch on June 8, 2018. InSight -- an acronym for "Interior Exploration using Seismic Investigations, Geodesy and Heat Transport" -- will study the deep interior of Mars to improve understanding about how rocky planets like Earth formed and evolved. http://photojournal.jpl.nasa.gov/catalog/PIA21489

The use of Global Positioning System units and ArcGIS Online to engage K-12 Students in Research Being Done in their Local Communities

NASA Astrophysics Data System (ADS)

Butcher, C. E.; Sparrow, E. B.; Clucas, T.

2015-12-01

Incorporating K-12 students in scientific research processes and opportunities in their communities is a great way to bridge the gap between research and education and to start building science research capacity at an early age. One goal of the Experimental Program to Stimulate Competitive Research (EPSCoR) Alaska Adapting to Changing Environments project is to engage the local community in the research as well as to share results with the people. By giving K-12 students Global Positioning System (GPS) units, and allowing them to collect and map their own data, they are being exposed to some of the research methods being used by scientists in the Alaska ACE project. This hands-on, minds-on method has been successfully used in formal education settings such as a Junior High School classroom in Nuiqsut, Alaska as well as in informal education settings such as summer camps in Barrow, Alaska and Kenai, Alaska. The students progress from mapping by hand to collecting location data with their GPS units and cameras, and imputing this information into ArcGIS Online to create map products. The data collected were from sites ranging from important places in the community to sites visited during summer camps, with students reflecting on data and site significance. Collecting data, using technology, and creating map products contribute to science skills and practices students need to conduct research of their own and to understand research being done around them. The goal of this education outreach implementation is to bring students closer to the research, understand the process of science, and have the students continue to collect data and contribute to research in their communities. Support provided for this work from the Alaska EPSCoR NSF Award #OIA-1208927 and the state of Alaska is gratefully acknowledged.

Involvement of Sp1 and Microsatellite Repressor Sequences in the Transcriptional Control of the Human CD30 Gene

PubMed Central

Croager, Emma J.; Gout, Alexander M.; Abraham, Lawrence J.

2000-01-01

CD30, as a member of the tumor necrosis factor (TNF) receptor family, is expressed on the surface of activated lymphoid cells. CD30 overexpression is a characteristic of lymphoproliferative diseases such as Hodgkin’s/non-Hodgkin’s lymphomas, embryonal carcinoma, and a number of Th2-associated diseases. The CD30 gene has been mapped to a region of the murine genome that is involved in susceptibility to systemic lupus erythematosus. Functionally, CD30 may play a role in the deletion of autoreactive T cells. We were interested in determining the molecular nature of CD30 overexpression. Sequence comparison has revealed significant identity between the TATA-less human and murine CD30 promoters; they share a number of common consensus binding motifs. Transfection assays identified three regions of transcriptional importance; the region between position −1.2 kb and −336 bp, containing a CCAT microsatellite sequence, a conserved Sp1 site at positions −43 to −38, and a downstream promoter element (DPE) at positions +24 to +29. EMSA and DNase I footprinting showed specific DNA-protein interactions of the CD30 promoter with the Sp1 site and the CCAT repeat region. The DPE element was shown to be essential for start site selection. We conclude that the conserved Sp1 site at −43 to −38 is associated with maximum reporter gene activity, the DPE element is required for start site selection, and the CCAT tetranucleotide repeats act to repress transcription. We also have shown that the microsatellite is multiallelic, when we screened a random healthy population. Further studies are required to determine whether microsatellite instability in the repressor predisposes susceptible individuals to CD30 overexpression. PMID:10793083

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity

PubMed Central

Song, Lingyun; Zhang, Zhancheng; Grasfeder, Linda L.; Boyle, Alan P.; Giresi, Paul G.; Lee, Bum-Kyu; Sheffield, Nathan C.; Gräf, Stefan; Huss, Mikael; Keefe, Damian; Liu, Zheng; London, Darin; McDaniell, Ryan M.; Shibata, Yoichiro; Showers, Kimberly A.; Simon, Jeremy M.; Vales, Teresa; Wang, Tianyuan; Winter, Deborah; Zhang, Zhuzhu; Clarke, Neil D.; Birney, Ewan; Iyer, Vishwanath R.; Crawford, Gregory E.; Lieb, Jason D.; Furey, Terrence S.

2011-01-01

The human body contains thousands of unique cell types, each with specialized functions. Cell identity is governed in large part by gene transcription programs, which are determined by regulatory elements encoded in DNA. To identify regulatory elements active in seven cell lines representative of diverse human cell types, we used DNase-seq and FAIRE-seq (Formaldehyde Assisted Isolation of Regulatory Elements) to map “open chromatin.” Over 870,000 DNaseI or FAIRE sites, which correspond tightly to nucleosome-depleted regions, were identified across the seven cell lines, covering nearly 9% of the genome. The combination of DNaseI and FAIRE is more effective than either assay alone in identifying likely regulatory elements, as judged by coincidence with transcription factor binding locations determined in the same cells. Open chromatin common to all seven cell types tended to be at or near transcription start sites and to be coincident with CTCF binding sites, while open chromatin sites found in only one cell type were typically located away from transcription start sites and contained DNA motifs recognized by regulators of cell-type identity. We show that open chromatin regions bound by CTCF are potent insulators. We identified clusters of open regulatory elements (COREs) that were physically near each other and whose appearance was coordinated among one or more cell types. Gene expression and RNA Pol II binding data support the hypothesis that COREs control gene activity required for the maintenance of cell-type identity. This publicly available atlas of regulatory elements may prove valuable in identifying noncoding DNA sequence variants that are causally linked to human disease. PMID:21750106

The Global Regulatory Architecture of Transcription during the Caulobacter Cell Cycle

PubMed Central

Zhou, Bo; Schrader, Jared M.; Kalogeraki, Virginia S.; Abeliuk, Eduardo; Dinh, Cong B.; Pham, James Q.; Cui, Zhongying Z.; Dill, David L.; McAdams, Harley H.; Shapiro, Lucy

2015-01-01

Each Caulobacter cell cycle involves differentiation and an asymmetric cell division driven by a cyclical regulatory circuit comprised of four transcription factors (TFs) and a DNA methyltransferase. Using a modified global 5′ RACE protocol, we globally mapped transcription start sites (TSSs) at base-pair resolution, measured their transcription levels at multiple times in the cell cycle, and identified their transcription factor binding sites. Out of 2726 TSSs, 586 were shown to be cell cycle-regulated and we identified 529 binding sites for the cell cycle master regulators. Twenty-three percent of the cell cycle-regulated promoters were found to be under the combinatorial control of two or more of the global regulators. Previously unknown features of the core cell cycle circuit were identified, including 107 antisense TSSs which exhibit cell cycle-control, and 241 genes with multiple TSSs whose transcription levels often exhibited different cell cycle timing. Cumulatively, this study uncovered novel new layers of transcriptional regulation mediating the bacterial cell cycle. PMID:25569173

A new clustering algorithm applicable to multispectral and polarimetric SAR images

NASA Technical Reports Server (NTRS)

Wong, Yiu-Fai; Posner, Edward C.

1993-01-01

We describe an application of a scale-space clustering algorithm to the classification of a multispectral and polarimetric SAR image of an agricultural site. After the initial polarimetric and radiometric calibration and noise cancellation, we extracted a 12-dimensional feature vector for each pixel from the scattering matrix. The clustering algorithm was able to partition a set of unlabeled feature vectors from 13 selected sites, each site corresponding to a distinct crop, into 13 clusters without any supervision. The cluster parameters were then used to classify the whole image. The classification map is much less noisy and more accurate than those obtained by hierarchical rules. Starting with every point as a cluster, the algorithm works by melting the system to produce a tree of clusters in the scale space. It can cluster data in any multidimensional space and is insensitive to variability in cluster densities, sizes and ellipsoidal shapes. This algorithm, more powerful than existing ones, may be useful for remote sensing for land use.

The global regulatory architecture of transcription during the Caulobacter cell cycle.

PubMed

Zhou, Bo; Schrader, Jared M; Kalogeraki, Virginia S; Abeliuk, Eduardo; Dinh, Cong B; Pham, James Q; Cui, Zhongying Z; Dill, David L; McAdams, Harley H; Shapiro, Lucy

2015-01-01

Each Caulobacter cell cycle involves differentiation and an asymmetric cell division driven by a cyclical regulatory circuit comprised of four transcription factors (TFs) and a DNA methyltransferase. Using a modified global 5' RACE protocol, we globally mapped transcription start sites (TSSs) at base-pair resolution, measured their transcription levels at multiple times in the cell cycle, and identified their transcription factor binding sites. Out of 2726 TSSs, 586 were shown to be cell cycle-regulated and we identified 529 binding sites for the cell cycle master regulators. Twenty-three percent of the cell cycle-regulated promoters were found to be under the combinatorial control of two or more of the global regulators. Previously unknown features of the core cell cycle circuit were identified, including 107 antisense TSSs which exhibit cell cycle-control, and 241 genes with multiple TSSs whose transcription levels often exhibited different cell cycle timing. Cumulatively, this study uncovered novel new layers of transcriptional regulation mediating the bacterial cell cycle.

Map of Nasca Geoglyphs

NASA Astrophysics Data System (ADS)

Hanzalová, K.; Pavelka, K.

2013-07-01

The Czech Technical University in Prague in the cooperation with the University of Applied Sciences in Dresden (Germany) work on the Nasca Project. The cooperation started in 2004 and much work has been done since then. All work is connected with Nasca lines in southern Peru. The Nasca project started in 1995 and its main target is documentation and conservation of the Nasca lines. Most of the project results are presented as WebGIS application via Internet. In the face of the impending destruction of the soil drawings, it is possible to preserve this world cultural heritage for the posterity at least in a digital form. Creating of Nasca lines map is very useful. The map is in a digital form and it is also available as a paper map. The map contains planimetric component of the map, map lettering and altimetry. Thematic folder in this map is a vector layer of the geoglyphs in Nasca/Peru. Basis for planimetry are georeferenced satellite images, altimetry is created from digital elevation model. This map was created in ArcGis software.

A VS30 map for California with geologic and topographic constraints

USGS Publications Warehouse

Thompson, Eric; Wald, David J.; Worden, Charles

2014-01-01

For many earthquake engineering applications, site response is estimated through empirical correlations with the time‐averaged shear‐wave velocity to 30 m depth (VS30). These applications therefore depend on the availability of either site‐specific VS30 measurements or VS30 maps at local, regional, and global scales. Because VS30 measurements are sparse, a proxy frequently is needed to estimate VS30 at unsampled locations. We present a new VS30 map for California, which accounts for observational constraints from multiple sources and spatial scales, such as geology, topography, and site‐specific VS30measurements. We apply the geostatistical approach of regression kriging (RK) to combine these constraints for predicting VS30. For the VS30 trend, we start with geology‐based VS30 values and identify two distinct trends between topographic gradient and the residuals from the geology VS30 model. One trend applies to deep and fine Quaternary alluvium, whereas the second trend is slightly stronger and applies to Pleistocene sedimentary units. The RK framework ensures that the resulting map of California is locally refined to reflect the rapidly expanding database of VS30 measurements throughout California. We compare the accuracy of the new mapping method to a previously developed map of VS30 for California. We also illustrate the sensitivity of ground motions to the new VS30 map by comparing real and scenario ShakeMaps with VS30 values from our new map to those for existingVS30 maps.

High spatial resolution mapping of water quality and bathymetry with an autonomous underwater vehicle

NASA Astrophysics Data System (ADS)

Pampalone, Vincenzo; Milici, Barbara

2015-12-01

The drone Ecomapper AUV (Autonomous Underwater Vehicle) is a rare example of highly technological instrument in the environmental coastal monitoring field. The YSI EcoMapper is a one-man deployable, Autonomous Underwater Vehicle (AUV) designed to collect bathymetry and water quality data. The submarine-like vehicle follows a programmed course and employs sensors mounted in the nose to record pertinent information. Once the vehicle has started its mission, it operates independently of the user and utilizes GPS waypoints navigation to complete its programmed course. Throughout the course, the vehicle constantly steers toward the line drawn in the mission planning software (VectorMap), essentially following a more accurate road of coordinates instead of transversing waypoint-to-waypoint. It has been equipped with a Doppler Velocity Log (DVL) to increase its underwater navigation accuracy. Potential EcoMapper applications include baseline environmental mapping in freshwater, estuarine or near-coastal environments, bathymetric mapping, dissolved oxygen studies, event monitoring (algal blooms, storm impacts, low dissolved oxygen), non-point source studies, point-source dispersion mapping, security, search & rescue, inspection, shallow water mapping, thermal dissipation mapping of cooling outfalls, trace-dye studies. The AUV is used in the coastal area of the Augusta Bay (Italy), located in the eastern part of Sicily. Due to the heavy contamination generated by the several chemical and petrochemical industries active in the zone, the harbour was declared a Contaminated Site of National Interest. The ecomapper allows for a simultaneous data collection of water quality and bathymetric data providing a complete environmental mapping system of the Harbour.

Identity of a peptide domain of human C9 that is bound by the cell-surface complement inhibitor, CD59.

PubMed

Chang, C P; Hüsler, T; Zhao, J; Wiedmer, T; Sims, P J

1994-10-21

The CD59 antigen is a plasma membrane glycoprotein that serves as an inhibitor of the C5b-9 complex of complement. This inhibitory activity appears related to the capacity of CD59 to bind with high affinity to sites that are nascently exposed in the alpha-chain subunit of human C8, as well as within the C9b domain (amino acid residues 245-538) of human C9, during assembly of the C5b-9 complex on the target membrane (Ninomiya, H., and Sims, P. J. (1992) J. Biol. Chem. 267, 13675-13680). The CD59 binding site in C9 was first investigated by N-terminal sequencing of CD59-binding peptides generated by limited digest of the isolated C9b domain. These experiments revealed a 17-kDa fragment (starting at C9 residue Thr-320) that retained affinity for CD59, suggesting the possibility for localizing the CD59 binding site by mapping with small C9-derived peptides. Peptides spanning the entire C9b sequence were expressed in Escherichia coli and then probed with CD59. CD59 bound specifically to all peptides starting N-terminal to C9 residue 359 with C termini extending beyond residue 411. Little to no CD59 binding was observed for various C9-derived peptides that started C-terminal to residue 359 or that were truncated N-terminal to residue 411. Affinity-purified antibody against C9 residues 320-411 inhibited CD59 binding to C9 by > 50% and completely inhibited its binding to the isolated C9b domain. Little to no specific binding of CD59 was detected for peptides restricted to the putative hinge domain within C9b (residues 245-271). These results indicate that a CD59 binding site is located between residues 320 and 411 of the C9 polypeptide and suggest that the affinity of this site is principally determined by residues 359-411.

Using maps in genealogy

USGS Publications Warehouse

,

2002-01-01

In genealogical research, maps can provide clues to where our ancestors may have lived and where to look for written records about them. Beginners should master basic genealogical research techniques before starting to use topographic maps.

Fast generation of spin-squeezed states in bosonic Josephson junctions

NASA Astrophysics Data System (ADS)

Juliá-Díaz, B.; Torrontegui, E.; Martorell, J.; Muga, J. G.; Polls, A.

2012-12-01

We describe methods for the fast production of highly coherent-spin-squeezed many-body states in bosonic Josephson junctions. We start from the known mapping of the two-site Bose-Hubbard (BH) Hamiltonian to that of a single effective particle evolving according to a Schrödinger-like equation in Fock space. Since, for repulsive interactions, the effective potential in Fock space is nearly parabolic, we extend recently derived protocols for shortcuts to adiabatic evolution in harmonic potentials to the many-body BH Hamiltonian. A comparison with current experiments shows that our methods allow for an important reduction in the preparation times of highly squeezed spin states.

Usability Evaluation of Public Web Mapping Sites

NASA Astrophysics Data System (ADS)

Wang, C.

2014-04-01

Web mapping sites are interactive maps that are accessed via Webpages. With the rapid development of Internet and Geographic Information System (GIS) field, public web mapping sites are not foreign to people. Nowadays, people use these web mapping sites for various reasons, in that increasing maps and related map services of web mapping sites are freely available for end users. Thus, increased users of web mapping sites led to more usability studies. Usability Engineering (UE), for instance, is an approach for analyzing and improving the usability of websites through examining and evaluating an interface. In this research, UE method was employed to explore usability problems of four public web mapping sites, analyze the problems quantitatively and provide guidelines for future design based on the test results. Firstly, the development progress for usability studies were described, and simultaneously several usability evaluation methods such as Usability Engineering (UE), User-Centered Design (UCD) and Human-Computer Interaction (HCI) were generally introduced. Then the method and procedure of experiments for the usability test were presented in detail. In this usability evaluation experiment, four public web mapping sites (Google Maps, Bing maps, Mapquest, Yahoo Maps) were chosen as the testing websites. And 42 people, who having different GIS skills (test users or experts), gender (male or female), age and nationality, participated in this test to complete the several test tasks in different teams. The test comprised three parts: a pretest background information questionnaire, several test tasks for quantitative statistics and progress analysis, and a posttest questionnaire. The pretest and posttest questionnaires focused on gaining the verbal explanation of their actions qualitatively. And the design for test tasks targeted at gathering quantitative data for the errors and problems of the websites. Then, the results mainly from the test part were analyzed. The success rate from different public web mapping sites was calculated and compared, and displayed by the means of diagram. And the answers from questionnaires were also classified and organized in this part. Moreover, based on the analysis, this paper expands the discussion about the layout, map visualization, map tools, search logic and etc. Finally, this paper closed with some valuable guidelines and suggestions for the design of public web mapping sites. Also, limitations for this research stated in the end.

Social.Water--Open Source Citizen Science Software for CrowdHydrology

NASA Astrophysics Data System (ADS)

Fienen, M. N.; Lowry, C.

2013-12-01

CrowdHydrology is a crowd-sourced citizen science project in which passersby near streams are encouraged to read a gage and send an SMS (text) message with the water level to a number indicated on a sign. The project was initially started using free services such as Google Voice, Gmail, and Google Maps to acquire and present the data on the internet. Social.Water is open-source software, using Python and JavaScript, that automates the acquisition, categorization, and presentation of the data. Open-source objectives pervade both the project and the software as the code is hosted at Github, only free scripting codes are used, and any person or organization can install a gage and join the CrowdHydrology network. In the first year, 10 sites were deployed in upstate New York, USA. In the second year, expansion to 44 sites throughout the upper Midwest USA was achieved. Comparison with official USGS and academic measurements have shown low error rates. Citizen participation varies greatly from site to site, so surveys or other social information is sought for insight into why some sites experience higher rates of participation than others.

Lidar Systems for Precision Navigation and Safe Landing on Planetary Bodies

NASA Technical Reports Server (NTRS)

Amzajerdian, Farzin; Pierrottet, Diego F.; Petway, Larry B.; Hines, Glenn D.; Roback, Vincent E.

2011-01-01

The ability of lidar technology to provide three-dimensional elevation maps of the terrain, high precision distance to the ground, and approach velocity can enable safe landing of robotic and manned vehicles with a high degree of precision. Currently, NASA is developing novel lidar sensors aimed at needs of future planetary landing missions. These lidar sensors are a 3-Dimensional Imaging Flash Lidar, a Doppler Lidar, and a Laser Altimeter. The Flash Lidar is capable of generating elevation maps of the terrain that indicate hazardous features such as rocks, craters, and steep slopes. The elevation maps collected during the approach phase of a landing vehicle, at about 1 km above the ground, can be used to determine the most suitable safe landing site. The Doppler Lidar provides highly accurate ground relative velocity and distance data allowing for precision navigation to the landing site. Our Doppler lidar utilizes three laser beams pointed to different directions to measure line of sight velocities and ranges to the ground from altitudes of over 2 km. Throughout the landing trajectory starting at altitudes of about 20 km, the Laser Altimeter can provide very accurate ground relative altitude measurements that are used to improve the vehicle position knowledge obtained from the vehicle navigation system. At altitudes from approximately 15 km to 10 km, either the Laser Altimeter or the Flash Lidar can be used to generate contour maps of the terrain, identifying known surface features such as craters, to perform Terrain relative Navigation thus further reducing the vehicle s relative position error. This paper describes the operational capabilities of each lidar sensor and provides a status of their development. Keywords: Laser Remote Sensing, Laser Radar, Doppler Lidar, Flash Lidar, 3-D Imaging, Laser Altimeter, Precession Landing, Hazard Detection

From the European indoor radon map towards an atlas of natural radiation.

PubMed

Tollefsen, T; Cinelli, G; Bossew, P; Gruber, V; De Cort, M

2014-11-01

In 2006, the Joint Research Centre of the European Commission launched a project to map radon at the European level, as part of a planned European Atlas of Natural Radiation. It started with a map of indoor radon concentrations. As of May 2014, this map includes data from 24 countries, covering a fair part of Europe. Next, a European map of geogenic radon, intended to show 'what earth delivers' in terms of radon potential (RP), was started in 2008. A first trial map has been created, and a database was established to collect all available data relevant to the RP. The Atlas should eventually display the geographical distribution of physical quantities related to natural radiation. In addition to radon, it will comprise maps of quantities such as cosmic rays and terrestrial gamma radiation. In this paper, the authors present the current state of the radon maps and the Atlas. © The Author 2014. Published by Oxford University Press.

The morbid anatomy of the human genome: chromosomal location of mutations causing disease.

PubMed Central

McKusick, V A; Amberger, J S

1993-01-01

Information is given in tabular form derived from a synopsis of the human gene map which has been updated continuously since 1973 as part of Mendelian Inheritance in Man (Johns Hopkins University Press, 10th ed, 1992) and of OMIM (Online Mendelian Inheritance in Man, available generally since 1987). The part of the synopsis reproduced here consists of chromosome by chromosome gene lists of loci for which there are associated disorders (table 1), a pictorial representation of this information (fig 1a-d), and an index of disorders for which the causative mutations have been mapped (table 2). In table 1, information on genes that have been located to specific chromosomal positions and are also the site of disease producing mutations is arranged by chromosome, starting with chromosome 1 and with the end of the short arm of the chromosome in each case. In table 2 an alphabetized list of these disorders and the chromosomal location of the mutation in each case are provided. Both in the 'Disorder' field of table 1 and in table 2, the numbers 1, 2, or 3 in parentheses after the name of the disorder indicate that its chromosomal location was determined by mapping of the wildtype gene (1), by mapping of the clinical phenotype (2), or by both strategies (3). PMID:8423603

A simulation of Earthquake Loss Estimation in Southeastern Korea using HAZUS and the local site classification Map

NASA Astrophysics Data System (ADS)

Kang, S.; Kim, K.

2013-12-01

Regionally varying seismic hazards can be estimated using an earthquake loss estimation system (e.g. HAZUS-MH). The estimations for actual earthquakes help federal and local authorities develop rapid, effective recovery measures. Estimates for scenario earthquakes help in designing a comprehensive earthquake hazard mitigation plan. Local site characteristics influence the ground motion. Although direct measurements are desirable to construct a site-amplification map, such data are expensive and time consuming to collect. Thus we derived a site classification map of the southern Korean Peninsula using geologic and geomorphologic data, which are readily available for the entire southern Korean Peninsula. Class B sites (mainly rock) are predominant in the area, although localized areas of softer soils are found along major rivers and seashores. The site classification map is compared with independent site classification studies to confirm our site classification map effectively represents the local behavior of site amplification during an earthquake. We then estimated the losses due to a magnitude 6.7 scenario earthquake in Gyeongju, southeastern Korea, with and without the site classification map. Significant differences in loss estimates were observed. The loss without the site classification map decreased without variation with increasing epicentral distance, while the loss with the site classification map varied from region to region, due to both the epicentral distance and local site effects. The major cause of the large loss expected in Gyeongju is the short epicentral distance. Pohang Nam-Gu is located farther from the earthquake source region. Nonetheless, the loss estimates in the remote city are as large as those in Gyeongju and are attributed to the site effect of soft soil found widely in the area.

Using maps in genealogy

USGS Publications Warehouse

,

1999-01-01

Maps are one of many sources you may need to complete a family tree. In genealogical research, maps can provide clues to where our ancestors may have lived and where to look for written records about them. Beginners should master basic genealogical research techniques before starting to use topographic maps.

Nucleotide sequence analysis of the L gene of Newcastle disease virus: homologies with Sendai and vesicular stomatitis viruses.

PubMed Central

Yusoff, K; Millar, N S; Chambers, P; Emmerson, P T

1987-01-01

The nucleotide sequence of the L gene of the Beaudette C strain of Newcastle disease virus (NDV) has been determined. The L gene is 6704 nucleotides long and encodes a protein of 2204 amino acids with a calculated molecular weight of 248822. Mung bean nuclease mapping of the 5' terminus of the L gene mRNA indicates that the transcription of the L gene is initiated 11 nucleotides upstream of the translational start site. Comparison with the amino acid sequences of the L genes of Sendai virus and vesicular stomatitis virus (VSV) suggests that there are several regions of homology between the sequences. These data provide further evidence for an evolutionary relationship between the Paramyxoviridae and the Rhabdoviridae. A non-coding sequence of 46 nucleotides downstream of the presumed polyadenylation site of the L gene may be part of a negative strand leader RNA. Images PMID:3035486

Interactive NCORP Map Details Community Research Sites | Division of Cancer Prevention

Cancer.gov

An interactive map of the NCI Community Oncology Research Program (NCORP) with detailed information on hundreds of community sites that take part in clinical trials is available on the NCORP website. NCORP Map NCORP Community Sites, Minority/Underserved Community Sites, and Research Bases |

A revised logistic regression equation and an automated procedure for mapping the probability of a stream flowing perennially in Massachusetts

USGS Publications Warehouse

Bent, Gardner C.; Steeves, Peter A.

2006-01-01

A revised logistic regression equation and an automated procedure were developed for mapping the probability of a stream flowing perennially in Massachusetts. The equation provides city and town conservation commissions and the Massachusetts Department of Environmental Protection a method for assessing whether streams are intermittent or perennial at a specific site in Massachusetts by estimating the probability of a stream flowing perennially at that site. This information could assist the environmental agencies who administer the Commonwealth of Massachusetts Rivers Protection Act of 1996, which establishes a 200-foot-wide protected riverfront area extending from the mean annual high-water line along each side of a perennial stream, with exceptions for some urban areas. The equation was developed by relating the observed intermittent or perennial status of a stream site to selected basin characteristics of naturally flowing streams (defined as having no regulation by dams, surface-water withdrawals, ground-water withdrawals, diversion, wastewater discharge, and so forth) in Massachusetts. This revised equation differs from the equation developed in a previous U.S. Geological Survey study in that it is solely based on visual observations of the intermittent or perennial status of stream sites across Massachusetts and on the evaluation of several additional basin and land-use characteristics as potential explanatory variables in the logistic regression analysis. The revised equation estimated more accurately the intermittent or perennial status of the observed stream sites than the equation from the previous study. Stream sites used in the analysis were identified as intermittent or perennial based on visual observation during low-flow periods from late July through early September 2001. The database of intermittent and perennial streams included a total of 351 naturally flowing (no regulation) sites, of which 85 were observed to be intermittent and 266 perennial. Stream sites included in the database had drainage areas that ranged from 0.04 to 10.96 square miles. Of the 66 stream sites with drainage areas greater than 2.00 square miles, 2 sites were intermittent and 64 sites were perennial. Thus, stream sites with drainage areas greater than 2.00 square miles were assumed to flow perennially, and the database used to develop the logistic regression equation included only those stream sites with drainage areas less than 2.00 square miles. The database for the equation included 285 stream sites that had drainage areas less than 2.00 square miles, of which 83 sites were intermittent and 202 sites were perennial. Results of the logistic regression analysis indicate that the probability of a stream flowing perennially at a specific site in Massachusetts can be estimated as a function of four explanatory variables: (1) drainage area (natural logarithm), (2) areal percentage of sand and gravel deposits, (3) areal percentage of forest land, and (4) region of the state (eastern region or western region). Although the equation provides an objective means of determining the probability of a stream flowing perennially at a specific site, the reliability of the equation is constrained by the data used in its development. The equation is not recommended for (1) losing stream reaches or (2) streams whose ground-water contributing areas do not coincide with their surface-water drainage areas, such as many streams draining the Southeast Coastal Region-the southern part of the South Coastal Basin, the eastern part of the Buzzards Bay Basin, and the entire area of the Cape Cod and the Islands Basins. If the equation were used on a regulated stream site, the estimated intermittent or perennial status would reflect the natural flow conditions for that site. An automated mapping procedure was developed to determine the intermittent or perennial status of stream sites along reaches throughout a basin. The procedure delineates the drainage area boundaries, determines values for the four explanatory variables, and solves the equation for estimating the probability of a stream flowing perennially at two locations on a headwater (first-order) stream reach-one near its confluence or end point and one near its headwaters or start point. The automated procedure then determines the intermittent or perennial status of the reach on the basis of the calculated probability values and a probability cutpoint (a stream is considered to flow perennially at a cutpoint of 0.56 or greater for this study) for the two locations or continues to loop upstream or downstream between locations less than and greater than the cutpoint of 0.56 to determine the transition point from an intermittent to a perennial stream. If the first-order stream reach is determined to be intermittent, the procedure moves to the next downstream reach and repeats the same process. The automated procedure then moves to the next first-order stream and repeats the process until the entire basin is mapped. A map of the intermittent and perennial stream reaches in the Shawsheen River Basin is provided on a CD-ROM that accompanies this report. The CD-ROM also contains ArcReader 9.0, a freeware product, that allows a user to zoom in and out, set a scale, pan, turn on and off map layers (such as a USGS topographic map), and print a map of the stream site with a scale bar. Maps of the intermittent and perennial stream reaches in Massachusetts will provide city and town conservation commissions and the Massachusetts Department of Environmental Protection with an additional method for assessing the intermittent or perennial status of stream sites.

Special-Status Plant Species Surveys and Vegetation Mapping at Lawrence Livermore National Laboratory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Preston, R E

This report presents the results of Jones & Stokes special-status plant surveys and vegetation mapping for the University of California, Lawrence Livermore National Laboratory (LLNL). Special-status plant surveys were conducted at Site 300 in April to May 1997 and in March to April 2002. Eight special-status plants were identified at Site 300: large-flowered fiddleneck, big tarplant, diamond-petaled poppy, round-leaved filaree, gypsum-loving larkspur, California androsace, stinkbells, and hogwallow starfish. Maps identifying the locations of these species, a discussion of the occurrence of these species at Site 300, and a checklist of the flora of Site 300 are presented. A reconnaissance surveymore » of the LLNL Livermore Site was conducted in June 2002. This survey concluded that no special-status plants occur at the Livermore Site. Vegetation mapping was conducted in 2001 at Site 300 to update a previous vegetation study done in 1986. The purpose of the vegetation mapping was to update and to delineate more precisely the boundaries between vegetation types and to map vegetation types that previously were not mapped. The vegetation map is presented with a discussion of the vegetation classification used.« less

Using Temporal Modulation Sensitivity to Select Stimulation Sites for Processor MAPs in Cochlear Implant Listeners

PubMed Central

Garadat, Soha N.; Zwolan, Teresa A.; Pfingst, Bryan E.

2013-01-01

Previous studies in our laboratory showed that temporal acuity as assessed by modulation detection thresholds (MDTs) varied across activation sites and that this site-to-site variability was subject specific. Using two 10-channel MAPs, the previous experiments showed that processor MAPs that had better across-site mean (ASM) MDTs yielded better speech recognition than MAPs with poorer ASM MDTs tested in the same subject. The current study extends our earlier work on developing more optimal fitting strategies to test the feasibility of using a site-selection approach in the clinical domain. This study examined the hypothesis that revising the clinical speech processor MAP for cochlear implant (CI) recipients by turning off selected sites that have poorer temporal acuity and reallocating frequencies to the remaining electrodes would lead to improved speech recognition. Twelve CI recipients participated in the experiments. We found that site selection procedure based on MDTs in the presence of a masker resulted in improved performance on consonant recognition and recognition of sentences in noise. In contrast, vowel recognition was poorer with the experimental MAP than with the clinical MAP, possibly due to reduced spectral resolution when sites were removed from the experimental MAP. Overall, these results suggest a promising path for improving recipient outcomes using personalized processor-fitting strategies based on a psychophysical measure of temporal acuity. PMID:23881208

Spatial resolution of pace mapping of idiopathic ventricular tachycardia/ectopy originating in the right ventricular outflow tract.

PubMed

Bogun, Frank; Taj, Majid; Ting, Michael; Kim, Hyungjin Myra; Reich, Stephen; Good, Eric; Jongnarangsin, Krit; Chugh, Aman; Pelosi, Frank; Oral, Hakan; Morady, Fred

2008-03-01

Pace mapping has been used to identify the site of origin of focal ventricular arrhythmias. The spatial resolution of pace mapping has not been adequately quantified using currently available three-dimensional mapping systems. The purpose of this study was to determine the spatial resolution of pace mapping in patients with idiopathic ventricular tachycardia or premature ventricular contractions originating in the right ventricular outflow tract. In 16 patients with idiopathic ventricular tachycardia/ectopy from the right ventricular outflow tract, comparisons and classifications of pace maps were performed by two observers (good pace map: match >10/12 leads; inadequate pace map: match < or =10/12 leads) and a customized MATLAB 6.0 program (assessing correlation coefficient and normalized root mean square of the difference (nRMSd) between test and template signals). With an electroanatomic mapping system, the correlation coefficient of each pace map was correlated with the distance between the pacing site and the effective ablation site. The endocardial area within the 10-ms activation isochrone was measured. The ablation procedure was effective in all patients. Sites with good pace maps had a higher correlation coefficient and lower nRMSd than sites with inadequate pace maps (correlation coefficient: 0.96 +/- 0.03 vs 0.76 +/- 0.18, P <.0001; nRMSd: 0.41 +/- 0.16 vs 0.89 +/- 0.39, P <.0001). Using receiver operating characteristic curves, appropriate cutoff values were >0.94 for correlation coefficient (sensitivity 81%, specificity 89%) and < or =0.54 for nRMSd (sensitivity 76%, specificity 80%). Good pace maps were located a mean of 7.3 +/- 5.0 mm from the effective ablation site and had a mean activation time of -24 +/- 7 ms. However, in 3 (18%) of 16 patients, the best pace map was inadequate at the effective ablation site, with an endocardial activation time at these sites of -25 +/- 12 ms. Pace maps with correlation coefficient > or =0.94 were confined to an area of 1.8 +/- 0.6 cm2. The 10-ms isochrone measured 1.2 +/- 0.7 cm2. The spatial resolution of a good pace map for targeting ventricular tachycardia/ectopy is 1.8 cm2 in the right ventricular outflow tract and therefore is inferior to the spatial resolution of activation mapping as assessed by isochronal activation. In approximately 20% of patients, pace mapping is unreliable in identifying the site of origin, possibly due a deeper site of origin and preferential conduction via fibers connecting the focus to the endocardial surface.

Mapping NEHRP VS30 site classes

USGS Publications Warehouse

Holzer, T.L.; Padovani, A.C.; Bennett, M.J.; Noce, T.E.; Tinsley, J. C.

2005-01-01

Site-amplification potential in a 140-km2 area on the eastern shore of San Francisco Bay, California, was mapped with data from 210 seismic cone penetration test (SCPT) soundings. NEHRP VS30 values were computed on a 50-m grid by both taking into account the thickness and using mean values of locally measured shear-wave velocities of shallow geologic units. The resulting map of NEHRP VS30 site classes differs from other published maps that (1) do not include unit thickness and (2) are based on regional compilations of velocity. Although much of the area in the new map is now classified as NEHRP Site Class D, the velocities of the geologic deposits within this area are either near the upper or lower VS30 boundary of Class D. If maps of NEHRP site classes are to be based on geologic maps, velocity distributions of geologic units may need to be considered in the definition of VS30 boundaries of NEHRP site classes. ?? 2005, Earthquake Engineering Research Institute.

Damage Assessment Map from Interferometric Coherence

NASA Astrophysics Data System (ADS)

Yun, S.; Fielding, E. J.; Simons, M.; Rosen, P. A.; Owen, S. E.; Webb, F.

2010-12-01

Large earthquakes cause buildings to collapse, which often claims the lives of many. For example, 2010 Haiti earthquake killed about 230,000 people, with about 280,000 buildings collapsed or severely damaged. When a major earthquake hits an urban area, one of the most critical information for rescue operations is rapid and accurate assessment of building-collapse areas. From a study on 2003 Bam earthquake in Iran, interferometric coherence was proved useful for earthquake damage assessment (Fielding et al., 2005) when similar perpendicular baselines can be found for pre- and coseismic interferometric pairs and when there is little temporal and volume decorrelation. In this study we develop a new algorithm to create a more robust and accurate damage assessment map using interferometric coherence despite different interferometric baselines and with other decorrelation sources. We test the algorithm on a building block that recently underwent demolition, which is a proxy for building collapse due to earthquakes, for new construction in the City of Pasadena, California. The size of the building block is about 150 m E-W and 300 m N-S, and the demolition project started on April 23, 2007 and continued until January 22, 2008. After we process Japanese L-band ALOS PALSAR data with ROI_PAC, an interferometric coherence map that spans the demolition period is registered to a coherence map before the demolition, and the relative bias of the coherence values are removed, then a causality constraint is applied to enhance the change due to demolition. The results show clear change in coherence at the demolition site. We improve the signal-to-noise ratio of the coherence change at the demolition site from 17.3 (for simple difference) to 44.6 (with the new algorithm). The damage assessment map algorithm will become more useful with the emergence of InSAR missions with more frequent data acquisition, such as Sentinel-1 and DESDynI.

INVESTIGATING THE EFFICACY OF CLINICAL TRIAL MONITORING STRATEGIES: Design and Implementation of the Cluster Randomized START Monitoring Substudy

PubMed Central

Hullsiek, Katherine Huppler; Kagan, Jonathan M; Engen, Nicole; Grarup, Jesper; Hudson, Fleur; Denning, Eileen T; Carey, Catherine; Courtney-Rodgers, David; Finley, Elizabeth B; Jansson, Per O; Pearson, Mary T; Peavy, Dwight E; Belloso, Waldo H

2014-01-01

Background Trial monitoring protects participant safety and study integrity. While monitors commonly go on-site to verify source data, there is little evidence that this practice is efficient or effective. An ongoing international HIV treatment trial (START) provides an opportunity to explore the usefulness of different monitoring approaches. Methods All START sites are centrally monitored and required to follow a local monitoring plan requiring specific quality assurance activities. Additionally, sites were randomized (1:1) to receive, or not receive, annual on-site monitoring. The study will determine if on-site monitoring increases the identification of major protocol deviations (eligibility or consent violations, improper study drug use, primary or serious event underreporting, data alteration or fraud). Results The START study completed enrollment in December 2013, with planned follow-up through December 2016. The monitoring study is ongoing at 196 sites in 34 countries. Results are expected when the START study concludes in December 2016. PMID:25973346

Effects of transcriptional start site sequence and position on nucleotide-sensitive selection of alternative start sites at the pyrC promoter in Escherichia coli.

PubMed Central

Liu, J; Turnbough, C L

1994-01-01

In Escherichia coli, expression of the pyrC gene is regulated primarily by a translational control mechanism based on nucleotide-sensitive selection of transcriptional start sites at the pyrC promoter. When intracellular levels of CTP are high, pyrC transcripts are initiated predominantly with CTP at a site 7 bases downstream of the Pribnow box. These transcripts form a stable hairpin at their 5' ends that blocks ribosome binding. When the CTP level is low and the GTP level is high, conditions found in pyrimidine-limited cells, transcripts are initiated primarily with GTP at a site 9 bases downstream of the Pribnow box. These shorter transcripts are unable to form a hairpin at their 5' ends and are readily translated. In this study, we examined the effects of nucleotide sequence and position on the selection of transcriptional start sites at the pyrC promoter. We characterized promoter mutations that systematically alter the sequence at position 7 or 9 downstream of the Pribnow box or vary the spacing between the Pribnow box and wild-type transcriptional initiation region. The results reveal preferences for particular initiating nucleotides (ATP > or = GTP > UTP >> CTP) and for starting positions downstream of the Pribnow box (7 >> 6 and 8 > 9 > 10). The results indicate that optimal nucleotide-sensitive start site switching at the wild-type pyrC promoter is the result of competition between the preferred start site (position 7) that uses the poorest initiating nucleotide (CTP) and a weak start site (position 9) that uses a good initiating nucleotide (GTP). The sequence of the pyrC promoter also minimizes the synthesis of untranslatable transcripts and provides for maximum stability of the regulatory transcript hairpin. In addition, the results show that the effects of the mutations on pyrC expression and regulation are consistent with the current model for translational control. Possible effects of preferences for initiating nucleotides and start sites on the expression and regulation of other genes are discussed. Images PMID:7910603

Direct optical mapping of transcription factor binding sites on field-stretched λ-DNA in nanofluidic devices

PubMed Central

Sriram, K. K.; Yeh, Jia-Wei; Lin, Yii-Lih; Chang, Yi-Ren; Chou, Chia-Fu

2014-01-01

Mapping transcription factor (TF) binding sites along a DNA backbone is crucial in understanding the regulatory circuits that control cellular processes. Here, we deployed a method adopting bioconjugation, nanofluidic confinement and fluorescence single molecule imaging for direct mapping of TF (RNA polymerase) binding sites on field-stretched single DNA molecules. Using this method, we have mapped out five of the TF binding sites of E. coli RNA polymerase to bacteriophage λ-DNA, where two promoter sites and three pseudo-promoter sites are identified with the corresponding binding frequency of 45% and 30%, respectively. Our method is quick, robust and capable of resolving protein-binding locations with high accuracy (∼ 300 bp), making our system a complementary platform to the methods currently practiced. It is advantageous in parallel analysis and less prone to false positive results over other single molecule mapping techniques such as optical tweezers, atomic force microscopy and molecular combing, and could potentially be extended to general mapping of protein–DNA interaction sites. PMID:24753422

Oligo kernels for datamining on biological sequences: a case study on prokaryotic translation initiation sites

PubMed Central

Meinicke, Peter; Tech, Maike; Morgenstern, Burkhard; Merkl, Rainer

2004-01-01

Background Kernel-based learning algorithms are among the most advanced machine learning methods and have been successfully applied to a variety of sequence classification tasks within the field of bioinformatics. Conventional kernels utilized so far do not provide an easy interpretation of the learnt representations in terms of positional and compositional variability of the underlying biological signals. Results We propose a kernel-based approach to datamining on biological sequences. With our method it is possible to model and analyze positional variability of oligomers of any length in a natural way. On one hand this is achieved by mapping the sequences to an intuitive but high-dimensional feature space, well-suited for interpretation of the learnt models. On the other hand, by means of the kernel trick we can provide a general learning algorithm for that high-dimensional representation because all required statistics can be computed without performing an explicit feature space mapping of the sequences. By introducing a kernel parameter that controls the degree of position-dependency, our feature space representation can be tailored to the characteristics of the biological problem at hand. A regularized learning scheme enables application even to biological problems for which only small sets of example sequences are available. Our approach includes a visualization method for transparent representation of characteristic sequence features. Thereby importance of features can be measured in terms of discriminative strength with respect to classification of the underlying sequences. To demonstrate and validate our concept on a biochemically well-defined case, we analyze E. coli translation initiation sites in order to show that we can find biologically relevant signals. For that case, our results clearly show that the Shine-Dalgarno sequence is the most important signal upstream a start codon. The variability in position and composition we found for that signal is in accordance with previous biological knowledge. We also find evidence for signals downstream of the start codon, previously introduced as transcriptional enhancers. These signals are mainly characterized by occurrences of adenine in a region of about 4 nucleotides next to the start codon. Conclusions We showed that the oligo kernel can provide a valuable tool for the analysis of relevant signals in biological sequences. In the case of translation initiation sites we could clearly deduce the most discriminative motifs and their positional variation from example sequences. Attractive features of our approach are its flexibility with respect to oligomer length and position conservation. By means of these two parameters oligo kernels can easily be adapted to different biological problems. PMID:15511290

Operator design and mechanism for CarA repressor-mediated down-regulation of the photoinducible carB operon in Myxococcus xanthus.

PubMed

López-Rubio, José Juan; Padmanabhan, S; Lázaro, Jose María; Salas, Margarita; Murillo, Francisco José; Elías-Arnanz, Montserrat

2004-07-09

The carB operon encodes all except one of the enzymes involved in light-induced carotenogenesis in Myxococcus xanthus. Expression of its promoter (P(B)) is repressed in the dark by sequence-specific DNA binding of CarA to a palindrome (pI) located between positions -47 and -64 relative to the transcription start site. This promotes subsequent binding of CarA to additional sites that remain to be defined. CarS, produced in the light, interacts physically with CarA, abrogates CarA-DNA binding, and thereby derepresses P(B). In this study, we delineate the operator design that exists for CarA by precisely mapping out the second operator element. For this, we examined how stepwise deletions and site-directed mutagenesis in the region between the palindrome and the transcription start site affect CarA binding around P(B) in vitro and expression of P(B) in vivo. These revealed the second operator element to be an imperfect interrupted palindrome (pII) spanning positions -26 to -40. In vitro assays using purified M. xanthus RNA polymerase showed that CarA abolishes P(B)-RNA polymerase binding and runoff transcription and that both were restored by CarS, thus rationalizing the observations in vivo. CarA binding to pII (after association with pI) effectively occludes RNA polymerase from P(B) and so provides the operative mechanism for the repression of the carB operon by CarA. The bipartite operator design, whereby transcription is blocked by the low affinity CarA-pII binding and is readily restored by CarS, may have evolved to match the needs for a rapid and an effective response to light.

ReadXplorer—visualization and analysis of mapped sequences

PubMed Central

Hilker, Rolf; Stadermann, Kai Bernd; Doppmeier, Daniel; Kalinowski, Jörn; Stoye, Jens; Straube, Jasmin; Winnebald, Jörn; Goesmann, Alexander

2014-01-01

Motivation: Fast algorithms and well-arranged visualizations are required for the comprehensive analysis of the ever-growing size of genomic and transcriptomic next-generation sequencing data. Results: ReadXplorer is a software offering straightforward visualization and extensive analysis functions for genomic and transcriptomic DNA sequences mapped on a reference. A unique specialty of ReadXplorer is the quality classification of the read mappings. It is incorporated in all analysis functions and displayed in ReadXplorer's various synchronized data viewers for (i) the reference sequence, its base coverage as (ii) normalizable plot and (iii) histogram, (iv) read alignments and (v) read pairs. ReadXplorer's analysis capability covers RNA secondary structure prediction, single nucleotide polymorphism and deletion–insertion polymorphism detection, genomic feature and general coverage analysis. Especially for RNA-Seq data, it offers differential gene expression analysis, transcription start site and operon detection as well as RPKM value and read count calculations. Furthermore, ReadXplorer can combine or superimpose coverage of different datasets. Availability and implementation: ReadXplorer is available as open-source software at http://www.readxplorer.org along with a detailed manual. Contact: rhilker@mikrobio.med.uni-giessen.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24790157

Mapping the spatial and temporal dynamics of the velvet mesquite with MODIS and AVIRIS: Case study at the Santa Rita Experimental Range

NASA Astrophysics Data System (ADS)

Kaurivi, Jorry Zebby Ujama

The general objective of this research is to develop a methodology that will allow mapping and quantifying shrub encroachment with remote sensing. The multitemporal properties of the Moderate Resolution Imaging Spectroradiometer (MODIS) -250m, 16-day vegetation index products were combined with the hyperspectral and high spatial resolution (3.6m) computation of the Airborne Visible-Infrared Imaging Spectrometer (AVIRIS) to detect the dynamics of mesquite and grass/soil matrix at two sites of high (19.5%) and low (5.7%) mesquite cover in the Santa Rita Experimental Range (SRER). MODIS results showed separability between grassland and mesquite based on phenology. Mesquite landscapes had longer green peak starting in April through February, while the grassland only peaked during the monsoon season (July through October). AVIRIS revealed spectral separability, but high variation in the data implicated high heterogeneity in the landscape. Nonetheless, the methodology for larger data was developed in this study and combines ground, air and satellite data.

High-resolution mapping of transcription factor binding sites on native chromatin

PubMed Central

Kasinathan, Sivakanthan; Orsi, Guillermo A.; Zentner, Gabriel E.; Ahmad, Kami; Henikoff, Steven

2014-01-01

Sequence-specific DNA-binding proteins including transcription factors (TFs) are key determinants of gene regulation and chromatin architecture. Formaldehyde cross-linking and sonication followed by Chromatin ImmunoPrecipitation (X-ChIP) is widely used for profiling of TF binding, but is limited by low resolution and poor specificity and sensitivity. We present a simple protocol that starts with micrococcal nuclease-digested uncross-linked chromatin and is followed by affinity purification of TFs and paired-end sequencing. The resulting ORGANIC (Occupied Regions of Genomes from Affinity-purified Naturally Isolated Chromatin) profiles of Saccharomyces cerevisiae Abf1 and Reb1 provide highly accurate base-pair resolution maps that are not biased toward accessible chromatin, and do not require input normalization. We also demonstrate the high specificity of our method when applied to larger genomes by profiling Drosophila melanogaster GAGA Factor and Pipsqueak. Our results suggest that ORGANIC profiling is a widely applicable high-resolution method for sensitive and specific profiling of direct protein-DNA interactions. PMID:24336359

Datum Transformation of Spatial Data and Application in Cadastre

NASA Astrophysics Data System (ADS)

Kısa, A.; Erkek, B.; Ekin, L.

2012-07-01

In Turkey, cadastral works have been started with local-based works in 1924 and speeded up after 1950's by using photogrammetry. Different measurement methods, coordinate systems and scales have been used in these works. As a result of primary cadastral activities two main products are generated; cadastral maps and title deeds. After this, cadastral data live on the maps, by cadastral activities carried out by cadastral offices and title deed data live on the registrations by land registration activities carried out by land registration offices. Up to 2005 different references systems such as local (graphic) and ED50 have been used for Cadastral maps production. 2000's Land Registry and Cadastre Information System (TAKBİS) Project has started as a pilot application by Land Registry and Cadastre (TKGM). After completion of pilot project spreading activities started in 2005 and still has been ongoing. On the other hand The government has taken the decision to finish primary cadastral activities within three years. The primary cadastral activities completed at the end of 2008. And also TKGM has completed metadata portal in 2008. At last, cadastral map updating (renovation) started in 2009 by using digital orthophoto with 30 cm GSD. Today people have great expectations in accomplishing digital cadastral services, they need correct, reliable, easy and quick accessible land register and cadastral survey information. Even such request expressed in INPIRE directive by using ISO 191XX data standards. This means we have great hard work for spatial data conversion, datum and data transformation for map and cadastral data harmonization. This paper presents results of investigation of used cadastral maps and used datums of the TKGM and possible transformation methods of datum and some recommendations for future applications.

Distinct p53 genomic binding patterns in normal and cancer-derived human cells

PubMed Central

McCorkle, Sean R; McCombie, WR; Dunn, John J

2011-01-01

Here, we report genome-wide analysis of the tumor suppressor p53 binding sites in normal human cells. 743 high-confidence ChIP-seq peaks representing putative genomic binding sites were identified in normal IMR90 fibroblasts using a reference chromatin sample. More than 40% were located within 2 kb of a transcription start site (TSS), a distribution similar to that documented for individually studied, functional p53 binding sites and, to date, not observed by previous p53 genome-wide studies. Nearly half of the high-confidence binding sites in the IMR90 cells reside in CpG islands in marked contrast to sites reported in cancer-derived cells. The distinct genomic features of the IMR90 binding sites do not reflect a distinct preference for specific sequences, since the de novo developed p53 motif based on our study is similar to those reported by genome-wide studies of cancer cells. More likely, the different chromatin landscape in normal, compared with cancer-derived cells, influences p53 binding via modulating availability of the sites. We compared the IMR90 ChIP-seq peaks to the recently published IMR90 methylome1 and demonstrated that they are enriched at hypomethylated DNA. Our study represents the first genome-wide, de novo mapping of p53 binding sites in normal human cells and reveals that p53 binding sites reside in distinct genomic landscapes in normal and cancer-derived human cells. PMID:22127205

Stewardship mapping and assessment project: a framework for understanding community-based environmental stewardship

Treesearch

Erika S. Svendsen; Lindsay K. Campbell; Dana R. Fisher; James J.T. Connolly; Michelle L. Johnson; Nancy Falxa Sonti; Dexter H. Locke; Lynne M. Westphal; Cherie LeBlanc Fisher; Morgan Grove; Michele Romolini; Dale J. Blahna; Kathleen L. Wolf

2016-01-01

The Stewardship Mapping and Assessment Project (STEW-MAP) is designed to answer who, where, why and how environmental stewardship groups are caring for our urbanized landscapes. This report is intended to be a guide for those who wish to start STEW-MAP in their own city. It contains step-by-step directions for how to plan and implement a STEW-MAP project. STEW-MAP is...

Post-transcriptional m6A editing of HIV-1 mRNAs enhances viral gene expression

PubMed Central

Kennedy, Edward M.; Bogerd, Hal P.; Kornepati, Anand V. R.; Kang, Dong; Ghoshal, Delta; Marshall, Joy B.; Poling, Brigid C.; Tsai, Kevin; Gokhale, Nandan S.; Horner, Stacy M.; Cullen, Bryan R.

2016-01-01

Summary Covalent addition of a methyl group to the adenosine N6 (m6A) is an evolutionarily conserved and common RNA modification that is thought to modulate several aspects of RNA metabolism. While the presence of multiple m6A editing sites on diverse viral RNAs was reported starting almost 40 years ago, how m6A editing affects virus replication has remained unclear. Here, we used photo-crosslinking-assisted m6A sequencing techniques to precisely map several m6A editing sites on the HIV-1 genome and report that they cluster in the HIV-1 3’ untranslated region (3'UTR). Viral 3'UTR m6A sites or analogous cellular m6A sites strongly enhanced mRNA expression in cis by recruiting the cellular YTHDF m6A “reader” proteins. Reducing YTHDF expression inhibited, while YTHDF overexpression enhanced, HIV-1 protein and RNA expression, and virus replication in CD4+ T cells. These data identify m6A editing, and the resultant recruitment of YTHDF proteins, as major positive regulators of HIV-1 mRNA expression. PMID:27117054

Language Mapping with Navigated Repetitive TMS: Proof of Technique and Validation

PubMed Central

Tarapore, Phiroz E.; Findlay, Anne M.; Honma, Susanne M.; Mizuiri, Danielle; Houde, John F.; Berger, Mitchel S.; Nagarajan, Srikantan S.

2013-01-01

Objective Lesion-based mapping of speech pathways has been possible only during invasive neurosurgical procedures using direct cortical stimulation (DCS). However, navigated transcranial magnetic stimulation (nTMS) may allow for lesion-based interrogation of language pathways noninvasively. Although not lesion-based, magnetoencephalographic imaging (MEGI) is another noninvasive modality for language mapping. In this study, we compare the accuracy of nTMS and MEGI with DCS. Methods Subjects with lesions around cortical language areas underwent preoperative nTMS and MEGI for language mapping. nTMS maps were generated using a repetitive TMS protocol to deliver trains of stimulations during a picture naming task. MEGI activation maps were derived from adaptive spatial filtering of beta-band power decreases prior to overt speech during picture naming and verb generation tasks. The subjects subsequently underwent awake language mapping via intraoperative DCS. The language maps obtained from each of the 3 modalities were recorded and compared. Results nTMS and MEGI were performed on 12 subjects. nTMS yielded 21 positive language disruption sites (11 speech arrest, 5 anomia, and 5 other) while DCS yielded 10 positive sites (2 speech arrest, 5 anomia, and 3 other). MEGI isolated 32 sites of peak activation with language tasks. Positive language sites were most commonly found in the pars opercularis for all three modalities. In 9 instances the positive DCS site corresponded to a positive nTMS site, while in 1 instance it did not. In 4 instances, a positive nTMS site corresponded to a negative DCS site, while 169 instances of negative nTMS and DCS were recorded. The sensitivity of nTMS was therefore 90%, specificity was 98%, the positive predictive value was 69% and the negative predictive value was 99% as compared with intraoperative DCS. MEGI language sites for verb generation and object naming correlated with nTMS sites in 5 subjects, and with DCS sites in 2 subjects. Conclusion Maps of language function generated with nTMS correlate well with those generated by DCS. Negative nTMS mapping also correlates with negative DCS mapping. In our study, MEGI lacks the same level of correlation with intraoperative mapping; nevertheless it provides useful adjunct information in some cases. nTMS may offer a lesion-based method for noninvasively interrogating language pathways and be valuable in managing patients with peri-eloquent lesions. PMID:23702420

SfiI genomic cleavage map of Escherichia coli K-12 strain MG1655.

PubMed Central

Perkins, J D; Heath, J D; Sharma, B R; Weinstock, G M

1992-01-01

An SfiI restriction map of Escherichia coli K-12 strain MG1655 is presented. The map contains thirty-one cleavage sites separating fragments ranging in size from 407 kb to 3.7 kb. Several techniques were used in the construction of this map, including CHEF pulsed field gel electrophoresis; physical analysis of a set of twenty-six auxotrophic transposon insertions; correlation with the restriction map of Kohara and coworkers using the commercially available E. coli Gene Mapping Membranes; analysis of publicly available sequence information; and correlation of the above data with the combined genetic and physical map developed by Rudd, et al. The combination of these techniques has yielded a map in which all but one site can be localized within a range of +/- 2 kb, and over half the sites can be localized precisely by sequence data. Two sites present in the EcoSeq5 sequence database are not cleaved in MG1655 and four sites are noted to be sensitive to methylation by the dcm methylase. This map, combined with the NotI physical map of MG1655, can aid in the rapid, precise mapping of several different types of genetic alterations, including transposon mediated mutations and other insertions, inversions, deletions and duplications. Images PMID:1312707

10 CFR 36.15 - Start of construction.

Code of Federal Regulations, 2010 CFR

2010-01-01

... Requirements § 36.15 Start of construction. The applicant may not begin construction of a new irradiator prior... work, purchase of a site, site surveys or soil testing, site preparation, site excavation, construction... license with respect to the requirements of the Atomic Energy Act of 1954, as amended, and rules...

47 CFR 73.4108 - FM transmitter site map submissions.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 47 Telecommunication 4 2011-10-01 2011-10-01 false FM transmitter site map submissions. 73.4108 Section 73.4108 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) BROADCAST RADIO SERVICES RADIO BROADCAST SERVICES Rules Applicable to All Broadcast Stations § 73.4108 FM transmitter site map...

Occupancy Grid Map Merging Using Feature Maps

DTIC Science & Technology

2010-11-01

each robot begins exploring at different starting points, once two robots can communicate, they send their odometry data, LIDAR observations, and maps...robots [11]. Moreover, it is relevant to mention that significant success has been achieved in solving SLAM problems when using hybrid maps [12...represents the environment by parametric features. Our method is capable of representing a LIDAR scanned environment map in a parametric fashion. In general

statement of significance, location map, site plan, landscape plan, site ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

statement of significance, location map, site plan, landscape plan, site sections, evolution of cemetery landscape. - San Francisco National Cemetery, 1 Lincoln Boulevard, San Francisco, San Francisco County, CA

Two alternative ways of start site selection in human norovirus reinitiation of translation.

PubMed

Luttermann, Christine; Meyers, Gregor

2014-04-25

The calicivirus minor capsid protein VP2 is expressed via termination/reinitiation. This process depends on an upstream sequence element denoted termination upstream ribosomal binding site (TURBS). We have shown for feline calicivirus and rabbit hemorrhagic disease virus that the TURBS contains three sequence motifs essential for reinitiation. Motif 1 is conserved among caliciviruses and is complementary to a sequence in the 18 S rRNA leading to the model that hybridization between motif 1 and 18 S rRNA tethers the post-termination ribosome to the mRNA. Motif 2 and motif 2* are proposed to establish a secondary structure positioning the ribosome relative to the start site of the terminal ORF. Here, we analyzed human norovirus (huNV) sequences for the presence and importance of these motifs. The three motifs were identified by sequence analyses in the region upstream of the VP2 start site, and we showed that these motifs are essential for reinitiation of huNV VP2 translation. More detailed analyses revealed that the site of reinitiation is not fixed to a single codon and does not need to be an AUG, even though this codon is clearly preferred. Interestingly, we were able to show that reinitiation can occur at AUG codons downstream of the canonical start/stop site in huNV and feline calicivirus but not in rabbit hemorrhagic disease virus. Although reinitiation at the original start site is independent of the Kozak context, downstream initiation exhibits requirements for start site sequence context known for linear scanning. These analyses on start codon recognition give a more detailed insight into this fascinating mechanism of gene expression.

Regional mapping of hydrothermally altered igneous rocks along the Urumieh-Dokhtar, Chagai, and Alborz Belts of western Asia using Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) data and Interactive Data Language (IDL) logical operators: a tool for porphyry copper exploration and assessment: Chapter O in Global mineral resource assessment

USGS Publications Warehouse

Mars, John L.; Zientek, M.L.; Hammarstrom, J.M.; Johnson, K.M.; Pierce, F.W.

2014-01-01

The ASTER alteration map and corresponding geologic maps were used to select circular to elliptical patterns of argillic- and phyllic-altered volcanic and intrusive rocks as potential porphyry copper sites. One hundred and seventy eight potential porphyry copper sites were mapped along the UDVB, and 23 sites were mapped along the CVB. The potential sites were selected to assist in further exploration and assessments of undiscovered porphyry copper deposits.

Sensitivity in error detection of patient specific QA tools for IMRT plans

NASA Astrophysics Data System (ADS)

Lat, S. Z.; Suriyapee, S.; Sanghangthum, T.

2016-03-01

The high complexity of dose calculation in treatment planning and accurate delivery of IMRT plan need high precision of verification method. The purpose of this study is to investigate error detection capability of patient specific QA tools for IMRT plans. The two H&N and two prostate IMRT plans with MapCHECK2 and portal dosimetry QA tools were studied. Measurements were undertaken for original and modified plans with errors introduced. The intentional errors composed of prescribed dose (±2 to ±6%) and position shifting in X-axis and Y-axis (±1 to ±5mm). After measurement, gamma pass between original and modified plans were compared. The average gamma pass for original H&N and prostate plans were 98.3% and 100% for MapCHECK2 and 95.9% and 99.8% for portal dosimetry, respectively. In H&N plan, MapCHECK2 can detect position shift errors starting from 3mm while portal dosimetry can detect errors started from 2mm. Both devices showed similar sensitivity in detection of position shift error in prostate plan. For H&N plan, MapCHECK2 can detect dose errors starting at ±4%, whereas portal dosimetry can detect from ±2%. For prostate plan, both devices can identify dose errors starting from ±4%. Sensitivity of error detection depends on type of errors and plan complexity.

Seismic Hazard Maps for Seattle, Washington, Incorporating 3D Sedimentary Basin Effects, Nonlinear Site Response, and Rupture Directivity

USGS Publications Warehouse

Frankel, Arthur D.; Stephenson, William J.; Carver, David L.; Williams, Robert A.; Odum, Jack K.; Rhea, Susan

2007-01-01

This report presents probabilistic seismic hazard maps for Seattle, Washington, based on over 500 3D simulations of ground motions from scenario earthquakes. These maps include 3D sedimentary basin effects and rupture directivity. Nonlinear site response for soft-soil sites of fill and alluvium was also applied in the maps. The report describes the methodology for incorporating source and site dependent amplification factors into a probabilistic seismic hazard calculation. 3D simulations were conducted for the various earthquake sources that can affect Seattle: Seattle fault zone, Cascadia subduction zone, South Whidbey Island fault, and background shallow and deep earthquakes. The maps presented in this document used essentially the same set of faults and distributed-earthquake sources as in the 2002 national seismic hazard maps. The 3D velocity model utilized in the simulations was validated by modeling the amplitudes and waveforms of observed seismograms from five earthquakes in the region, including the 2001 M6.8 Nisqually earthquake. The probabilistic seismic hazard maps presented here depict 1 Hz response spectral accelerations with 10%, 5%, and 2% probabilities of exceedance in 50 years. The maps are based on determinations of seismic hazard for 7236 sites with a spacing of 280 m. The maps show that the most hazardous locations for this frequency band (around 1 Hz) are soft-soil sites (fill and alluvium) within the Seattle basin and along the inferred trace of the frontal fault of the Seattle fault zone. The next highest hazard is typically found for soft-soil sites in the Duwamish Valley south of the Seattle basin. In general, stiff-soil sites in the Seattle basin exhibit higher hazard than stiff-soil sites outside the basin. Sites with shallow bedrock outside the Seattle basin have the lowest estimated hazard for this frequency band.

The Westfield River Watershed Interactive Atlas: mapping recreation data on the web

Treesearch

Robert S. Bristow; Steven Riberdy

2002-01-01

Imagine searching the web to create a map to your house. You could use one of the many Internet mapping sites like MapBlast™ or MapQuest™ to create such a map. But maybe you wish to get a map of trails for the Grand Canyon. The National Park Service web site could serve that need. Or you may wish to get a map to show you the way from the Orlando...

Using Concept Maps to Assess Interdisciplinary Integration of Green Engineering Knowledge

ERIC Educational Resources Information Center

Borrego, Maura; Newswander, Chad B.; McNair, Lisa D.; McGinnis, Sean; Paretti, Marie C.

2009-01-01

Engineering education, like many fields, has started to explore the benefits of concept maps as an assessment technique for knowledge integration. Because they allow students to graphically link topics and represent complex interconnections among diverse concepts, we argue that concept maps are particularly appropriate for assessing…

Mapping and analysis of phosphorylation sites: a quick guide for cell biologists

PubMed Central

Dephoure, Noah; Gould, Kathleen L.; Gygi, Steven P.; Kellogg, Douglas R.

2013-01-01

A mechanistic understanding of signaling networks requires identification and analysis of phosphorylation sites. Mass spectrometry offers a rapid and highly sensitive approach to mapping phosphorylation sites. However, mass spectrometry has significant limitations that must be considered when planning to carry out phosphorylation-site mapping. Here we provide an overview of key information that should be taken into consideration before beginning phosphorylation-site analysis, as well as a step-by-step guide for carrying out successful experiments. PMID:23447708

47 CFR 73.4108 - FM transmitter site map submissions.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 47 Telecommunication 4 2010-10-01 2010-10-01 false FM transmitter site map submissions. 73.4108... RADIO BROADCAST SERVICES Rules Applicable to All Broadcast Stations § 73.4108 FM transmitter site map submissions. See Memorandum Opinion and Order and Public Notice, adopted October 24, 1986. 1 FCC Rcd 381 (1986...

Temporal and spatial structure in a daily wildfire-start data set from the western United States (198696)

USGS Publications Warehouse

Bartlein, P.J.; Hostetler, S.W.; Shafer, S.L.; Holman, J.O.; Solomon, A.M.

2008-01-01

The temporal and spatial structure of 332 404 daily fire-start records from the western United States for the period 1986 through 1996 is illustrated using several complimentary visualisation techniques. We supplement maps and time series plots with Hovmo??ller diagrams that reduce the spatial dimensionality of the daily data in order to reveal the underlying space?time structure. The mapped distributions of all lightning- and human-started fires during the 11-year interval show similar first-order patterns that reflect the broad-scale distribution of vegetation across the West and the annual cycle of climate. Lightning-started fires are concentrated in the summer half-year and occur in widespread outbreaks that last a few days and reflect coherent weather-related controls. In contrast, fires started by humans occur throughout the year and tend to be concentrated in regions surrounding large-population centres or intensive-agricultural areas. Although the primary controls of human-started fires are their location relative to burnable fuel and the level of human activity, spatially coherent, weather-related variations in their incidence can also be noted. ?? IAWF 2008.

The new geographic information system in ETVA VI.PE.

NASA Astrophysics Data System (ADS)

Xagoraris, Zafiris; Soulis, George

2016-08-01

ETVA VI.PE. S.A. is a member of the Piraeus Bank Group of Companies and its activities include designing, developing, exploiting and managing Industrial Areas throughout Greece. Inside ETVA VI.PE.'s thirty-one Industrial Parks there are currently 2,500 manufacturing companies established, with 40,000 employees and € 2.5 billion of invested funds. In each one of the industrial areas ETVA VI.PE guarantees the companies industrial lots of land (sites) with propitious building codes and complete infrastructure networks of water supply, sewerage, paved roads, power supply, communications, cleansing services, etc. The development of Geographical Information System for ETVA VI.PE.'s Industrial Parks started at the beginning of 1992 and consists of three subsystems: Cadastre, that manages the information for the land acquisition of Industrial Areas; Street Layout - Sites, that manages the sites sold to manufacturing companies; Networks, that manages the infrastructure networks (roads, water supply, sewerage etc). The mapping of each Industrial Park is made incorporating state-of-the-art photogrammetric, cartographic and surveying methods and techniques. Passing through the phases of initial design (hybrid GIS) and system upgrade (integrated Gis solution with spatial database), the system is currently operating on a new upgrade (integrated gIS solution with spatial database) that includes redesigning and merging the system's database schemas, along with the creation of central security policies, and the development of a new web GIS application for advanced data entry, highly customisable and standard reports, and dynamic interactive maps. The new GIS bring the company to advanced levels of productivity and introduce the new era for decision making and business management.

Mapping resource use over a Russian landscape: an integrated look at harvesting of a non-timber forest product in central Kamchatka

NASA Astrophysics Data System (ADS)

Hitztaler, Stephanie K.; Bergen, Kathleen M.

2013-12-01

Small-scale resource use became an important adaptive mechanism in remote logging communities in Russia at the onset of the post-Soviet period in 1991. We focused on harvesting of a non-timber forest product, lingonberry (Vaccinium vitis-idaea), in the forests of the Kamchatka Peninsula (Russian Far East). We employed an integrated geographical approach to make quantifiable connections between harvesting and the landscape, and to interpret these relationships in their broader contexts. Landsat TM images were used for a new classification; the resulting land-cover map was the basis for linking non-spatial data on harvesters’ gathering behaviors to spatial data within delineated lingonberry gathering sites. Several significant relationships emerged: (1) mature forests negatively affected harvesters’ initial choice to gather in a site, while young forests had a positive effect; (2) land-cover type was critical in determining how and why gathering occurred: post-disturbance young and maturing forests were significantly associated with higher gathering intensity and with the choice to market harvests; and (3) distance from gathering sites to villages and main roads also mattered: longer distances were significantly correlated to more time spent gathering and to increased marketing of harvests. We further considered our findings in light of the larger ecological and social dynamics at play in central Kamchatka. This unique study is an important starting point for conservation- and sustainable development-based work, and for additional research into the drivers of human-landscape interactions in the Russian Far East.

National Airspace System (NAS)

DTIC Science & Technology

2013-12-01

signed at Ft. Hood, Texas (Army Site) on August 29, 2013. DASR Installation and Check-Out ( INCO ) started at Dobbins AFB, Georgia (AF Site) on February 25...2013, with SAT completed on July 17, 2013 and DD250 signed on September 17, 2013. DASR INCO at Aviano AB, Italy started on September 9, 2013...Island (Navy site) on December 16, 2013. DASR INCO at Lajes Field, Portugal started on June 12, 2013; DASR SAT was completed on January 30, 2014

Spatial Organization of the Core Region of Yeast TFIIIB-DNA Complexes

PubMed Central

Persinger, Jim; Sengupta, Sarojini M.; Bartholomew, Blaine

1999-01-01

The interaction of yeast TFIIIB with the region upstream of the SUP4 tRNATyr gene was extensively probed by use of photoreactive phosphodiesters, deoxyuridines, and deoxycytidines that are site specifically incorporated into DNA. The TATA binding protein (TBP) was found to be in close proximity to the minor groove of a TATA-like DNA sequence that starts 30 nucleotides upstream of the start site of transcription. TBP was cross-linked to the phosphate backbone of DNA from bp −30 to −20 in the nontranscribed strand and from bp −28 to −24 in the transcribed strand (+1 denotes the start site of transcription). Most of the major groove of DNA in this region was shown not to be in close proximity to TBP, thus resembling the binding of TBP to the TATA box, with one notable exception. TBP was shown to interact with the major groove of DNA primarily at bp −23 and to a lesser degree at bp −25 in the transcribed strand. The stable interaction of TBP with the major groove at bp −23 was shown to require the B" subunit of TFIIIB. The S4 helix and flanking region of TBP were shown to be proximal to the major groove of DNA by peptide mapping of the region of TBP cross-linked at bp −23. Thus, TBP in the TFIIIB-SUP4 gene promoter region is bound in the same direction as TBP bound to the TATA box with respect to the transcription start site. The B" and TFIIB-related factor (BRF) subunits of TFIIIB are positioned on opposite sides of the TBP-DNA core of the TFIIIB complex, as indicated by correlation of cross-linking data to the crystal structure of the TBP-TATA box complex. Evidence is given for BRF binding near the C-terminal stirrup of TBP, similar to that of TFIIB near the TBP-TATA box complex. The protein clamp formed around the TBP-DNA complex by BRF and B" would help explain the long half-life of the TFIIIB-DNA complex and its resistance to polyanions and high salt. The path of DNA traversing the surface of TBP at the 3′ end of the TATA-like element in the SUP4 tRNA gene is not the same as that of TBP bound to a TATA box element, as shown by the cross-linking of TBP at bp −23. PMID:10373570

Myh7b/miR-499 gene expression is transcriptionally regulated by MRFs and Eos

PubMed Central

Yeung, Fan; Chung, Eunhee; Guess, Martin G.; Bell, Matthew L.; Leinwand, Leslie A.

2012-01-01

The sarcomeric myosin gene, Myh7b, encodes an intronic microRNA, miR-499, which regulates cardiac and skeletal muscle biology, yet little is known about its transcriptional regulation. To identify the transcription factors involved in regulating Myh7b/miR-499 gene expression, we have mapped the transcriptional start sites and identified an upstream 6.2 kb region of the mouse Myh7b gene whose activity mimics the expression pattern of the endogenous Myh7b gene both in vitro and in vivo. Through promoter deletion analysis, we have mapped a distal E-box element and a proximal Ikaros site that are essential for Myh7b promoter activity in muscle cells. We show that the myogenic regulatory factors, MyoD, Myf5 and Myogenin, bind to the E-box, while a lymphoid transcription factor, Ikaros 4 (Eos), binds to the Ikaros motif. Further, we show that through physical interaction, MyoD and Eos form an active transcriptional complex on the chromatin to regulate the expression of the endogenous Myh7b/miR-499 gene in muscle cells. We also provide the first evidence that Eos can regulate expression of additional myosin genes (Myosin 1 and β-Myosin) via the miR-499/Sox6 pathway. Therefore, our results indicate a novel role for Eos in the regulation of the myofiber gene program. PMID:22638570

Inhibition of Non-ATG Translational Events in Cells via Covalent Small Molecules Targeting RNA.

PubMed

Yang, Wang-Yong; Wilson, Henry D; Velagapudi, Sai Pradeep; Disney, Matthew D

2015-04-29

One major class of disease-causing RNAs is expanded repeating transcripts. These RNAs cause diseases via multiple mechanisms, including: (i) gain-of-function, in which repeating RNAs bind and sequester proteins involved in RNA biogenesis and (ii) repeat associated non-ATG (RAN) translation, in which repeating transcripts are translated into toxic proteins without use of a canonical, AUG, start codon. Herein, we develop and study chemical probes that bind and react with an expanded r(CGG) repeat (r(CGG)(exp)) present in a 5' untranslated region that causes fragile X-associated tremor/ataxia syndrome (FXTAS). Reactive compounds bind to r(CGG)(exp) in cellulo as shown with Chem-CLIP-Map, an approach to map small molecule binding sites within RNAs in cells. Compounds also potently improve FXTAS-associated pre-mRNA splicing and RAN translational defects, while not affecting translation of the downstream open reading frame. In contrast, oligonucleotides affect both RAN and canonical translation when they bind to r(CGG)(exp), which is mechanistically traced to a decrease in polysome loading. Thus, designer small molecules that react with RNA targets can be used to profile the RNAs to which they bind in cells, including identification of binding sites, and can modulate several aspects of RNA-mediated disease pathology in a manner that may be more beneficial than oligonucleotides.

Characterization of the human peroxisome proliferator activated receptor delta gene and its expression.

PubMed

Skogsberg, J; Kannisto, K; Roshani, L; Gagne, E; Hamsten, A; Larsson, C; Ehrenborg, E

2000-07-01

Peroxisome proliferator activated receptors (PPARs) are nuclear receptors regulating the expression of genes involved in lipid and glucose metabolism. Three different PPARs; alpha (PPARA), gamma (PPARG) and delta (PPARD) have been characterized and they are distinguished from each other by tissue distribution and cell activation. In this study, the structure and detailed chromosomal localization of the human PPARD gene was determined. Three genomic clones containing the PPARD gene was isolated from a human P1 library. The gene spans approximately 85 kb of DNA and consists of 9 exons and 8 introns with exons ranging in size from 84 bp to 2.3 kb and introns ranging from 180 bp to 50 kb. All splice acceptor and donor sites conform to the consensus sequences including the AG-GT motif. Although PPARD lacks a TATA box, the gene is transcribed from a unique start site located 380 bp upstream of the ATG initiation codon. The 5' and 3' ends were mapped by rapid amplification of cDNA ends and the mRNA size of PPARD based upon the structure of the gene is 3803 bp. In addition, the chromosomal sublocalization of PPARD was determined by radiation hybrid mapping. The PPARD gene is located at 14 cR from the colipase gene and 15 cR from the serine kinase gene at chromosomal region 6p21.2.

Evaluation of the varying Naturally Occurring Asbestos mitigation measures at School and Commercial construction projects in California

NASA Astrophysics Data System (ADS)

Kalika, S.

2012-12-01

In commercial development or K-12 school construction, project sites are often purchased and much of the planning process completed prior to an assessment of the soils proposed for excavation or potential offhaul. Geologic maps, while initially helpful for identifying potential hazards such as landslides and earthquake faults, are less helpful in the identification of naturally occurring hazardous minerals, such as the seven regulated minerals currently classified as asbestos. Geologic maps identify mafic and ultramafic bedrock zones; however, a skilled geologist with knowledge of asbestos hazards will further visualize the earth-shaping processes that may have resulted in the deposition of naturally occurring asbestos in locations outside mapped ultramafic zones including the base of an alluvial fan or within streambed channels. When sampled as an afterthought prior to disposal, property owners are surprised by the budget-crippling costs of waste handling and disposal of NOA, as well as mitigations required to protect the health of construction workers, the public, and future site occupants. The California Air Resources Board (CARB) continues to lead the way in evaluation and regulation of NOA, through development of the CARB 435 preparation and laboratory analytical method, local enforcement of the Asbestos Airborne Toxic Control Measure for Construction, Grading, Quarrying, and Surface Mining Operations (ATCM), and implementation of dust control measures to protect public health. A thorough site evaluation and construction design includes utilization of the sampling methods developed by the California Geological Survey, laboratory analytical methods within CARB 435, and mitigation measures required by CARB, DTSC, and OSHA for the protection of worker and public health after NOA is discovered. The site evaluation should additionally include an assessment of the future site usage, as regulations differ based on potential health affects to future occupants. Construction and long-term monitoring at an elementary school differs in regulatory requirements from construction of a commercial property. This presentation will highlight two case studies: a school project with several years of advance planning versus a commercial property where NOA was discovered weeks before the start of construction. The presentation will analyze the regulatory differences, mitigation measures, and consideration of the financial impacts that the discovery of NOA can have on a school versus a commercial project.

Site-specific microtubule-associated protein 4 dephosphorylation causes microtubule network densification in pressure overload cardiac hypertrophy.

PubMed

Chinnakkannu, Panneerselvam; Samanna, Venkatesababa; Cheng, Guangmao; Ablonczy, Zsolt; Baicu, Catalin F; Bethard, Jennifer R; Menick, Donald R; Kuppuswamy, Dhandapani; Cooper, George

2010-07-09

In severe pressure overload-induced cardiac hypertrophy, a dense, stabilized microtubule network forms that interferes with cardiocyte contraction and microtubule-based transport. This is associated with persistent transcriptional up-regulation of cardiac alpha- and beta-tubulin and microtubule-stabilizing microtubule-associated protein 4 (MAP4). There is also extensive microtubule decoration by MAP4, suggesting greater MAP4 affinity for microtubules. Because the major determinant of this affinity is site-specific MAP4 dephosphorylation, we characterized this in hypertrophied myocardium and then assessed the functional significance of each dephosphorylation site found by mimicking it in normal cardiocytes. We first isolated MAP4 from normal and pressure overload-hypertrophied feline myocardium; volume-overloaded myocardium, which has an equal degree and duration of hypertrophy but normal functional and cytoskeletal properties, served as a control for any nonspecific growth-related effects. After cloning cDNA-encoding feline MAP4 and obtaining its deduced amino acid sequence, we characterized by mass spectrometry any site-specific MAP4 dephosphorylation. Solely in pressure overload-hypertrophied myocardium, we identified striking MAP4 dephosphorylation at Ser-472 in the MAP4 N-terminal projection domain and at Ser-924 and Ser-1056 in the assembly-promoting region of the C-terminal microtubule-binding domain. Site-directed mutagenesis of MAP4 cDNA was then used to switch each serine to non-phosphorylatable alanine. Wild-type and mutated cDNAs were used to construct adenoviruses; microtubule network density, stability, and MAP4 decoration were assessed in normal cardiocytes following an equivalent level of MAP4 expression. The Ser-924 --> Ala MAP4 mutant produced a microtubule phenotype indistinguishable from that seen in pressure overload hypertrophy, such that Ser-924 MAP4 dephosphorylation during pressure overload hypertrophy may be central to this cytoskeletal abnormality.

Updating the Geologic Maps of the Apollo 15, 16, and 17 Landing Sites

NASA Astrophysics Data System (ADS)

Garry, W. B.; Mest, S. C.; Yingst, R. A.; Ostrach, L. R.; Petro, N. E.; Cohen, B. A.

2018-06-01

Our team is funded through NASA's Planetary Data Archiving, Restoration, and Tools (PDART) program to produce two new USGS Special Investigation Maps (SIM) for the Apollo 15, 16, and 17 missions: a regional map (1:200K) and a landing-site map (1:24K).

27 CFR 9.192 - Wahluke Slope.

Code of Federal Regulations, 2011 CFR

2011-04-01

... boundary line of section 15, which forms a portion of the boundary line of the Hanford Site, T15N/R26E, Wahatis Peak map; then (4) Proceed generally southwest along the Hanford Site boundary in a series of 90... Bridge map, and continue onto the Priest Rapids NE map to the intersection of the Hanford Site boundary...

27 CFR 9.192 - Wahluke Slope.

Code of Federal Regulations, 2010 CFR

2010-04-01

... boundary line of section 15, which forms a portion of the boundary line of the Hanford Site, T15N/R26E, Wahatis Peak map; then (4) Proceed generally southwest along the Hanford Site boundary in a series of 90... Bridge map, and continue onto the Priest Rapids NE map to the intersection of the Hanford Site boundary...

27 CFR 9.192 - Wahluke Slope.

Code of Federal Regulations, 2012 CFR

2012-04-01

... boundary line of section 15, which forms a portion of the boundary line of the Hanford Site, T15N/R26E, Wahatis Peak map; then (4) Proceed generally southwest along the Hanford Site boundary in a series of 90... Bridge map, and continue onto the Priest Rapids NE map to the intersection of the Hanford Site boundary...

27 CFR 9.192 - Wahluke Slope.

Code of Federal Regulations, 2013 CFR

2013-04-01

... boundary line of section 15, which forms a portion of the boundary line of the Hanford Site, T15N/R26E, Wahatis Peak map; then (4) Proceed generally southwest along the Hanford Site boundary in a series of 90... Bridge map, and continue onto the Priest Rapids NE map to the intersection of the Hanford Site boundary...

27 CFR 9.192 - Wahluke Slope.

Code of Federal Regulations, 2014 CFR

2014-04-01

... boundary line of section 15, which forms a portion of the boundary line of the Hanford Site, T15N/R26E, Wahatis Peak map; then (4) Proceed generally southwest along the Hanford Site boundary in a series of 90... Bridge map, and continue onto the Priest Rapids NE map to the intersection of the Hanford Site boundary...

Molecular cloning and expression of a gene for a factor which stabilizes formation of inhibitor-mitochondrial ATPase complex from Saccharomyces cerevisiae.

PubMed

Akashi, A; Yoshida, Y; Nakagoshi, H; Kuroki, K; Hashimoto, T; Tagawa, K; Imamoto, F

1988-10-01

Stabilizing factor, a 9 kDa protein, stabilizes and facilitates formation of the complex between mitochondrial ATP synthase and its intrinsic inhibitor protein. A clone containing the gene encoding the 9 kDa protein was selected from a yeast genomic library to determine the structure of its precursor protein. As deduced from the nucleotide sequence, the precursor of the yeast 9 kDa stabilizing factor contains 86 amino acid residues and has a molecular weight of 10,062. From the predicted sequence we infer that the stabilizing factor precursor contains a presequence of 23 amino acid residues at its amino terminus. We also used S1 mapping to determine the initiation site of transcription under glucose-repressed or derepressed conditions. These experiments suggest that transcription of this gene starts at three different sites and that only one of them is not affected by the presence of glucose.

Across-site patterns of modulation detection: Relation to speech recognitiona)

PubMed Central

Garadat, Soha N.; Zwolan, Teresa A.; Pfingst, Bryan E.

2012-01-01

The aim of this study was to identify across-site patterns of modulation detection thresholds (MDTs) in subjects with cochlear implants and to determine if removal of sites with the poorest MDTs from speech processor programs would result in improved speech recognition. Five hundred millisecond trains of symmetric-biphasic pulses were modulated sinusoidally at 10 Hz and presented at a rate of 900 pps using monopolar stimulation. Subjects were asked to discriminate a modulated pulse train from an unmodulated pulse train for all electrodes in quiet and in the presence of an interleaved unmodulated masker presented on the adjacent site. Across-site patterns of masked MDTs were then used to construct two 10-channel MAPs such that one MAP consisted of sites with the best masked MDTs and the other MAP consisted of sites with the worst masked MDTs. Subjects’ speech recognition skills were compared when they used these two different MAPs. Results showed that MDTs were variable across sites and were elevated in the presence of a masker by various amounts across sites. Better speech recognition was observed when the processor MAP consisted of sites with best masked MDTs, suggesting that temporal modulation sensitivity has important contributions to speech recognition with a cochlear implant. PMID:22559376

Sen2-Agri country level demonstration for Ukraine

NASA Astrophysics Data System (ADS)

Kussul, N.; Kolotii, A.; Shelestov, A.; Lavreniuk, M. S.

2016-12-01

Due to launch of Sentinel-2 mission European Space Agency (ESA) started Sentinel-2 for Agriculture (Sen2-Agri) project coordinated by Universite catholique de Louvain (UCL). Ukraine is selected as one of 3 country level demonstration sites for benchmarking Sentinel-2 data due to wide range of main crops (both winter and summer), big fields and high enough climate variability over the territory [1-2]. Within this county level demonstration main objectives are following: i) Sentinel's products quality assessment and their suitability estimation for the territory of Ukraine [2]; ii) demonstration in order to convince decision makers and state authorities; iii) assessment of the personnel and facilities required to run the Sen2-Agri system and creation of Sen-2 Agri products (crop type maps and such essential climatic variable as Leaf Area Index - LAI [3]). During this project ground data were collected for crop land mapping and crop type classification along the roads within main agro-climatic zones of Ukraine. For LAI estimation we used indirect non-destructive method which is based on DHP-images and VALERI protocol. Products created with use of Sen2-Agri system deployed during project execution and results of neural-network approach utilization will be compared. References Kussul, N., Lemoine, G., Gallego, F. J., Skakun, S. V., Lavreniuk, M., & Shelestov, A. Y. Parcel-Based Crop Classification in Ukraine Using Landsat-8 Data and Sentinel-1A Data. IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing , 9 (6), 2500-2508. Kussul, N., Skakun, S., Shelestov, A., Lavreniuk, M., Yailymov, B., & Kussul, O. (2015). Regional scale crop mapping using multi-temporal satellite imagery. The International Archives of Photogrammetry, Remote Sensing and Spatial Information Sciences, 40(7), 45-52. Shelestov, A., Kolotii, A., Camacho, F., Skakun, S., Kussul, O., Lavreniuk, M., & Kostetsky, O. (2015, July). Mapping of biophysical parameters based on high resolution EO imagery for JECAM test site in Ukraine. In 2015 IEEE International Geoscience and Remote Sensing Symposium (IGARSS), 1733-1736

Global Real-Time Nowcasting of Ionosphere with Giro-Driven Assimilative IRI

NASA Astrophysics Data System (ADS)

Galkin, I. A.; Reinisch, B. W.; Huang, X. A.; Vesnin, A.; Bilitza, D.; Song, P.

2014-12-01

Real-time prediction of the ionosphere beyond its quiet-time median behavior has proved to be a great challenge: low-latency sensor data streams are scarce, and early comparisons conducted within the CEDAR ETI Assessment framework showed that, on average, the assimilative physics-based models perform on par with the long-term empirical predictions. This rather surprising result led to the formation of the Real-Time Task Force of the International Reference Ionosphere (IRI) science team in 2011, with a simple objective to develop a method for correcting the IRI long-term climatology definitions on the fly, i.e., in near real-time, using suitable observations. Three years later, a pilot version of the IRI-based Real-Time Assimilative Model "IRTAM" started its continuous operations at the Global Ionosphere Radio Observatory (GIRO) Data Center, using online feeds from the ionosondes contributing data to GIRO. The IRTAM version 0.1B builds and publishes every 15-minutes an updated "global weather" map of the peak density and height in the ionosphere, as well as a map of deviations from the classic IRI climate. Incidentally, the IRTAM verification and validation efforts shed light on the forecasting capabilities of the assimilative IRI extension, even though it has not yet involved external activity indicators. At the core of the assimilative computations, a Non-linear Error Compensation Technique for Associative Restoration (NECTAR) seeks agreement between IRI prediction and the 24-hour history of latest observations at GIRO sensor sites to produce the one map frame. The NECTAR first evaluates the diurnal harmonics of the observed deviations from the IRI climatology at each GIRO site to then independently compute the spatial maps for each diurnal harmonic. Thus obtained "corrective" coefficients of the spatial-diurnal expansion are added to the original IRI set of coefficients to obtain the IRTAM specification. We are intrigued by the IRTAM capability to glean ionospheric dynamics over no-data areas, and the potential for short-term forecasting.

Wide-area mapping of snow water equivalent by Sentinel-1&2 data

NASA Astrophysics Data System (ADS)

Conde, Vasco; Nico, Giovanni; Catalao, Joao; Kontu, Anna; Gritsevich, Maria

2017-04-01

The mapping of snow physical properties over large mountain areas of remote areas is an important topic in both climatological studies and hydrological models where the effects of snow melting are modeled and used to forecast extreme flood events. Usually, these models are run using in-situ measurements of snow which are expensive and statistically not representative of the spatial distribution of snow properties due to slope orientation of terrain, local terrain morphology and height as well as vegetation cover. In this work we investigate the use of data acquired by Sentinel-1 and 2 missions using a C-band SAR and multispectral sensor, respectively. The Sentinel-1 SAR data are processed to estimate the Snow Water Equivalent (SWE) using both the radar amplitude and the output of the SAR interferometry processing. Both approaches need in-situ data to process SAR data and calibrate SWE estimates. The use of SAR amplitude to estimate the SWE is well established and the basic idea is that the radar signal backscattered by snow is related to the SWE so, after modeling the relationship between these two quantities at the site of in-situ measurements this relationship can be used to map the SWE at all site where the SAR amplitude information is available. The physical principle used by SAR interferometry is that of phase delay due to propagation in a non-dispersive medium. This implies that the snow is supposed to be dry in order to allow the propagation of the SAR signal. Sentinel-2 images have been used to get land-use maps and identify areas covered by vegetation. Finland has been chosen as a study region with in-situ measurements acquired thanks to the availability of rich database of in-situ measurements of SWE. Sentinel data used in this work have been acquired starting from November 2015. Publication supported by FCT- project UID/GEO/50019/2013 - Instituto Dom Luiz.

Surface-material maps of Viking landing sites on Mars

NASA Technical Reports Server (NTRS)

Moore, H. J.; Keller, J. M.

1991-01-01

Researchers mapped the surface materials at the Viking landing sites on Mars to gain a better understanding of the materials and rock populations at the sites and to provide information for future exploration. The maps extent to about 9 m in front of each lander and are about 15 m wide - an area comparable to the area of a pixel in high resolution Viking Orbiter images. The maps are divided into the near and far fields. Data for the near fields are from 1/10 scale maps, umpublished maps, and lander images. Data for the far fields are from 1/20 scale contour maps, contoured lander camera mosaics, and lander images. Rocks are located on these maps using stereometric measurements and the contour maps. Frequency size distribution of rocks and the responses of soil-like materials to erosion by engine exhausts during landings are discussed.

Transposon Tn10 contains two structural genes with opposite polarity between tetA and IS10R.

PubMed Central

Schollmeier, K; Hillen, W

1984-01-01

The nucleotide sequence of the central part of Tn10 has been determined from the rightmost HindIII site to IS10R. This sequence contains two open reading frames with opposite polarity. The in vivo transcription start points in this sequence have been determined by S1 mapping. These results define one minor and two major promoters. The transcription starts of the two major promoters are only 18 base pairs apart, and the transcripts show different polarity and overlap by 18 base pairs. The nucleotide sequence reveals two regions with palindromic symmetry which may serve as operators. Their possible involvement in the regulation of transcription of both genes is discussed. Taken together these results allow for a maximal coding capacity of 138 amino acids directed toward IS10R and 197 amino acids directed toward tetA. The possible function of these gene products is discussed. The accompanying article (Braus et al., J. Bacteriol. 160:504-509, 1984) presents evidence that these genes are expressed. Images PMID:6094471

Acoustic mapping of the regional seafloor geology in and around Hawaiian ocean dredged-material disposal sites

USGS Publications Warehouse

Torresan, Michael E.; Gardner, James V.

2000-01-01

During January and February 1998 the U.S. Geological Survey Coastal and Marine Geology Team (USGS) conducted regional high-resolution multibeam mapping surveys of the area surrounding EPA-designated ocean disposal sites located offshore of the Hawaiian Islands of Oahu, Kauai, Maui, and Hawaii. The sites are all located within 5 nautical miles of shore on insular shelves or slopes. Regional maps were required of areas much larger than the disposal sites themselves to assess both the regional seafloor geology and the immediate vicinity of the disposal sites. The purpose of the disposal site surveys was to delimit the extent of disposal material by producing detailed bathymetric and backscatter maps of the seafloor with a ± 1 m spatial accuracy and <1% depth error. The advantage of using multibeam over conventional towed, single-beam sidescan sonar is that the multibeam data are accurately georeferenced for precise location of all imaged features. The multibeam produces a coregistered acoustic-backscatter map that is often required to locate individual disposal deposits. These data were collected by the USGS as part of its regional seafloor mapping and in support of ocean disposal site monitoring studies conducted in cooperation with the US Environmental Protection Agency (EPA) and the US Army Corps of Engineers (COE).

Mentoring for NHS doctors: perceived benefits across the personal–professional interface

PubMed Central

Steven, A; Oxley, J; Fleming, WG

2008-01-01

Summary Objective To investigate NHS doctors' perceived benefits of being involved in mentoring schemes and to explore the overlaps and relationships between areas of benefit. Design Extended qualitative analysis of a multi-site interview study following an interpretivist approach. Setting Six NHS mentoring schemes across England. Main outcome measures Perceived benefits. Results While primary analysis resulted in lists of perceived benefits, the extended analysis revealed three overarching areas: professional practice, personal well-being and development. Benefits appear to go beyond a doctor's professional role to cross the personal–professional interface. Problem solving and change management seem to be key processes underpinning the raft of personal and professional benefits reported. A conceptual map was developed to depict these areas and relationships. In addition secondary analysis suggests that in benefitting one area mentoring may lead to consequential benefits in others. Conclusions Prior research into mentoring has mainly taken place in a single health care sector. This multi-site study suggests that the perceived benefits of involvement in mentoring may cross the personal/professional interface and may override organizational differences. Furthermore the map developed highlights the complex relationships which exist between the three areas of professional practice, personal wellbeing and personal and professional development. Given the consistency of findings across several studies it seems probable that organizations would be strengthened by doctors who feel more satisfied and confident in their professional roles as a result of participation in mentoring. Mentoring may have the potential to take us beyond individual limits to greater benefits and the conceptual map may offer a starting point for the development of outcome criteria and evaluation tools for mentoring schemes. PMID:19029356

Mid-2017 Map of NASA's Curiosity Mars Rover Mission

NASA Image and Video Library

2017-07-11

This map shows the route driven by NASA's Curiosity Mars rover, from the location where it landed in August 2012 to its location in July 2017, and its planned path to additional geological layers of lower Mount Sharp. The blue star near top center marks "Bradbury Landing," the site where Curiosity arrived on Mars on Aug. 5, 2012, PDT (Aug. 6, EDT and Universal Time). Blue triangles mark waypoints investigated by Curiosity on the floor of Gale Crater and, starting with "Pahrump Hills," on Mount Sharp. The Sol 1750 label identifies the rover's location on July 9, 2017, the 1,750th Martian day, or sol, since the landing. In July 2017, the mission is examining "Vera Rubin Ridge" from the downhill side of the ridge. Spectrometry observations from NASA's Mars Reconnaissance Orbiter have detected hematite, an iron-oxide mineral, in the ridge. Curiosity's planned route continues to the top of the ridge and then to geological units where clay minerals and sulfate minerals have been detected from orbit. The base image for the map is from the High Resolution Imaging Science Experiment (HiRISE) camera on the Mars Reconnaissance Orbiter. North is up. "Bagnold Dunes" form a band of dark, wind-blown material at the foot of Mount Sharp. https://photojournal.jpl.nasa.gov/catalog/PIA21720

South American regional ionospheric maps computed by GESA: A pilot service in the framework of SIRGAS

NASA Astrophysics Data System (ADS)

Brunini, C.; Meza, A.; Gende, M.; Azpilicueta, F.

2008-08-01

SIRGAS (Geocentric Reference Frame for the Americas) is an international enterprise of the geodetic community that aims to realize the Terrestrial Reference Frame in the America's countries. In order to fulfill this commitment, SIRGAS manages a network of continuously operational GNSS receivers totalling around one hundred sites in the Caribbean, Central, and South American region. Although the network was not planed for ionospheric studies, its potential to be used for such a purpose was recently recognized and SIRGAS started a pilot experiment devoted to establish a regular service for computing and releasing regional vertical TEC (vTEC) maps based on GNSS data. Since July, 2005, the GESA (Geodesia Espacial y Aeronomía) laboratory belonging to the Facultad de Ciencias Astronómicas y Geofísicas of the Universidad Nacional de La Plata computes hourly maps of vertical Total Electron Content (vTEC) in the framework of the SIRGAS pilot experiment. These maps exploit all the GNSS data available in the South American region and are computed with the LPIM (La Plata Ionospheric Model). LPIM implements a de-biasing procedure that improves data calibration in relation to other procedures commonly used for such purposes. After calibration, slant TEC measurements are converted to vertical and mapped using local-time and modip latitude. The use of modip latitude smoothed the spatial variability of vTEC, especially in the South American low latitude region and hence allows for a better vTEC interpolation. This contribution summarizes the results obtained by GESA in the framework of the SIRGAS pilot experiment.

Reported consent processes and demographics: a substudy of the INSIGHT Strategic Timing of AntiRetroviral Treatment (START) trial.

PubMed

Denning, E; Sharma, S; Smolskis, M; Touloumi, G; Walker, S; Babiker, A; Clewett, M; Emanuel, E; Florence, E; Papadopoulos, A; Sánchez, A; Tavel, J; Grady, C

2015-04-01

Efforts are needed to improve informed consent of participants in research. The Strategic Timing of AntiRetroviral Therapy (START) study provides a unique opportunity to study the effect of length and complexity of informed consent documents on understanding and satisfaction among geographically diverse participants. Interested START sites were randomized to use either the standard consent form or the concise consent form for all of the site's participants. A total of 4473 HIV-positive participants at 154 sites world-wide took part in the Informed Consent Substudy, with consent given in 11 primary languages. Most sites sent written information to potential participants in advance of clinic visits, usually including the consent form. At about half the sites, staff reported spending less than an hour per participant in the consent process. The vast majority of sites assessed participant understanding using informal nonspecific questions or clinical judgment. These data reflect the interest of START research staff in evaluating the consent process and improving informed consent. The START Informed Consent Substudy is by far the largest study of informed consent intervention ever conducted. Its results have the potential to impact how consent forms are written around the world. © 2015 British HIV Association.

For Parents: Vaccines for Your Children

MedlinePlus

... content Start of Search Controls Search Form Controls Vaccines site Cancel Submit CDC A-Z Index MENU ... Z # Start of Search Controls Search Form Controls Vaccines site Cancel Submit For Parents: Vaccines for Your ...

Landuse Controls Fate and Transport of Radionulides in Fukushima Rivers

NASA Astrophysics Data System (ADS)

Onda, Y.; Taniguchi, K.; Yoshimura, K.; Smith, H.; Brake, W.

2017-12-01

The Fukushima Daiichi Nuclear Power Plant accident has released massive amount of radiocesium into the terrestrial environment, and the radiocecium have been moved through rainfall and erosional processes. Especially, radiocesium (Cs-137) transfer and flux through river network is important to understand the redistribution of radiocesium in terrestrial environment, which is essential for assessing the external and internal radiological doses.An intensive field monitoring campaign has been started including mapping project, immediately after the Fukushima NPP accident including detailed monitoring site in upstream (Yamakiya site), and 30 monitoring sites in downstream river sites. The activity concentration of radiocesium of suspended sediment declining rapidly, and the effective half-life and had high correlation with land cover ratio by different land use of the catchments during the 1st year after the fallout. The total measured flux to the ocean of radiocesium from the Abukuma River at Iwanuma was 14 TBq for the period from August 2011 to October 2014. The detailed monitoring of activity concentration of radiocesium and their flux, which can be applicable for the fate and flux of the radionuclide transfer in humid temperate environment. We also found that land use controls most of the transport and then fate of Cs-137 in terrestrial environment.

A simultaneous multichannel monophasic action potential electrode array for in vivo epicardial repolarization mapping.

PubMed

Sahakian, A V; Peterson, M S; Shkurovich, S; Hamer, M; Votapka, T; Ji, T; Swiryn, S

2001-03-01

While the recording of extracellular monophasic action potentials (MAPs) from single epicardial or endocardial sites has been performed for over a century, we are unaware of any previous successful attempt to record MAPs simultaneously from a large number of sites in vivo. We report here the design and validation of an array of MAP electrodes which records both depolarization and repolarization simultaneously at up to 16 epicardial sites in a square array on the heart in vivo. The array consists of 16 sintered Ag-AgCl electrodes mounted in a common housing with individual suspensions allowing each electrode to exert a controlled pressure on the epicardial surface. The electrodes are arranged in a square array, with each quadrant of four having an additional recessed sintered Ag-AgCl reference electrode at its center. A saline-soaked sponge establishes ionic contact between the reference electrodes and the tissue. The array was tested on six anesthetized open-chested pigs. Simultaneous diagnostic-quality MAP recordings were obtained from up to 13 out of 16 ventricular sites. Ventricular MAPs had amplitudes of 10-40 mV with uniform morphologies and stable baselines for up to 30 min. MAP duration at 90% repolarization was measured and shown to vary as expected with cycle length during sustained pacing. The relationship between MAP duration and effective refractory period was also confirmed. The ability of the array to detect local differences in repolarization was tested in two ways. Placement of the array straddling the atrioventricular (AV) junction yielded simultaneous atrial or ventricular recordings at corresponding sites during 1:1 and 2:1 AV conduction. Localized ischemia via constriction of a coronary artery branch resulted in shortening of the repolarization phase at the ischemic, but not the nonischemic, sites. In conclusion, these results indicate that the simultaneous multichannel MAP electrode array is a viable method for in vivo epicardial repolarization mapping. The array has the potential to be expanded to increase the number of sites and spatial resolution.

CERT Research Annual Report 2009

DTIC Science & Technology

2009-01-01

Domain Name System (DNS), which maps names to IP addresses, is a vital component of the Internet. Nearly every transaction on the Internet begins by...many different ASNs (Autonomous System Numbers, which map to Internet Service Providers) there are. If there are more than 20, then it is extremely...functions, that is, mappings from their domains to ranges, or inputs to outputs. These mappings are pre-defined as a starting point for the FX

Whole Sky Imager Characterization of Sky Obscuration by Clouds for the Starfire Optical Range

DTIC Science & Technology

2010-01-11

9.3 Further Algorithm Development and Evaluation 58 9.4 Analysis of the Data Base 58 10.0 DISCUSSION OF CONTRACT REQUIREMENTS 59 10.1...clouds, Site 5 Feb 14 2008 0900 28 21 Transmittance map, Moonlight , clear sky, Site 5 Feb 3 2008 0700 28 22 Transmittance map, Moonlight , thin...clouds, Site 5 Feb 8 2008 1200 29 23 Transmittance map, Moonlight , broken clouds, Site 5 Feb 2 2008 0800 29 24 Cloud Algorithm Results, Moonlight

Quantitative susceptibility mapping of human brain at 3T: a multisite reproducibility study.

PubMed

Lin, P-Y; Chao, T-C; Wu, M-L

2015-03-01

Quantitative susceptibility mapping of the human brain has demonstrated strong potential in examining iron deposition, which may help in investigating possible brain pathology. This study assesses the reproducibility of quantitative susceptibility mapping across different imaging sites. In this study, the susceptibility values of 5 regions of interest in the human brain were measured on 9 healthy subjects following calibration by using phantom experiments. Each of the subjects was imaged 5 times on 1 scanner with the same procedure repeated on 3 different 3T systems so that both within-site and cross-site quantitative susceptibility mapping precision levels could be assessed. Two quantitative susceptibility mapping algorithms, similar in principle, one by using iterative regularization (iterative quantitative susceptibility mapping) and the other with analytic optimal solutions (deterministic quantitative susceptibility mapping), were implemented, and their performances were compared. Results show that while deterministic quantitative susceptibility mapping had nearly 700 times faster computation speed, residual streaking artifacts seem to be more prominent compared with iterative quantitative susceptibility mapping. With quantitative susceptibility mapping, the putamen, globus pallidus, and caudate nucleus showed smaller imprecision on the order of 0.005 ppm, whereas the red nucleus and substantia nigra, closer to the skull base, had a somewhat larger imprecision of approximately 0.01 ppm. Cross-site errors were not significantly larger than within-site errors. Possible sources of estimation errors are discussed. The reproducibility of quantitative susceptibility mapping in the human brain in vivo is regionally dependent, and the precision levels achieved with quantitative susceptibility mapping should allow longitudinal and multisite studies such as aging-related changes in brain tissue magnetic susceptibility. © 2015 by American Journal of Neuroradiology.

[New drugs of abuse on the Web: the role of the Psychonaut Web Mapping Project].

PubMed

Schifano, Fabrizio; Ricciardi, Alessandra; Corazza, Ornella; Deluca, Paolo; Davey, Zoe; Rafanelli, Chiara

2010-01-01

In the rapid change of drug scenarios, as the powerful development in the drug market, particularly in the number and the kind of the compound available, Internet plays a dominant role to become one of the major "drug market". The European Commission funded the Psychonaut Web Mapping Project (carried out in the time-frame January 2008-December 2009), with the aim to start/implement an Early Warning System (through the data/information collected from the Web virtual market), to identify and categorise novel recreational drugs/psychoactive compounds (synthetical/herbal drugs), and new trends in drug use to provide information for immediate and prevention intervention. The Psychonaut is a multi-site research project involving 8 research centres (De Sleutel, Belgium; University of Hertfordshire School of Pharmacy, St George's University of London, England; A-klinikkasäätiö, Finlandia; Klinik für Psychiatrie und Psychotherapie, Germany; Assessorato Salute Regione Marche, Italy; Drug Abuse Unit, Spain; Centre of Competence Bergen Clinics Foundation, Norway) based in 7 European Countries (England, Italy, Belgium, Finland, Germany, Spain, Norway).

A Middle to Late Holocene avulsion history of the Euphrates river: a case study from Tell ed-Dēr, Iraq, Lower Mesopotamia

NASA Astrophysics Data System (ADS)

An Heyvaert, Vanessa Mary; Baeteman, Cecile

2008-12-01

Geoarchaeological research was performed to reconstruct the floodplain history in the surroundings of two ancient Mesopotamian cities: Tell ed-Dēr and Sippar. The mapping of the floodplain is based on facies analyses of the sedimentary succession of 225 hand-operated boreholes. The archaeological sites Tell ed-Dēr and Sippar are closely linked to a palaeochannelbelt of the Euphrates, located in the western part of the study area. Channel activity started at least in ca 3100 BC/5050 cal BP, until ca 1400-1000 BC/3350-2950 cal BP. The channel belt was part of an avulsion driven multiple Euphrates channel network that gradually became abandoned from the second half of the 2nd millennium BC. A second mapped Euphrates, Tigris or Joint Euphrates -Tigris palaeochannel belt became abandoned well before 3100 BC. Examples of natural processes as well as human interactions triggering avulsion are given. Moreover, textual, archaeological and geological data show clearly that flood-control techniques and the construction of large-scale dikes seemed to be a common practice.

Defining the location of promoter-associated R-loops at near-nucleotide resolution using bisDRIP-seq

PubMed Central

Dumelie, Jason G

2017-01-01

R-loops are features of chromatin consisting of a strand of DNA hybridized to RNA, as well as the expelled complementary DNA strand. R-loops are enriched at promoters where they have recently been shown to have important roles in modifying gene expression. However, the location of promoter-associated R-loops and the genomic domains they perturb to modify gene expression remain unclear. To resolve this issue, we developed a bisulfite-based approach, bisDRIP-seq, to map R-loops across the genome at near-nucleotide resolution in MCF-7 cells. We found the location of promoter-associated R-loops is dependent on the presence of introns. In intron-containing genes, R-loops are bounded between the transcription start site and the first exon-intron junction. In intronless genes, the 3' boundary displays gene-specific heterogeneity. Moreover, intronless genes are often associated with promoter-associated R-loop formation. Together, these studies provide a high-resolution map of R-loops and identify gene structure as a critical determinant of R-loop formation. PMID:29072160

Retrotransposon profiling of RNA polymerase III initiation sites.

PubMed

Qi, Xiaojie; Daily, Kenneth; Nguyen, Kim; Wang, Haoyi; Mayhew, David; Rigor, Paul; Forouzan, Sholeh; Johnston, Mark; Mitra, Robi David; Baldi, Pierre; Sandmeyer, Suzanne

2012-04-01

Although retroviruses are relatively promiscuous in choice of integration sites, retrotransposons can display marked integration specificity. In yeast and slime mold, some retrotransposons are associated with tRNA genes (tDNAs). In the Saccharomyces cerevisiae genome, the long terminal repeat retrotransposon Ty3 is found at RNA polymerase III (Pol III) transcription start sites of tDNAs. Ty1, 2, and 4 elements also cluster in the upstream regions of these genes. To determine the extent to which other Pol III-transcribed genes serve as genomic targets for Ty3, a set of 10,000 Ty3 genomic retrotranspositions were mapped using high-throughput DNA sequencing. Integrations occurred at all known tDNAs, two tDNA relics (iYGR033c and ZOD1), and six non-tDNA, Pol III-transcribed types of genes (RDN5, SNR6, SNR52, RPR1, RNA170, and SCR1). Previous work in vitro demonstrated that the Pol III transcription factor (TF) IIIB is important for Ty3 targeting. However, seven loci that bind the TFIIIB loader, TFIIIC, were not targeted, underscoring the unexplained absence of TFIIIB at those sites. Ty3 integrations also occurred in two open reading frames not previously associated with Pol III transcription, suggesting the existence of a small number of additional sites in the yeast genome that interact with Pol III transcription complexes.

Functional analysis of the promoter of the molt-inhibiting hormone (mih) gene in mud crab Scylla paramamosain.

PubMed

Zhang, Xin; Huang, Danping; Jia, Xiwei; Zou, Zhihua; Wang, Yilei; Zhang, Ziping

2018-04-01

In this study, the 5'-flanking region of molt-inhibiting hormone (MIH) gene was cloned by Tail-PCR. It is 2024 bp starting from the translation initiation site, and 1818 bp starting from the predicted transcription start site. Forecast analysis results by the bioinformatics software showed that the transcription start site is located at 207 bp upstream of the start codon ATG, and TATA box is located at 240 bp upstream of the start codon ATG. Potential transcription factor binding sites include Sp1, NF-1, Oct-1, Sox-2, RAP1, and so on. There are two CpG islands, located at -25- +183 bp and -1451- -1316 bp respectively. The transfection results of luciferase reporter constructs showed that the core promoter region was located in the fragment -308 bp to -26 bp. NF-kappaB and RAP1 were essential for mih basal transcriptional activity. There are three kinds of polymorphism CA in the 5'-flanking sequence, and they can influence mih promoter activity. These findings provide a genetic foundation of the further research of mih transcription regulation. Copyright © 2017 Elsevier Inc. All rights reserved.

An archiving system for Planetary Mapping Data - Availability of derived information and knowledge in Planetary Science!

NASA Astrophysics Data System (ADS)

Nass, A.

2017-12-01

Since the late 1950s a huge number of planetary missions started to explore our solar system. The data resulting from this robotic exploration and remote sensing varies in data type, resolution and target. After data preprocessing, and referencing, the released data are available for the community on different portals and archiving systems, e.g. PDS or PSA. One major usage for these data is mapping, i.e. the extraction and filtering of information by combining and visualizing different kind of base data. Mapping itself is conducted either for mission planning (e.g. identification of landing site) or fundamental research (e.g. reconstruction of surface). The mapping results for mission planning are directly managed within the mission teams. The derived data for fundamental research - also describable as maps, diagrams, or analysis results - are mainly project-based and exclusively available in scientific papers. Within the last year, first steps have been taken to ensure a sustainable use of these derived data by finding an archiving system comparable to the data portals, i.e. reusable, well-documented, and sustainable. For the implementation three tasks are essential. Two tasks have been treated in the past 1. Comparability and interoperability has been made possible by standardized recommendations for visual, textual, and structural description of mapping data. 2. Interoperability between users, information- and graphic systems is possible by templates and guidelines for digital GIS-based mapping. These two steps are adapted e.g. within recent mapping projects for the Dawn mission. The third task hasn`t been implemented thus far: Establishing an easily detectable and accessible platform that holds already acquired information and published mapping results for future investigations or mapping projects. An archive like this would support the scientific community significantly by a constant rise of knowledge and understanding based on recent discussions within Information Science and Management, and Data Warehousing. This contribution describes the necessary map archive components that have to be considered for an efficient establishment and user-oriented accessibility. It will be described how already existing developments could be used, and which components will have to be developed yet.

Space Archeology Overview at Gordion: 2010 to 2012

NASA Technical Reports Server (NTRS)

Tucker, Compton J.; Slayback, Daniel; Nigro, Joseph D.; Yager, Karina A.

2014-01-01

In fiscal years 2010, 2011, and 2012, Compton Tucker was the principal investigator of a NASA Space Archaeology project that worked at Gordion, in Central Turkey. Tucker was assisted by an excellent team of co-workers including Joseph Nigro and Daniel Slayback of Science Systems Applications Incorporated, Jenny Strum of the University of New Mexico, and Karina Yager, a post doctoral fellow at NASA/GSFC. This report summaries their research activities at Gordion for the field seasons of 2010, 2011, and 2012. Because of the possible use of our findings at Gordion for tomb robbing there and/or the encouragement of potential tomb robbers using our geophysical survey methods to locate areas to loot, we have not published any of our survey results in the open literature nor placed any of these results on any web sites. These 2010- 2012 survey results remain in the confidential archives of the University of Pennsylvania's University Museum of Archaeology and Anthropology, the group that leads the Gordion Excavation and Research Project. Excavations are planned for 2013 at Gordion, including several that will be based upon the research results in this report. The site of Gordion in central Turkey, famous as the home of King Midas, whose father's intricately tied knot gave the site its name, also served as the center of the Phrygian kingdom that ruled much of Central Anatolia in Asia Minor during the early first millennium B.C. Gordion has been a University of Pennsylvania Museum of Archaeology and Anthropology excavation project since 1950, yet the site is incompletely published despite six decades of research. The primary obstacles related to the site and its preservation were two problems that NASA technology could address: (1) critical survey errors in the hundreds of maps and plans produced by the earlier excavators, most of which used mutually incompatible geospatial referencing systems, that prevented any systematic understanding of the site; and (2) agricultural encroachment upon the site that was compromising its archaeological integrity. Our NASA Space Archaeology proposal was written to address both of these problems. When we started working at Gordion in 2010, we added a third objective, (3) ground penetrating radar and magnetic geophysical surveys of threatened areas. The first objective our NASA Space Archaeology Project was to provide the University of Pennsylvania's Museum of Archaeology and Anthropology a system to rectify and incorporate all existing survey data from Gordion, including previous aerial photographs of the site, detailed site surveys, maps, and excavation plans, into a common mapping system. This was accomplished with a Geographic Information System (GIS) based upon a 60 cm Quickbird satellite image ortho-rectified using Shuttle Radar Topographic Mission (SRTM) 30 m digital elevation data and tied to a known datum at Gordion. This enabled the first accurate, multi-layer plan of this complex site, occupied almost continuously from the Bronze Age to the 1st millennium CE, and made possible Gordion's three-dimensional development for the first time.

Survey of protein–DNA interactions in Aspergillus oryzae on a genomic scale

PubMed Central

Wang, Chao; Lv, Yangyong; Wang, Bin; Yin, Chao; Lin, Ying; Pan, Li

2015-01-01

The genome-scale delineation of in vivo protein–DNA interactions is key to understanding genome function. Only ∼5% of transcription factors (TFs) in the Aspergillus genus have been identified using traditional methods. Although the Aspergillus oryzae genome contains >600 TFs, knowledge of the in vivo genome-wide TF-binding sites (TFBSs) in aspergilli remains limited because of the lack of high-quality antibodies. We investigated the landscape of in vivo protein–DNA interactions across the A. oryzae genome through coupling the DNase I digestion of intact nuclei with massively parallel sequencing and the analysis of cleavage patterns in protein–DNA interactions at single-nucleotide resolution. The resulting map identified overrepresented de novo TF-binding motifs from genomic footprints, and provided the detailed chromatin remodeling patterns and the distribution of digital footprints near transcription start sites. The TFBSs of 19 known Aspergillus TFs were also identified based on DNase I digestion data surrounding potential binding sites in conjunction with TF binding specificity information. We observed that the cleavage patterns of TFBSs were dependent on the orientation of TF motifs and independent of strand orientation, consistent with the DNA shape features of binding motifs with flanking sequences. PMID:25883143

The B-cell identity factor Pax5 regulates distinct transcriptional programmes in early and late B lymphopoiesis

PubMed Central

Revilla-i-Domingo, Roger; Bilic, Ivan; Vilagos, Bojan; Tagoh, Hiromi; Ebert, Anja; Tamir, Ido M; Smeenk, Leonie; Trupke, Johanna; Sommer, Andreas; Jaritz, Markus; Busslinger, Meinrad

2012-01-01

Pax5 controls the identity and development of B cells by repressing lineage-inappropriate genes and activating B-cell-specific genes. Here, we used genome-wide approaches to identify Pax5 target genes in pro-B and mature B cells. In these cell types, Pax5 bound to 40% of the cis-regulatory elements defined by mapping DNase I hypersensitive (DHS) sites, transcription start sites and histone modifications. Although Pax5 bound to 8000 target genes, it regulated only 4% of them in pro-B and mature B cells by inducing enhancers at activated genes and eliminating DHS sites at repressed genes. Pax5-regulated genes in pro-B cells account for 23% of all expression changes occurring between common lymphoid progenitors and committed pro-B cells, which identifies Pax5 as an important regulator of this developmental transition. Regulated Pax5 target genes minimally overlap in pro-B and mature B cells, which reflects massive expression changes between these cell types. Hence, Pax5 controls B-cell identity and function by regulating distinct target genes in early and late B lymphopoiesis. PMID:22669466

Planetary Cartography and Mapping: where we are Today, and where we are Heading For?

NASA Astrophysics Data System (ADS)

Naß, A.; Di, K.; Elgner, S.; van Gasselt, S.; Hare, T.; Hargitai, H.; Karachevtseva, I.; Kersten, E.; Manaud, N.; Roatsch, T.; Rossi, A. P.; Skinner, J., Jr.; Wählisch, M.

2017-07-01

Planetary Cartography does not only provides the basis to support planning (e.g., landing-site selection, orbital observations, traverse planning) and to facilitate mission conduct during the lifetime of a mission (e.g., observation tracking and hazard avoidance). It also provides the means to create science products after successful termination of a planetary mission by distilling data into maps. After a mission's lifetime, data and higher level products like mosaics and digital terrain models (DTMs) are stored in archives - and eventually into maps and higher-level data products - to form a basis for research and for new scientific and engineering studies. The complexity of such tasks increases with every new dataset that has been put on this stack of information, and in the same way as the complexity of autonomous probes increases, also tools that support these challenges require new levels of sophistication. In planetary science, cartography and mapping have a history dating back to the roots of telescopic space exploration and are now facing new technological and organizational challenges with the rise of new missions, new global initiatives, organizations and opening research markets. The focus of this contribution is to summarize recent activities in Planetary Cartography, highlighting current issues the community is facing to derive the future opportunities in this field. By this we would like to invite cartographers/researchers to join this community and to start thinking about how we can jointly solve some of these challenges.

Site-specific Microtubule-associated Protein 4 Dephosphorylation Causes Microtubule Network Densification in Pressure Overload Cardiac Hypertrophy*

PubMed Central

Chinnakkannu, Panneerselvam; Samanna, Venkatesababa; Cheng, Guangmao; Ablonczy, Zsolt; Baicu, Catalin F.; Bethard, Jennifer R.; Menick, Donald R.; Kuppuswamy, Dhandapani; Cooper, George

2010-01-01

In severe pressure overload-induced cardiac hypertrophy, a dense, stabilized microtubule network forms that interferes with cardiocyte contraction and microtubule-based transport. This is associated with persistent transcriptional up-regulation of cardiac α- and β-tubulin and microtubule-stabilizing microtubule-associated protein 4 (MAP4). There is also extensive microtubule decoration by MAP4, suggesting greater MAP4 affinity for microtubules. Because the major determinant of this affinity is site-specific MAP4 dephosphorylation, we characterized this in hypertrophied myocardium and then assessed the functional significance of each dephosphorylation site found by mimicking it in normal cardiocytes. We first isolated MAP4 from normal and pressure overload-hypertrophied feline myocardium; volume-overloaded myocardium, which has an equal degree and duration of hypertrophy but normal functional and cytoskeletal properties, served as a control for any nonspecific growth-related effects. After cloning cDNA-encoding feline MAP4 and obtaining its deduced amino acid sequence, we characterized by mass spectrometry any site-specific MAP4 dephosphorylation. Solely in pressure overload-hypertrophied myocardium, we identified striking MAP4 dephosphorylation at Ser-472 in the MAP4 N-terminal projection domain and at Ser-924 and Ser-1056 in the assembly-promoting region of the C-terminal microtubule-binding domain. Site-directed mutagenesis of MAP4 cDNA was then used to switch each serine to non-phosphorylatable alanine. Wild-type and mutated cDNAs were used to construct adenoviruses; microtubule network density, stability, and MAP4 decoration were assessed in normal cardiocytes following an equivalent level of MAP4 expression. The Ser-924 → Ala MAP4 mutant produced a microtubule phenotype indistinguishable from that seen in pressure overload hypertrophy, such that Ser-924 MAP4 dephosphorylation during pressure overload hypertrophy may be central to this cytoskeletal abnormality. PMID:20436166

Starting Labor-Management Quality of Work Life Programs.

ERIC Educational Resources Information Center

Brower, Michael

This report summarizes the experiences of the Massachusetts Quality of Working Life Center in assisting the attempted and actual start-up of a number of quality of work life (QWL) programs in 1976 and 1977 and in providing ongoing assistance. Lessons learned by the three sites the center launched, other sites, as well as those sites that chose not…

Modeling forest site productivity using mapped geospatial attributes within a South Carolina landscape, USA

Treesearch

B.R. Parresol; D.A. Scott; S.J. Zarnoch; L.A. Edwards; J.I. Blake

2017-01-01

Spatially explicit mapping of forest productivity is important to assess many forest management alternatives. We assessed the relationship between mapped variables and site index of forests ranging from southern pine plantations to natural hardwoods on a 74,000-ha landscape in South Carolina, USA. Mapped features used in the analysis were soil association, land use...

A short region of the promoter of the breast cancer associated PLU-1 gene can regulate transcription in vitro and in vivo.

PubMed

Catteau, Aurélie; Rosewell, Ian; Solomon, Ellen; Taylor-Papadimitriou, Joyce

2004-07-01

The recently cloned gene PLU-1 shows restricted expression in adult tissues, with high expression being found in testis, and transiently in the pregnant mammary gland. However, both the gene and the protein product are specifically up-regulated in breast cancer. To investigate the control of expression of the PLU-1 gene, we have cloned and functionally characterised the 5' flanking region of the gene, which was found to contain another putative gene. Two transcription start sites of the PLU-1 gene were mapped by 5' RACE. A short proximal 249 bp region was defined using reporter gene assays, which encompasses the major transcription start site and exhibits a strong constitutive promoter activity in all cell lines tested. However, regions upstream of this sequence repress transcription more effectively in a non-malignant breast cell line as compared to breast cancer cell lines. The 249 bp region is GC-rich and includes consensus Sp1 sites, GC boxes, cAMP-responsive element (CRE) and other putative cis-elements. Mutational analysis showed that two intact conserved Sp1 binding sites (shown here to bind Sp1 and/or Sp3) are critical for constitutive promoter activity, while a negative role for a neighbouring GC box is indicated. The sequence of the core promoter is highly conserved in the mouse and Plu-1 expression in the mouse embryo has been documented. Using transgenesis, we therefore examined the ability of the 249 bp fragment to control expression of a reporter gene during embryogenesis. We found that not only is the core promoter sufficient to activate transcription in vivo, but that the expression of the reporter gene coincides both temporally and spatially with regions where endogenous Plu-1 is highly expressed. This suggests that tissue specific controlling elements are found within the short fragment and are functional in the embryonic environment.

CLIP-seq analysis of multi-mapped reads discovers novel functional RNA regulatory sites in the human transcriptome.

PubMed

Zhang, Zijun; Xing, Yi

2017-09-19

Crosslinking or RNA immunoprecipitation followed by sequencing (CLIP-seq or RIP-seq) allows transcriptome-wide discovery of RNA regulatory sites. As CLIP-seq/RIP-seq reads are short, existing computational tools focus on uniquely mapped reads, while reads mapped to multiple loci are discarded. We present CLAM (CLIP-seq Analysis of Multi-mapped reads). CLAM uses an expectation-maximization algorithm to assign multi-mapped reads and calls peaks combining uniquely and multi-mapped reads. To demonstrate the utility of CLAM, we applied it to a wide range of public CLIP-seq/RIP-seq datasets involving numerous splicing factors, microRNAs and m6A RNA methylation. CLAM recovered a large number of novel RNA regulatory sites inaccessible by uniquely mapped reads. The functional significance of these sites was demonstrated by consensus motif patterns and association with alternative splicing (splicing factors), transcript abundance (AGO2) and mRNA half-life (m6A). CLAM provides a useful tool to discover novel protein-RNA interactions and RNA modification sites from CLIP-seq and RIP-seq data, and reveals the significant contribution of repetitive elements to the RNA regulatory landscape of the human transcriptome. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Comprehensive human transcription factor binding site map for combinatory binding motifs discovery.

PubMed

Müller-Molina, Arnoldo J; Schöler, Hans R; Araúzo-Bravo, Marcos J

2012-01-01

To know the map between transcription factors (TFs) and their binding sites is essential to reverse engineer the regulation process. Only about 10%-20% of the transcription factor binding motifs (TFBMs) have been reported. This lack of data hinders understanding gene regulation. To address this drawback, we propose a computational method that exploits never used TF properties to discover the missing TFBMs and their sites in all human gene promoters. The method starts by predicting a dictionary of regulatory "DNA words." From this dictionary, it distills 4098 novel predictions. To disclose the crosstalk between motifs, an additional algorithm extracts TF combinatorial binding patterns creating a collection of TF regulatory syntactic rules. Using these rules, we narrowed down a list of 504 novel motifs that appear frequently in syntax patterns. We tested the predictions against 509 known motifs confirming that our system can reliably predict ab initio motifs with an accuracy of 81%-far higher than previous approaches. We found that on average, 90% of the discovered combinatorial binding patterns target at least 10 genes, suggesting that to control in an independent manner smaller gene sets, supplementary regulatory mechanisms are required. Additionally, we discovered that the new TFBMs and their combinatorial patterns convey biological meaning, targeting TFs and genes related to developmental functions. Thus, among all the possible available targets in the genome, the TFs tend to regulate other TFs and genes involved in developmental functions. We provide a comprehensive resource for regulation analysis that includes a dictionary of "DNA words," newly predicted motifs and their corresponding combinatorial patterns. Combinatorial patterns are a useful filter to discover TFBMs that play a major role in orchestrating other factors and thus, are likely to lock/unlock cellular functional clusters.

Comprehensive Human Transcription Factor Binding Site Map for Combinatory Binding Motifs Discovery

PubMed Central

Müller-Molina, Arnoldo J.; Schöler, Hans R.; Araúzo-Bravo, Marcos J.

2012-01-01

To know the map between transcription factors (TFs) and their binding sites is essential to reverse engineer the regulation process. Only about 10%–20% of the transcription factor binding motifs (TFBMs) have been reported. This lack of data hinders understanding gene regulation. To address this drawback, we propose a computational method that exploits never used TF properties to discover the missing TFBMs and their sites in all human gene promoters. The method starts by predicting a dictionary of regulatory “DNA words.” From this dictionary, it distills 4098 novel predictions. To disclose the crosstalk between motifs, an additional algorithm extracts TF combinatorial binding patterns creating a collection of TF regulatory syntactic rules. Using these rules, we narrowed down a list of 504 novel motifs that appear frequently in syntax patterns. We tested the predictions against 509 known motifs confirming that our system can reliably predict ab initio motifs with an accuracy of 81%—far higher than previous approaches. We found that on average, 90% of the discovered combinatorial binding patterns target at least 10 genes, suggesting that to control in an independent manner smaller gene sets, supplementary regulatory mechanisms are required. Additionally, we discovered that the new TFBMs and their combinatorial patterns convey biological meaning, targeting TFs and genes related to developmental functions. Thus, among all the possible available targets in the genome, the TFs tend to regulate other TFs and genes involved in developmental functions. We provide a comprehensive resource for regulation analysis that includes a dictionary of “DNA words,” newly predicted motifs and their corresponding combinatorial patterns. Combinatorial patterns are a useful filter to discover TFBMs that play a major role in orchestrating other factors and thus, are likely to lock/unlock cellular functional clusters. PMID:23209563

Development of a 3D Model for the Assessment of Vulnerability Due to Sea Level Rise on the Historic Strawbery Banke

NASA Astrophysics Data System (ADS)

Jefferson, M.; Curran, B.; Routhier, M.; Mulukutla, G. K.; Hall, C. L.

2011-12-01

The study of climate change is now starting to be widely researched around the world. One prominent exception to this fact is within the discipline of Historic Preservation. With the likelihood of climate change causing sea levels to rise over decades to come, historical preservationists are now looking for data and information which can help them mitigate potential threats to our cultural heritage along our sea coasts. Some such information that can be helpful in understanding these threats includes geographic information such as the locations of artifacts, fossils, and historic structures as well as their vertical elevation above mean sea level. In an effort to build a set of protocols to help preservations study these threats, our work is currently focusing on a historic living history museum site known as Strawbery Banke in Portsmouth, New Hampshire. This poster features a subset of this work that was completed through undergraduate student internships funded by the Joan and James Leitzel Center at the University of New Hampshire. This subset of work focused on the creation a 3D model of the study site. Two aspects of the creation of this model involved the completion of a topographic ground survey and the 3D digital mapping of the site itself. The ground survey was completed with the use of standard surveying techniques and tools and the 3D digital mapping was completed with the use of ArcScene, a software which is part of the ArcGIS suite. This work was completed in conjunction with a larger study funded by the National Geographic Society to better understand how sea level rise and the effects of storm surges are putting the historic structures at Strawbery Banke at risk.

Participation in the Journey to Life Conversation Map Improves Control of Hypertension, Diabetes, and Hypercholesterolemia.

PubMed

Crawford, Paul; Wiltz, Scott

2015-01-01

The Diabetes Conversation Map program includes 4 "board game-like" education tools. We describe how the Journey to Life Conversation Map Education Class improves diabetes performance measures of hemoglobin A1c (HbA1c), low-density lipoprotein (LDL), and blood pressure (BP). Retrospective case-control study in a military family medicine clinic from January 2007 to January 2010. We included 202 patients who completed ≥1 conversation map class and a comparison group of 209 patients who did not attend. Attendees started with HbA1c 8.25 (95% confidence interval [CI], 7.86-8.64) and decreased to 6.96 (95% CI, 6.69-7.23). Patients in the comparison group started at 8.57 (95% CI, 8.18-8.95) and decreased to 8.27 (95% CI, 8.01-8.54) (P < .001). Attendees began with LDL of 111 mg/dL (95% CI, 103-119) and decreased to 94 mg/dL (95% CI, 81-106). Patients in the comparison group started at 89 mg/dL (95% CI, 81-98) and increased to 98 mg/dL (95% CI, 85-110) (P < .007). Systolic BP decreased 5.4 mmHg among attendees versus 0.8 mmHg among those in the comparison group (P = .014), whereas diastolic BP was unchanged (P = .110). The Journey to Life Healthy Interactions Conversation Map Education Class for diabetes improves diabetes performance measures. © Copyright 2015 by the American Board of Family Medicine.

Transcription Start Site Evolution in Drosophila

PubMed Central

Main, Bradley J.; Smith, Andrew D.; Jang, Hyosik; Nuzhdin, Sergey V.

2013-01-01

Transcription start site (TSS) evolution remains largely undescribed in Drosophila, likely due to limited annotations in non-melanogaster species. In this study, we introduce a concise new method that selectively sequences from the 5′-end of mRNA and used it to identify TSS in four Drosophila species, including Drosophila melanogaster, D. simulans, D. sechellia, and D. pseudoobscura. For verification, we compared our results in D. melanogaster with known annotations, published 5′-rapid amplification of cDNA ends data, and with RNAseq from the same mRNA pool. Then, we paired 2,849 D. melanogaster TSS with its closest equivalent TSS in each species (likely to be its true ortholog) using the available multiple sequence alignments. Most of the D. melanogaster TSSs were successfully paired with an ortholog in each species (83%, 86%, and 55% for D. simulans, D. sechellia, and D. pseudoobscura, respectively). On the basis of the number and distribution of reads mapped at each TSS, we also estimated promoter-specific expression (PSE) and TSS peak shape, respectively. Among paired TSS orthologs, the location and promoter activity were largely conserved. TSS location appears important as PSE, and TSS peak shape was more frequently divergent among TSS that had moved. Unpaired TSS were surprisingly common in D. pseudoobscura. An increased mutation rate upstream of TSS might explain this pattern. We found an enrichment of ribosomal protein genes among diverged TSS, suggesting that TSS evolution is not uniform across the genome. PMID:23649539

Minimal invasive epicardial lead implantation: optimizing cardiac resynchronization with a new mapping device for epicardial lead placement.

PubMed

Maessen, J G; Phelps, B; Dekker, A L A J; Dijkman, B

2004-05-01

To optimize resynchronization in biventricular pacing with epicardial leads, mapping to determine the best pacing site, is a prerequisite. A port access surgical mapping technique was developed that allowed multiple pace site selection and reproducible lead evaluation and implantation. Pressure-volume loops analysis was used for real time guidance in targeting epicardial lead placement. Even the smallest changes in lead position revealed significantly different functional results. Optimizing the pacing site with this technique allowed functional improvement up to 40% versus random pace site selection.

Prediction and analysis of three gene families related to leaf rust (Puccinia triticina) resistance in wheat (Triticum aestivum L.).

PubMed

Peng, Fred Y; Yang, Rong-Cai

2017-06-20

The resistance to leaf rust (Lr) caused by Puccinia triticina in wheat (Triticum aestivum L.) has been well studied over the past decades with over 70 Lr genes being mapped on different chromosomes and numerous QTLs (quantitative trait loci) being detected or mapped using DNA markers. Such resistance is often divided into race-specific and race-nonspecific resistance. The race-nonspecific resistance can be further divided into resistance to most or all races of the same pathogen and resistance to multiple pathogens. At the molecular level, these three types of resistance may cover across the whole spectrum of pathogen specificities that are controlled by genes encoding different protein families in wheat. The objective of this study is to predict and analyze genes in three such families: NBS-LRR (nucleotide-binding sites and leucine-rich repeats or NLR), START (Steroidogenic Acute Regulatory protein [STaR] related lipid-transfer) and ABC (ATP-Binding Cassette) transporter. The focus of the analysis is on the patterns of relationships between these protein-coding genes within the gene families and QTLs detected for leaf rust resistance. We predicted 526 ABC, 1117 NLR and 144 START genes in the hexaploid wheat genome through a domain analysis of wheat proteome. Of the 1809 SNPs from leaf rust resistance QTLs in seedling and adult stages of wheat, 126 SNPs were found within coding regions of these genes or their neighborhood (5 Kb upstream from transcription start site [TSS] or downstream from transcription termination site [TTS] of the genes). Forty-three of these SNPs for adult resistance and 18 SNPs for seedling resistance reside within coding or neighboring regions of the ABC genes whereas 14 SNPs for adult resistance and 29 SNPs for seedling resistance reside within coding or neighboring regions of the NLR gene. Moreover, we found 17 nonsynonymous SNPs for adult resistance and five SNPs for seedling resistance in the ABC genes, and five nonsynonymous SNPs for adult resistance and six SNPs for seedling resistance in the NLR genes. Most of these coding SNPs were predicted to alter encoded amino acids and such information may serve as a starting point towards more thorough molecular and functional characterization of the designated Lr genes. Using the primer sequences of 99 known non-SNP markers from leaf rust resistance QTLs, we found candidate genes closely linked to these markers, including Lr34 with distances to its two gene-specific markers being 1212 bases (to cssfr1) and 2189 bases (to cssfr2). This study represents a comprehensive analysis of ABC, NLR and START genes in the hexaploid wheat genome and their physical relationships with QTLs for leaf rust resistance at seedling and adult stages. Our analysis suggests that the ABC (and START) genes are more likely to be co-located with QTLs for race-nonspecific, adult resistance whereas the NLR genes are more likely to be co-located with QTLs for race-specific resistance that would be often expressed at the seedling stage. Though our analysis was hampered by inaccurate or unknown physical positions of numerous QTLs due to the incomplete assembly of the complex hexaploid wheat genome that is currently available, the observed associations between (i) QTLs for race-specific resistance and NLR genes and (ii) QTLs for nonspecific resistance and ABC genes will help discover SNP variants for leaf rust resistance at seedling and adult stages. The genes containing nonsynonymous SNPs are promising candidates that can be investigated in future studies as potential new sources of leaf rust resistance in wheat breeding.

Trail Orienteering: An Effective Way To Practice Map Interpretation.

ERIC Educational Resources Information Center

Horizons, 1999

1999-01-01

Discusses a type of orienteering developed in Great Britain to allow people with physical disabilities to compete on equal terms. Sites are viewed from a wheelchair-accessible main route. The main skill is interpreting the maps at each site, not finding the sites. Describes differences from standard orienteering, how sites work, and essential…

The Family Map: A Tool for Understanding the Risks for Children in Families with Substance Abuse

ERIC Educational Resources Information Center

Bokony, Patti A.; Conners-Burrow, Nicola A.; Whiteside-Mansell, Leanne; Johnson, Danya; McKelvey, Lorraine; Bradley, Robert H.

2010-01-01

This article reviews the findings from our assessments of children and their families in two Head Start programs using the Family Map. Specifically, we used the Family Map assessment tool to identify risks to children associated with alcohol and drug use in families with young children. Practical suggestions are offered to administrators about the…

Environmental psychology: Mapping landscape meanings for ecosystem management

Treesearch

Daniel R. Williams; Michael E. Patterson

1999-01-01

An intellectual map is a good starting point for any effort to integrate research on the human dimensions of ecosystem management. We must remember going into such exercises, however, that every map maker imposes a certain point of view, sense of order, or set of conventions in the effort to represent the world. Just as there are competing ways to divide the landscape...

National Park Service Vegetation Inventory Program, Cuyahoga Valley National Park, Ohio

USGS Publications Warehouse

Hop, Kevin D.; Drake, J.; Strassman, Andrew C.; Hoy, Erin E.; Menard, Shannon; Jakusz, J.W.; Dieck, J.J.

2013-01-01

The National Park Service (NPS) Vegetation Inventory Program (VIP) is an effort to classify, describe, and map existing vegetation of national park units for the NPS Natural Resource Inventory and Monitoring (I&M) Program. The NPS VIP is managed by the NPS Biological Resources Management Division and provides baseline vegetation information to the NPS Natural Resource I&M Program. The U.S. Geological Survey (USGS) Vegetation Characterization Program lends a cooperative role in the NPS VIP. The USGS Upper Midwest Environmental Sciences Center, NatureServe, and NPS Cuyahoga Valley National Park (CUVA) have completed vegetation classification and mapping of CUVA.Mappers, ecologists, and botanists collaborated to identify and describe vegetation types within the National Vegetation Classification Standard (NVCS) and to determine how best to map them by using aerial imagery. The team collected data from 221 vegetation plots within CUVA to develop detailed descriptions of vegetation types. Data from 50 verification sites were also collected to test both the key to vegetation types and the application of vegetation types to a sample set of map polygons. Furthermore, data from 647 accuracy assessment (AA) sites were collected (of which 643 were used to test accuracy of the vegetation map layer). These data sets led to the identification of 45 vegetation types at the association level in the NVCS at CUVA.A total of 44 map classes were developed to map the vegetation and general land cover of CUVA, including the following: 29 map classes represent natural/semi-natural vegetation types in the NVCS, 12 map classes represent cultural vegetation (agricultural and developed) in the NVCS, and 3 map classes represent non-vegetation features (open-water bodies). Features were interpreted from viewing color-infrared digital aerial imagery dated October 2010 (during peak leaf-phenology change of trees) via digital onscreen three-dimensional stereoscopic workflow systems in geographic information systems (GIS). The interpreted data were digitally and spatially referenced, thus making the spatial database layers usable in GIS. Polygon units were mapped to either a 0.5 ha or 0.25 ha minimum mapping unit, depending on vegetation type.A geodatabase containing various feature-class layers and tables shows the locations of vegetation types and general land cover (vegetation map), vegetation plot samples, verification sites, AA sites, project boundary extent, and aerial photographic centers. The feature-class layer and relate tables for the CUVA vegetation map provides 4,640 polygons of detailed attribute data covering 13,288.4 ha, with an average polygon size of 2.9 ha.Summary reports generated from the vegetation map layer show map classes representing natural/semi-natural types in the NVCS apply to 4,151 polygons (89.4% of polygons) and cover 11,225.0 ha (84.5%) of the map extent. Of these polygons, the map layer shows CUVA to be 74.4% forest (9,888.8 ha), 2.5% shrubland (329.7 ha), and 7.6% herbaceous vegetation cover (1,006.5 ha). Map classes representing cultural types in the NVCS apply to 435 polygons (9.4% of polygons) and cover 1,825.7 ha (13.7%) of the map extent. Map classes representing non-NVCS units (open water) apply to 54 polygons (1.2% of polygons) and cover 237.7 ha (1.8%) of the map extent.A thematic AA study was conducted of map classes representing natural/semi-natural types in the NVCS. Results present an overall accuracy of 80.7% (kappa index of 79.5%) based on data from 643 of the 647 AA sites. Most individual map-class themes exceed the NPS VIP standard of 80% with a 90% confidence interval.The CUVA vegetation mapping project delivers many geospatial and vegetation data products in hardcopy and/or digital formats. These products consist of an in-depth project report discussing methods and results, which include descriptions and a dichotomous key to vegetation types, map classification and map-class descriptions, and a contingency table showing AA results. The suite of products also includes a database of vegetation plots, verification sites, and AA sites; digital pictures of field sites; field data sheets; aerial photographic imagery; hardcopy and digital maps; and a geodatabase of vegetation types and land cover (map layer), fieldwork locations (vegetation plots, verification sites, and AA sites), aerial photographic index, project boundary, and metadata. All geospatial products are projected in Universal Transverse Mercator, Zone 17, by using the North American Datum of 1983. Information on the NPS VIP and completed park mapping projects are located on the Internet at and .

QuickMap: a public tool for large-scale gene therapy vector insertion site mapping and analysis.

PubMed

Appelt, J-U; Giordano, F A; Ecker, M; Roeder, I; Grund, N; Hotz-Wagenblatt, A; Opelz, G; Zeller, W J; Allgayer, H; Fruehauf, S; Laufs, S

2009-07-01

Several events of insertional mutagenesis in pre-clinical and clinical gene therapy studies have created intense interest in assessing the genomic insertion profiles of gene therapy vectors. For the construction of such profiles, vector-flanking sequences detected by inverse PCR, linear amplification-mediated-PCR or ligation-mediated-PCR need to be mapped to the host cell's genome and compared to a reference set. Although remarkable progress has been achieved in mapping gene therapy vector insertion sites, public reference sets are lacking, as are the possibilities to quickly detect non-random patterns in experimental data. We developed a tool termed QuickMap, which uniformly maps and analyzes human and murine vector-flanking sequences within seconds (available at www.gtsg.org). Besides information about hits in chromosomes and fragile sites, QuickMap automatically determines insertion frequencies in +/- 250 kb adjacency to genes, cancer genes, pseudogenes, transcription factor and (post-transcriptional) miRNA binding sites, CpG islands and repetitive elements (short interspersed nuclear elements (SINE), long interspersed nuclear elements (LINE), Type II elements and LTR elements). Additionally, all experimental frequencies are compared with the data obtained from a reference set, containing 1 000 000 random integrations ('random set'). Thus, for the first time a tool allowing high-throughput profiling of gene therapy vector insertion sites is available. It provides a basis for large-scale insertion site analyses, which is now urgently needed to discover novel gene therapy vectors with 'safe' insertion profiles.

Multiple mobile promoter regions for the rare carbapenem resistance gene of Bacteroides fragilis.

PubMed

Podglajen, I; Breuil, J; Rohaut, A; Monsempes, C; Collatz, E

2001-06-01

Two novel insertion sequences (IS), IS1187 and IS1188, are described upstream from the carbapenem resistance gene cfiA in strains of Bacteroides fragilis. Mapping, with the RACE procedure, of transcription start sites of cfiA in these and two other previously reported IS showed that transcription of this rarely encountered gene is initiated close to a variety of B. fragilis consensus promoter sequences, as recently defined (D. P. Bayley, E. R. Rocha, and C. J. Smith, FEMS Microbiol. Lett. 193:149-154, 2000). In the cases of IS1186 and IS1188, these sequences overlap with putative Esigma(70) promoter sequences, while in IS942 and IS1187 such sequences can be observed either upstream or downstream of the B. fragilis promoters.

Site Map | USDA Plant Hardiness Zone Map

Science.gov Websites

Acknowledgments & Citation Copyright Map & Data Downloads Map Downloads Geography (GIS) Downloads Multi ; Citation Copyright Map & Data Downloads Map Downloads Geography (GIS) Downloads Multi-ZIP Code Finder

77 FR 74266 - Review of National Environmental Policy Act Categorical Exclusion Survey Posted on DOT/FHWA Web Site

Federal Register 2010, 2011, 2012, 2013, 2014

2012-12-13

... of National Environmental Policy Act Categorical Exclusion Survey Posted on DOT/FHWA Web Site AGENCY... review is now available on the FHWA Web site, http://www.fhwa.dot.gov/map21 , and FTA Web site, http://www.fta.dot.gov/map21 . DATES: These reports were posted on the Web site on December 7, 2012...

Cruise report: RV Ocean Alert Cruise A2-98-SC: mapping the southern California continental margin; March 26 through April 11, 1998; San Diego to Long Beach, California

USGS Publications Warehouse

Gardner, James V.; Mayer, Larry A.

1998-01-01

The major objective of cruise A2-98 was to map portions of the southern California continental margin, including mapping in detail US Environmental Protection Agency (USEPA) ocean dumping sites. Mapping was accomplished using a high-resolution multibeam mapping system. The cruise was a jointly funded project between the USEPA and the US Geological Survey (USGS). The USEPA is specifically interested in a series of ocean dump sites off San Diego, Newport Beach, and Long Beach (see Fig. 1 in report) that require high-resolution base maps for site monitoring purposes. The USGS Coastal and Marine Geology Program has several on-going projects off southern California that lack high-precision base maps for a variety of ongoing geological studies. The cruise was conducted under a Cooperative Agreement between the USGS and the Ocean Mapping Group, University of New Brunswick, Canada.

An integrated remote sensing approach for identifying ecological range sites. [parker mountain

NASA Technical Reports Server (NTRS)

Jaynes, R. A.

1983-01-01

A model approach for identifying ecological range sites was applied to high elevation sagebrush-dominated rangelands on Parker Mountain, in south-central Utah. The approach utilizes map information derived from both high altitude color infrared photography and LANDSAT digital data, integrated with soils, geological, and precipitation maps. Identification of the ecological range site for a given area requires an evaluation of all relevant environmental factors which combine to give that site the potential to produce characteristic types and amounts of vegetation. A table is presented which allows the user to determine ecological range site based upon an integrated use of the maps which were prepared. The advantages of identifying ecological range sites through an integrated photo interpretation/LANDSAT analysis are discussed.

Computational Prediction and Experimental Verification of New MAP Kinase Docking Sites and Substrates Including Gli Transcription Factors

PubMed Central

Whisenant, Thomas C.; Ho, David T.; Benz, Ryan W.; Rogers, Jeffrey S.; Kaake, Robyn M.; Gordon, Elizabeth A.; Huang, Lan; Baldi, Pierre; Bardwell, Lee

2010-01-01

In order to fully understand protein kinase networks, new methods are needed to identify regulators and substrates of kinases, especially for weakly expressed proteins. Here we have developed a hybrid computational search algorithm that combines machine learning and expert knowledge to identify kinase docking sites, and used this algorithm to search the human genome for novel MAP kinase substrates and regulators focused on the JNK family of MAP kinases. Predictions were tested by peptide array followed by rigorous biochemical verification with in vitro binding and kinase assays on wild-type and mutant proteins. Using this procedure, we found new ‘D-site’ class docking sites in previously known JNK substrates (hnRNP-K, PPM1J/PP2Czeta), as well as new JNK-interacting proteins (MLL4, NEIL1). Finally, we identified new D-site-dependent MAPK substrates, including the hedgehog-regulated transcription factors Gli1 and Gli3, suggesting that a direct connection between MAP kinase and hedgehog signaling may occur at the level of these key regulators. These results demonstrate that a genome-wide search for MAP kinase docking sites can be used to find new docking sites and substrates. PMID:20865152

Identifying suitable sites for Florida panther reintroduction

USGS Publications Warehouse

Thatcher, Cindy A.; van Manen, Frank T.; Clark, Joseph D.

2006-01-01

A major objective of the 1995 Florida Panther (Puma concolor cory) Recovery Plan is the establishment of 2 additional panther populations within the historic range. Our goal was to identify prospective sites for Florida panther reintroduction within the historic range based on quantitative landscape assessments. First, we delineated 86 panther home ranges using telemetry data collected from 1981 to 2001 in south Florida to develop a Mahalanobis distance (D2) habitat model, using 4 anthropogenic variables and 3 landscape variables mapped at a 500-m resolution. From that analysis, we identified 9 potential reintroduction sites of sufficient size to support a panther population. We then developed a similar D2 model at a higher spatial resolution to quantify the area of favorable panther habitat at each site. To address potential for the population to expand, we calculated the amount of favorable habitat adjacent to each prospective reintroduction site within a range of dispersal distances of female panthers. We then added those totals to the contiguous patches to estimate the total amount of effective panther habitat at each site. Finally, we developed an expert-assisted model to rank and incorporate potentially important habitat variables that were not appropriate for our empirical analysis (e.g., area of public lands, livestock density). Anthropogenic factors heavily influenced both the landscape and the expert-assisted models. Of the 9 areas we identified, the Okefenokee National Wildlife Refuge, Ozark National Forest, and Felsenthal National Wildlife Refuge regions had the highest combination of effective habitat area and expert opinion scores. Sensitivity analyses indicated that variability among key model parameters did not affect the high ranking of those sites. Those sites should be considered as starting points for the field evaluation of potential reintroduction sites.

How to Differentiate an Integer Modulo n

ERIC Educational Resources Information Center

Emmons, Caleb; Krebs, Mike; Shaheen, Anthony

2009-01-01

A number derivative is a numerical mapping that satisfies the product rule. In this paper, we determine all number derivatives on the set of integers modulo n. We also give a list of undergraduate research projects to pursue using these maps as a starting point.

Measurement of sitting balance using the Manchester Active Position Seat (MAPS): a feasibility study.

PubMed

Powell, E S; Pyburn, R E; Hill, E; Smith, K S; Ribbands, M S; Mickelborough, J; Pomeroy, V M

2002-09-01

Evaluation of the effectiveness of therapy to improve sitting balance has been hampered by the limited number of sensitive objective clinical measures. We developed the Manchester Active Position Seat (MAPS) to provide a portable system to track change in the position of centre of force over time. (1) To investigate whether there is correspondence between the measurement of position change by a forceplate and by MAPS. (2) To explore whether and how MAPS measures changes in position when seated healthy adults change posture. A feasibility study. (1) An adult subject sat on MAPS placed on top of a forceplate. The x and y coordinates of the centre of pressure recorded from the forceplate and centre of force from MAPS during movement were compared graphically. (2) Four adults sat on MAPS using a standardized starting position and moving into six sets of six standardized target postures in a predetermined randomized order. The absolute shift in centre of force from the starting position was calculated. (1) The pattern of change of position over time was similar for the forceplate and for MAPS although there was a measurement difference, which increased with distance from the centre. (2) The direction of change of position corresponded to the direction of movement to the target postures but the amount of change varied between subjects. MAPS shows promise as an objective clinical measure of sitting balance, but peripheral accuracy of measurement needs to be improved.

Program Setup Time and Learning Curves associated with "ready to fly" Drone Mapping Hardware and Software.

NASA Astrophysics Data System (ADS)

Wilcox, T.

2016-12-01

How quickly can students (and educators) get started using a "ready to fly" UAS and popular publicly available photogrammetric mapping software for student research at the undergraduate level? This poster presentation focuses on the challenges of starting up your own drone-mapping program for undergraduate research in a compressed timescale of three months. Particular focus will be given to learning the operation of the platforms, hardware and software interface challenges, and using these electronic systems in real-world field settings that pose a range of physical challenges to both operators and equipment. We will be using a combination of the popular DJI Phantom UAS and Pix4D mapping software to investigate mass wasting processes and potential hazards present in public lands popular with recreational users. Projects are aimed at characterizing active geological hazards that operate on short timescales and may include gully headwall erosion in Flaming Geyser State Park and potential landslide instability within Capital State Forest, both in the Puget Sound region of Washington State.

AAPG-CSD geologic provinces code map

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meyer, R.F.; Wallace, L.G.; Wagner, F.J. Jr.

1991-10-01

This article provides the history of a revised geologic map which was drawn based on both surface geology and petroleum occurrence. The map includes offshore maps for California and the Gulf Coast of Texas and Louisiana. For onshore sites it provides geologic province boundaries which were drawn along county boundaries to approximate their position relative to oil and gas production. The offshore sites are drawn based on the universal transverse Mercator system.

Regional hydrogeological screening characteristics used for siting near-surface waste-disposal facilities in Oklahoma, U.S.A.

USGS Publications Warehouse

Johnson, K.S.

1991-01-01

The Oklahoma Geological Survey has developed several maps and reports for preliminary screening of the state of Oklahoma to identify areas that are generally acceptable or unacceptable for disposal of a wide variety of waste materials. These maps and reports focus on the geologic and hydrogeologic parameters that must be evaluated in the screening process. One map (and report) shows the outcrop distribution of 35 thick shale or clay units that are generally suitable for use as host rocks for surface disposal of wastes. A second map shows the distribution of unconsolidated alluvial and terrace-deposit aquifers, and a third map shows the distribution and hydrologic character of bedrock aquifers and their recharge areas. These latter two maps show the areas in the state where special attention must be exercised in permitting storage or disposal of waste materials that could degrade the quality of groundwater. State regulatory agencies and industry are using these maps and reports in preliminary screening of the state to identify potential disposal sites. These maps in no way replace the need for site-specific investigations to prove (or disprove) the adequacy of a site to safely contain waste materials. ?? 1991 Springer-Verlag New York Inc.

Estimating forest species abundance through linear unmixing of CHRIS/PROBA imagery

NASA Astrophysics Data System (ADS)

Stagakis, Stavros; Vanikiotis, Theofilos; Sykioti, Olga

2016-09-01

The advancing technology of hyperspectral remote sensing offers the opportunity of accurate land cover characterization of complex natural environments. In this study, a linear spectral unmixing algorithm that incorporates a novel hierarchical Bayesian approach (BI-ICE) was applied on two spatially and temporally adjacent CHRIS/PROBA images over a forest in North Pindos National Park (Epirus, Greece). The scope is to investigate the potential of this algorithm to discriminate two different forest species (i.e. beech - Fagus sylvatica, pine - Pinus nigra) and produce accurate species-specific abundance maps. The unmixing results were evaluated in uniformly distributed plots across the test site using measured fractions of each species derived by very high resolution aerial orthophotos. Landsat-8 images were also used to produce a conventional discrete-type classification map of the test site. This map was used to define the exact borders of the test site and compare the thematic information of the two mapping approaches (discrete vs abundance mapping). The required ground truth information, regarding training and validation of the applied mapping methodologies, was collected during a field campaign across the study site. Abundance estimates reached very good overall accuracy (R2 = 0.98, RMSE = 0.06). The most significant source of error in our results was due to the shadowing effects that were very intense in some areas of the test site due to the low solar elevation during CHRIS acquisitions. It is also demonstrated that the two mapping approaches are in accordance across pure and dense forest areas, but the conventional classification map fails to describe the natural spatial gradients of each species and the actual species mixture across the test site. Overall, the BI-ICE algorithm presented increased potential to unmix challenging objects with high spectral similarity, such as different vegetation species, under real and not optimum acquisition conditions. Its full potential remains to be investigated in further and more complex study sites in view of the upcoming satellite hyperspectral missions.

Validation of a novel mapping system and utility for mapping complex atrial tachycardias.

PubMed

Honarbakhsh, S; Hunter, R J; Dhillon, G; Ullah, W; Keating, E; Providencia, R; Chow, A; Earley, M J; Schilling, R J

2018-03-01

This study sought to validate a novel wavefront mapping system utilizing whole-chamber basket catheters (CARTOFINDER, Biosense Webster). The system was validated in terms of (1) mapping atrial-paced beats and (2) mapping complex wavefront patterns in atrial tachycardia (AT). Patients undergoing catheter ablation for AT and persistent AF were included. A 64-pole-basket catheter was used to acquire unipolar signals that were processed by CARTOFINDER mapping system to generate dynamic wavefront propagation maps. The left atrium was paced from four sites to demonstrate focal activation. ATs were mapped with the mechanism confirmed by conventional mapping, entrainment, and response to ablation. Twenty-two patients were included in the study (16 with AT and 6 with AF initially who terminated to AT during ablation). In total, 172 maps were created with the mapping system. It correctly identified atrial-pacing sites in all paced maps. It accurately mapped 9 focal/microreentrant and 18 macroreentrant ATs both in the left and right atrium. A third and fourth observer independently identified the sites of atrial pacing and the AT mechanism from the CARTOFINDER maps, while being blinded to the conventional activation maps. This novel mapping system was effectively validated by mapping focal activation patterns from atrial-paced beats. The system was also effective in mapping complex wavefront patterns in a range of ATs in patients with scarred atria. The system may therefore be of practical use in the mapping and ablation of AT and could have potential for mapping wavefront activations in AF. © 2018 Wiley Periodicals, Inc.

Fine-scale maps of recombination rates and hotspots in the mouse genome.

PubMed

Brunschwig, Hadassa; Levi, Liat; Ben-David, Eyal; Williams, Robert W; Yakir, Benjamin; Shifman, Sagiv

2012-07-01

Recombination events are not uniformly distributed and often cluster in narrow regions known as recombination hotspots. Several studies using different approaches have dramatically advanced our understanding of recombination hotspot regulation. Population genetic data have been used to map and quantify hotspots in the human genome. Genetic variation in recombination rates and hotspots usage have been explored in human pedigrees, mouse intercrosses, and by sperm typing. These studies pointed to the central role of the PRDM9 gene in hotspot modulation. In this study, we used single nucleotide polymorphisms (SNPs) from whole-genome resequencing and genotyping studies of mouse inbred strains to estimate recombination rates across the mouse genome and identified 47,068 historical hotspots--an average of over 2477 per chromosome. We show by simulation that inbred mouse strains can be used to identify positions of historical hotspots. Recombination hotspots were found to be enriched for the predicted binding sequences for different alleles of the PRDM9 protein. Recombination rates were on average lower near transcription start sites (TSS). Comparing the inferred historical recombination hotspots with the recent genome-wide mapping of double-strand breaks (DSBs) in mouse sperm revealed a significant overlap, especially toward the telomeres. Our results suggest that inbred strains can be used to characterize and study the dynamics of historical recombination hotspots. They also strengthen previous findings on mouse recombination hotspots, and specifically the impact of sequence variants in Prdm9.

Rapid Mapping for Built Heritage at Risk Using Low-Cost and Cots Sensors. a Test in the Duomo Vecchio of San Severino Marche

NASA Astrophysics Data System (ADS)

Calantropio, A.; Colucci, E.; Teppati Losè, L.

2017-11-01

In the last years, the researchers in the field of Geomatics have focused their attention in the experimentation and validation of new methodologies and techniques, stressing especially the potential of low-cost and COTS (Commercial Off The Shelf) solutions and sensors. In particular, these tools have been used with purposes of rapid mapping in different contexts (ranging from the construction industry, environmental monitoring, mining activities, etc.). The Built Heritage, due to its intrinsic nature of endangered artefact, can largely benefit from the technological and methodological innovations in this research field. The contribute presented in this paper will highlight these main topics: the rapid mapping of the Built Heritage (in particular the one subjected to different types of risk) using low-cost and COTS solutions. Different sensors and techniques were chosen to be evaluated on a specific test site: the Duomo Vecchio of San Severino Marche (MC - Italy), that was partially affected by the earthquake swarm that hit the area of Central Italy starting from the 24th of August 2016. One of the main aims of this work is to demonstrate how low-cost and COTS sensors can contribute to the documentation of the Built Heritage for its safeguard, for damage assessment in case of disastrous events and operations of restoration and preservation.

Evaluating the impact of geologic heritage on Earth science literacy: Adapting best practices from pedagogy and interpretation (Invited)

NASA Astrophysics Data System (ADS)

Semken, S. C.

2013-12-01

How might we authentically and practically evaluate the effects of a geologic heritage place or program on public Earth science literacy? This pedagogical form of evaluation is distinct from the evaluation of a place for its geological importance, heritage value, economic or cultural impact, and so on. Best evaluation practices from the realms of formal education, informal education, and interpretation start with a coherent set of evaluable learning outcomes, ideally recapitulated in one or more 'big ideas' that capture the essential attributes of the place or program. Learning outcomes may be classified as cognitive, affective, or psychomotor. Cognitive learning outcomes in a geoheritage context are the Earth-science concepts a visitor or student would be expected to uncover through on-site or virtual exploration of the stratigraphy, structure, landforms, and processes in a place. The Earth Science Literacy Principles (ESLP), and similar literacy documents relating to atmosphere, oceans, and climate; offer a template for mapping localized concepts onto more global ones. Quantitative instruments to evaluate understanding of the ESLP are in development, and the ESLP also map directly onto measures used in formal educational assessment, notably the Next Generation Science Standards in the USA. Nongeological place meanings (a component of sense of place) may suggest other cognitive outcomes. Affective learning outcomes for visitors and students in geoheritage sites are less readily defined, but may include place attachment (also a component of sense of place), attitudes, and interest. Multiple quantitative and qualitative methods of evaluating these outcomes exist. Psychomotor learning outcomes are even muddier, but accessibility (defined by statutes) offers a potential starting point. In practice, evaluation may be conducted synchronously or asynchronously with visitors' or students' interaction with the geoheritage place or program. Evaluation programs are typically constrained by access and practicality. Synchronous methods include observation, semi-structured interviews, rapid prototyping and surveys. Asynchronous methods include interviews, surveys, and tracking. Evaluation tools may require content or instrument validation for the specific context in which they are used. Illustrative examples from evaluation of public engagement with geoheritage places (National Parks) in the Southwest USA will be offered.

Research Networks Map | Division of Cancer Prevention

Cancer.gov

The Division of Cancer Prevention supports major scientific collaborations and research networks at more than 100 sites across the United States. Seven Major Programs' sites are shown on this map. | The Division of Cancer Prevention supports major scientific collaborations and research networks at more than 100 sites across the United States.

Characteristics, Access, Utilization, Satisfaction, and Outcomes of Healthy Start Participants in Eight Sites

PubMed Central

O’Neil, So; Cook, Benjamin; Trebino, Lisa; Walker, Deborah Klein

2009-01-01

To describe the characteristics, access, utilization, satisfaction, and outcomes of Healthy Start participants in eight selected sites, a survey of Healthy Start participants with infants ages 6–12-months-old at time of interview was conducted between October 2006 and January 2007. The response rate was 66% (n = 646), ranging from 37% in one site to >70% in seven sites. Healthy Start participants’ outcomes were compared to two national benchmarks. Healthy Start participants reported that they were satisfied with the program (>90% on five measures). Level of unmet need was 6% or less for most services, except for dental appointments (11%), housing (13%), and child care (11%). Infants had significantly better access to medical care than did their mothers, with higher rates of insurance coverage, medical homes, and checkups, and fewer unmet needs for health care. Healthy Start participants’ rates of ever breastfeeding (72%) and putting infants to sleep on their backs (70%) were at or near the Healthy People 2010 objectives, and considerably higher than rates among low-income mothers in the ECLS. The high rate of health education (>90%) may have contributed to these outcomes. Elimination of smoking among Healthy Start participants (46%) fell short of the Healthy People 2010 objective (99%). The low-birth weight (LBW) rate among Black Healthy Start participants (14%) was three times higher than the rate for Whites and Hispanics (5% each). Overall, the LBW rate in the eight sites (7.5%) was similar to the rate for low-income mothers in the ECLS, but both rates were above the Healthy People 2010 objective (5%). Challenges remain in reducing disparities in maternal and child health outcomes. Further attention to risk factors associated with LBW (especially smoking) may help close the gaps. The life course theory suggests that improved outcomes may require longer-term investments. Healthy Start’s emerging focus on interconception care has the potential to address longer-term needs of participants. PMID:19590941

The Epstein-Barr Virus Regulome in Lymphoblastoid Cells.

PubMed

Jiang, Sizun; Zhou, Hufeng; Liang, Jun; Gerdt, Catherine; Wang, Chong; Ke, Liangru; Schmidt, Stefanie C S; Narita, Yohei; Ma, Yijie; Wang, Shuangqi; Colson, Tyler; Gewurz, Benjamin; Li, Guoliang; Kieff, Elliott; Zhao, Bo

2017-10-11

Epstein-Barr virus (EBV) transforms B cells to continuously proliferating lymphoblastoid cell lines (LCLs), which represent an experimental model for EBV-associated cancers. EBV nuclear antigens (EBNAs) and LMP1 are EBV transcriptional regulators that are essential for LCL establishment, proliferation, and survival. Starting with the 3D genome organization map of LCL, we constructed a comprehensive EBV regulome encompassing 1,992 viral/cellular genes and enhancers. Approximately 30% of genes essential for LCL growth were linked to EBV enhancers. Deleting EBNA2 sites significantly reduced their target gene expression. Additional EBV super-enhancer (ESE) targets included MCL1, IRF4, and EBF. MYC ESE looping to the transcriptional stat site of MYC was dependent on EBNAs. Deleting MYC ESEs greatly reduced MYC expression and LCL growth. EBNA3A/3C altered CDKN2A/B spatial organization to suppress senescence. EZH2 inhibition decreased the looping at the CDKN2A/B loci and reduced LCL growth. This study provides a comprehensive view of the spatial organization of chromatin during EBV-driven cellular transformation. Copyright © 2017 Elsevier Inc. All rights reserved.

BOREAS TE-23 Map Plot Data

NASA Technical Reports Server (NTRS)

Rich, Paul M.; Fournier, Robert; Hall, Forrest G. (Editor); Papagno, Andrea (Editor)

2000-01-01

The Boreal Ecosystem-Atmospheric Study (BOREAS) TE-23 (Terrestrial Ecology) team collected map plot data in support of its efforts to characterize and interpret information on canopy architecture and understory cover at the BOREAS tower flux sites and selected auxiliary sites from May to August 1994. Mapped plots (typical dimensions 50 m x 60 m) were set up and characterized at all BOREAS forested tower flux and selected auxiliary sites. Detailed measurement of the mapped plots included: (1) stand characteristics (location, density, basal area); (2) map locations diameter at breast height (DBH) of all trees; (3) detailed geometric measures of a subset of trees (height, crown dimensions); and (4) understory cover maps. The data are stored in tabular ASCII files. The data files are available on a CD-ROM (see document number 20010000884), or from the Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC).

Transcriptional analysis of the bglP gene from Streptococcus mutans.

PubMed

Cote, Christopher K; Honeyman, Allen L

2006-04-21

An open reading frame encoding a putative antiterminator protein, LicT, was identified in the genomic sequence of Streptococcus mutans. A potential ribonucleic antitermination (RAT) site to which the LicT protein would potentially bind has been identified immediately adjacent to this open reading frame. The licT gene and RAT site are both located 5' to a beta-glucoside PTS regulon previously described in S. mutans that is responsible for esculin utilization in the presence of glucose. It was hypothesized that antitermination is the regulatory mechanism that is responsible for the control of the bglP gene expression, which encodes an esculin-specific PTS enzyme II. To localize the promoter activity associated with the bglP locus, a series of transcriptional lacZ gene fusions was formed on a reporter shuttle vector using various DNA fragments from the bglP promoter region. Subsequent beta-galactosidase assays in S. mutans localized the bglP promoter region and identified putative -35 and -10 promoter elements. Primer extension analysis identified the bglP transcriptional start site. In addition, a terminated bglP transcript formed by transcriptional termination was identified via transcript mapping experiments. The physical location of these genetic elements, the RAT site and the promoter regions, and the identification of a short terminated mRNA support the hypothesis that antitermination regulates the bglP transcript.

Transcriptional analysis of the bglP gene from Streptococcus mutans

PubMed Central

Cote, Christopher K; Honeyman, Allen L

2006-01-01

Background An open reading frame encoding a putative antiterminator protein, LicT, was identified in the genomic sequence of Streptococcus mutans. A potential ribonucleic antitermination (RAT) site to which the LicT protein would potentially bind has been identified immediately adjacent to this open reading frame. The licT gene and RAT site are both located 5' to a beta-glucoside PTS regulon previously described in S. mutans that is responsible for esculin utilization in the presence of glucose. It was hypothesized that antitermination is the regulatory mechanism that is responsible for the control of the bglP gene expression, which encodes an esculin-specific PTS enzyme II. Results To localize the promoter activity associated with the bglP locus, a series of transcriptional lacZ gene fusions was formed on a reporter shuttle vector using various DNA fragments from the bglP promoter region. Subsequent beta-galactosidase assays in S. mutans localized the bglP promoter region and identified putative -35 and -10 promoter elements. Primer extension analysis identified the bglP transcriptional start site. In addition, a terminated bglP transcript formed by transcriptional termination was identified via transcript mapping experiments. Conclusion The physical location of these genetic elements, the RAT site and the promoter regions, and the identification of a short terminated mRNA support the hypothesis that antitermination regulates the bglP transcript. PMID:16630357

Preferential cleavage sites for Sau3A restriction endonuclease in human ribosomal DNA.

PubMed

Kupriyanova, N S; Kirilenko, P M; Netchvolodov, K K; Ryskov, A P

2000-07-21

Previous studies of cloned ribosomal DNA (rDNA) variants isolated from the cosmid library of human chromosome 13 have revealed some disproportion in representativity of different rDNA regions (N. S. Kupriyanova, K. K. Netchvolodov, P. M. Kirilenko, B. I. Kapanadze, N. K. Yankovsky, and A. P. Ryskov, Mol. Biol. 30, 51-60, 1996). Here we show nonrandom cleavage of human rDNA with Sau3A or its isoshizomer MboI under mild hydrolysis conditions. The hypersensitive cleavage sites were found to be located in the ribosomal intergenic spacer (rIGS), especially in the regions of about 5-5.5 and 11 kb upstream of the rRNA transcription start point. This finding is based on sequencing mapping of the rDNA insert ends in randomly selected cosmid clones of human chromosome 13 and on the data of digestion kinetics of cloned and noncloned human genomic rDNA with Sau3A and MboI. The results show that a methylation status and superhelicity state of the rIGS have no effect on cleavage site sensitivity. It is interesting that all primary cleavage sites are adjacent to or entering into Alu or Psi cdc 27 retroposons of the rIGS suggesting a possible role of neighboring sequences in nuclease accessibility. The results explain nonequal representation of rDNA sequences in the human genomic DNA library used for this study. Copyright 2000 Academic Press.

Enhancers Are Major Targets for Murine Leukemia Virus Vector Integration

PubMed Central

De Ravin, Suk See; Su, Ling; Theobald, Narda; Choi, Uimook; Macpherson, Janet L.; Poidinger, Michael; Symonds, Geoff; Pond, Susan M.; Ferris, Andrea L.; Hughes, Stephen H.

2014-01-01

ABSTRACT Retroviral vectors have been used in successful gene therapies. However, in some patients, insertional mutagenesis led to leukemia or myelodysplasia. Both the strong promoter/enhancer elements in the long terminal repeats (LTRs) of murine leukemia virus (MLV)-based vectors and the vector-specific integration site preferences played an important role in these adverse clinical events. MLV integration is known to prefer regions in or near transcription start sites (TSS). Recently, BET family proteins were shown to be the major cellular proteins responsible for targeting MLV integration. Although MLV integration sites are significantly enriched at TSS, only a small fraction of the MLV integration sites (<15%) occur in this region. To resolve this apparent discrepancy, we created a high-resolution genome-wide integration map of more than one million integration sites from CD34+ hematopoietic stem cells transduced with a clinically relevant MLV-based vector. The integration sites form ∼60,000 tight clusters. These clusters comprise ∼1.9% of the genome. The vast majority (87%) of the integration sites are located within histone H3K4me1 islands, a hallmark of enhancers. The majority of these clusters also have H3K27ac histone modifications, which mark active enhancers. The enhancers of some oncogenes, including LMO2, are highly preferred targets for integration without in vivo selection. IMPORTANCE We show that active enhancer regions are the major targets for MLV integration; this means that MLV preferentially integrates in regions that are favorable for viral gene expression in a variety of cell types. The results provide insights for MLV integration target site selection and also explain the high risk of insertional mutagenesis that is associated with gene therapy trials using MLV vectors. PMID:24501411

Army Aviation Operations in the Pacific Theater

DTIC Science & Technology

2014-12-04

unveiled the day before in Darwin . Alongside the Australian Prime Minister, Julia Gillard, President Barack Obama disclosed the details of a new defense...deployments) to Darwin starting in mid-2012.8 On 4 April 2012, the first contingent of approximately 200 Marines arrived in Darwin to signal the start of...and the start of rotational Marine deployments to Darwin , the American rebalancing to Asia-Pacific appeared to begin in earnest. Looking at a map

Building America Top Innovations 2012: Building Science-Based Climate Maps

DOE Office of Scientific and Technical Information (OSTI.GOV)

none,

2013-01-01

This Building America Top Innovations profile describes the Building America-developed climate zone map, which serves as a consistent framework for energy-efficiency requirements in the national model energy code starting with the 2004 IECC Supplement and the ASHRAE 90.1 2004 edition. The map also provides a critical foundation for climate-specific guidance in the widely disseminated EEBA Builder Guides and Building America Best Practice Guides.

Good Seeing: Best Practices for Sustainable Operations at the Air Force Maui Optical and Supercomputing Site

DTIC Science & Technology

2016-01-01

supportive of this work from the start . This research would not have been possible without the contributions made by a number of individuals throughout...and funding structures. We started with these questions in particular based on the primary concerns at AMOS identified in the results of Phase I...from the start . Keck maintains connections with a series of other sites within a remote observing network. Remote observing from the mainland

GIS and Time-Series Integration in the Kennedy Space Center Environmental Information System

NASA Technical Reports Server (NTRS)

Hinkle, Ross; Costa, Joao Ribeiro da; Engel, Bernard

1996-01-01

NASA started the Ecological Program 14 years ago to collect environmental data which can be used in making environmental management decisions. The EP team created the Mapping Analysis and Planning System (MAPS) to store all the data, including the appropriate tools for data analysis and exploration.

Rumination disorder

MedlinePlus

... MedlinePlus GO GO About MedlinePlus Site Map FAQs Customer Support Health Topics Drugs & Supplements Videos & Tools Español ... ADAM Health Solutions. About MedlinePlus Site Map FAQs Customer Support Get email updates Subscribe to RSS Follow ...

7 CFR 1940.309 - Responsibilities of the prospective applicant.

Code of Federal Regulations, 2014 CFR

2014-01-01

... project elements and the proposed site(s) to include location maps, topographic maps, and photographs when... agency under Public Law 103-354 of a Soil Conservation Service (SCS) environmental assessment or...

Email Updates

MedlinePlus

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A GIS-BASED MULTI-CRITERIA EVALUATION SYSTEM FOR SELECTION OF LANDFILL SITES: a case study from Abu Dhabi, United Arab Emirates

NASA Astrophysics Data System (ADS)

Issa, S. M.; Shehhi, B. Al

2012-07-01

Landfill sites receive 92% of total annual solid waste produced by municipalities in the emirate of Abu Dhabi. In this study, candidate sites for an appropriate landfill location for the Abu Dhabi municipal area are determined by integrating geographic information systems (GIS) and multi-criteria evaluation (MCE) analysis. To identify appropriate landfill sites, eight input map layers including proximity to urban areas, proximity to wells and water table depth, geology and topography, proximity to touristic and archeological sites, distance from roads network, distance from drainage networks, and land slope are used in constraint mapping. A final map was generated which identified potential areas showing suitability for the location of the landfill site. Results revealed that 30% of the study area was identified as highly suitable, 25% as suitable, and 45% as unsuitable. The selection of the final landfill site, however, requires further field research.

A randomized trial comparing concise and standard consent forms in the START trial

PubMed Central

Touloumi, Giota; Walker, A. Sarah; Smolskis, Mary; Sharma, Shweta; Babiker, Abdel G.; Pantazis, Nikos; Tavel, Jorge; Florence, Eric; Sanchez, Adriana; Hudson, Fleur; Papadopoulos, Antonios; Emanuel, Ezekiel; Clewett, Megan; Munroe, David; Denning, Eileen

2017-01-01

Background Improving the effectiveness and efficiency of research informed consent is a high priority. Some express concern about longer, more complex, written consent forms creating barriers to participant understanding. A recent meta-analysis concluded that randomized comparisons were needed. Methods We conducted a cluster-randomized non-inferiority comparison of a standard versus concise consent form within a multinational trial studying the timing of starting antiretroviral therapy in HIV+ adults (START). Interested sites were randomized to standard or concise consent forms for all individuals signing START consent. Participants completed a survey measuring comprehension of study information and satisfaction with the consent process. Site personnel reported usual site consent practices. The primary outcome was comprehension of the purpose of randomization (pre-specified 7.5% non-inferiority margin). Results 77 sites (2429 participants) were randomly allocated to use standard consent and 77 sites (2000 participants) concise consent, for an evaluable cohort of 4229. Site and participant characteristics were similar for the two groups. The concise consent was non-inferior to the standard consent on comprehension of randomization (80.2% versus 82%, site adjusted difference: 0.75% (95% CI -3.8%, +5.2%)); and the two groups did not differ significantly on total comprehension score, satisfaction, or voluntariness (p>0.1). Certain independent factors, such as education, influenced comprehension and satisfaction but not differences between consent groups. Conclusions An easier to read, more concise consent form neither hindered nor improved comprehension of study information nor satisfaction with the consent process among a large number of participants. This supports continued efforts to make consent forms more efficient. Trial registration Informed consent substudy was registered as part of START study in clinicaltrials.gov #NCT00867048, and EudraCT # 2008-006439-12 PMID:28445471

Project Developmental Continuity Evaluation: Site Visitors' Manual.

ERIC Educational Resources Information Center

Morris, Mary; Smith, Allen

This site visitors' manual is part of a series of documents on the evaluation of Project Developmental Continuity (PDC), a Head Start demonstration program aimed at providing educational and developmental continuity between children's Head Start and primary school experiences. The PDC evaluation documents and analyzes the process of program…

PhosphOrtholog: a web-based tool for cross-species mapping of orthologous protein post-translational modifications.

PubMed

Chaudhuri, Rima; Sadrieh, Arash; Hoffman, Nolan J; Parker, Benjamin L; Humphrey, Sean J; Stöckli, Jacqueline; Hill, Adam P; James, David E; Yang, Jean Yee Hwa

2015-08-19

Most biological processes are influenced by protein post-translational modifications (PTMs). Identifying novel PTM sites in different organisms, including humans and model organisms, has expedited our understanding of key signal transduction mechanisms. However, with increasing availability of deep, quantitative datasets in diverse species, there is a growing need for tools to facilitate cross-species comparison of PTM data. This is particularly important because functionally important modification sites are more likely to be evolutionarily conserved; yet cross-species comparison of PTMs is difficult since they often lie in structurally disordered protein domains. Current tools that address this can only map known PTMs between species based on known orthologous phosphosites, and do not enable the cross-species mapping of newly identified modification sites. Here, we addressed this by developing a web-based software tool, PhosphOrtholog ( www.phosphortholog.com ) that accurately maps protein modification sites between different species. This facilitates the comparison of datasets derived from multiple species, and should be a valuable tool for the proteomics community. Here we describe PhosphOrtholog, a web-based application for mapping known and novel orthologous PTM sites from experimental data obtained from different species. PhosphOrtholog is the only generic and automated tool that enables cross-species comparison of large-scale PTM datasets without relying on existing PTM databases. This is achieved through pairwise sequence alignment of orthologous protein residues. To demonstrate its utility we apply it to two sets of human and rat muscle phosphoproteomes generated following insulin and exercise stimulation, respectively, and one publicly available mouse phosphoproteome following cellular stress revealing high mapping and coverage efficiency. Although coverage statistics are dataset dependent, PhosphOrtholog increased the number of cross-species mapped sites in all our example data sets by more than double when compared to those recovered using existing resources such as PhosphoSitePlus. PhosphOrtholog is the first tool that enables mapping of thousands of novel and known protein phosphorylation sites across species, accessible through an easy-to-use web interface. Identification of conserved PTMs across species from large-scale experimental data increases our knowledgebase of functional PTM sites. Moreover, PhosphOrtholog is generic being applicable to other PTM datasets such as acetylation, ubiquitination and methylation.

A Bayesian-Based Novel Methodology to Generate Reliable Site Response Mapping Sensitive to Data Uncertainties

NASA Astrophysics Data System (ADS)

Chakraborty, A.; Goto, H.

2017-12-01

The 2011 off the Pacific coast of Tohoku earthquake caused severe damage in many areas further inside the mainland because of site-amplification. Furukawa district in Miyagi Prefecture, Japan recorded significant spatial differences in ground motion even at sub-kilometer scales. The site responses in the damage zone far exceeded the levels in the hazard maps. A reason why the mismatch occurred is that mapping follow only the mean value at the measurement locations with no regard to the data uncertainties and thus are not always reliable. Our research objective is to develop a methodology to incorporate data uncertainties in mapping and propose a reliable map. The methodology is based on a hierarchical Bayesian modeling of normally-distributed site responses in space where the mean (μ), site-specific variance (σ2) and between-sites variance(s2) parameters are treated as unknowns with a prior distribution. The observation data is artificially created site responses with varying means and variances for 150 seismic events across 50 locations in one-dimensional space. Spatially auto-correlated random effects were added to the mean (μ) using a conditionally autoregressive (CAR) prior. The inferences on the unknown parameters are done using Markov Chain Monte Carlo methods from the posterior distribution. The goal is to find reliable estimates of μ sensitive to uncertainties. During initial trials, we observed that the tau (=1/s2) parameter of CAR prior controls the μ estimation. Using a constraint, s = 1/(k×σ), five spatial models with varying k-values were created. We define reliability to be measured by the model likelihood and propose the maximum likelihood model to be highly reliable. The model with maximum likelihood was selected using a 5-fold cross-validation technique. The results show that the maximum likelihood model (μ*) follows the site-specific mean at low uncertainties and converges to the model-mean at higher uncertainties (Fig.1). This result is highly significant as it successfully incorporates the effect of data uncertainties in mapping. This novel approach can be applied to any research field using mapping techniques. The methodology is now being applied to real records from a very dense seismic network in Furukawa district, Miyagi Prefecture, Japan to generate a reliable map of the site responses.

7 CFR 12.31 - On-site wetland identification criteria.

Code of Federal Regulations, 2011 CFR

2011-01-01

... CONSERVATION Wetland Conservation § 12.31 On-site wetland identification criteria. (a) Hydric soils. (1) NRCS shall identify hydric soils through the use of published soil maps which reflect soil surveys completed by NRCS or through the use of on-site reviews. If a published soil map is unavailable for a given...

7 CFR 12.31 - On-site wetland identification criteria.

Code of Federal Regulations, 2014 CFR

2014-01-01

... CONSERVATION Wetland Conservation § 12.31 On-site wetland identification criteria. (a) Hydric soils. (1) NRCS shall identify hydric soils through the use of published soil maps which reflect soil surveys completed by NRCS or through the use of on-site reviews. If a published soil map is unavailable for a given...

7 CFR 12.31 - On-site wetland identification criteria.

Code of Federal Regulations, 2010 CFR

2010-01-01

... CONSERVATION Wetland Conservation § 12.31 On-site wetland identification criteria. (a) Hydric soils. (1) NRCS shall identify hydric soils through the use of published soil maps which reflect soil surveys completed by NRCS or through the use of on-site reviews. If a published soil map is unavailable for a given...

7 CFR 12.31 - On-site wetland identification criteria.

Code of Federal Regulations, 2013 CFR

2013-01-01

... CONSERVATION Wetland Conservation § 12.31 On-site wetland identification criteria. (a) Hydric soils. (1) NRCS shall identify hydric soils through the use of published soil maps which reflect soil surveys completed by NRCS or through the use of on-site reviews. If a published soil map is unavailable for a given...

7 CFR 12.31 - On-site wetland identification criteria.

Code of Federal Regulations, 2012 CFR

2012-01-01

... CONSERVATION Wetland Conservation § 12.31 On-site wetland identification criteria. (a) Hydric soils. (1) NRCS shall identify hydric soils through the use of published soil maps which reflect soil surveys completed by NRCS or through the use of on-site reviews. If a published soil map is unavailable for a given...

Chromosome segregation drives division site selection in Streptococcus pneumoniae.

PubMed

van Raaphorst, Renske; Kjos, Morten; Veening, Jan-Willem

2017-07-18

Accurate spatial and temporal positioning of the tubulin-like protein FtsZ is key for proper bacterial cell division. Streptococcus pneumoniae (pneumococcus) is an oval-shaped, symmetrically dividing opportunistic human pathogen lacking the canonical systems for division site control (nucleoid occlusion and the Min-system). Recently, the early division protein MapZ was identified and implicated in pneumococcal division site selection. We show that MapZ is important for proper division plane selection; thus, the question remains as to what drives pneumococcal division site selection. By mapping the cell cycle in detail, we show that directly after replication both chromosomal origin regions localize to the future cell division sites, before FtsZ. Interestingly, Z-ring formation occurs coincidently with initiation of DNA replication. Perturbing the longitudinal chromosomal organization by mutating the condensin SMC, by CRISPR/Cas9-mediated chromosome cutting, or by poisoning DNA decatenation resulted in mistiming of MapZ and FtsZ positioning and subsequent cell elongation. Together, we demonstrate an intimate relationship between DNA replication, chromosome segregation, and division site selection in the pneumococcus, providing a simple way to ensure equally sized daughter cells.

Coastline Mapping and Cultural Review to Predict Sea Level Rise Impact on Hawaiian Archeological Sites

NASA Astrophysics Data System (ADS)

Clinton, J.

2017-12-01

Much of Hawaii's history is recorded in archeological sites. Researchers and cultural practitioners have been studying and reconstructing significant archeological sites for generations. Climate change, and more specifically, sea level rise may threaten these sites. Our research records current sea levels and then projects possible consequences to these cultural monuments due to sea level rise. In this mixed methods study, research scientists, cultural practitioners, and secondary students use plane-table mapping techniques to create maps of coastlines and historic sites. Students compare historical records to these maps, analyze current sea level rise trends, and calculate future sea levels. They also gather data through interviews with community experts and kupuna (elders). If climate change continues at projected rates, some historic sites will be in danger of negative impact due to sea level rise. Knowing projected sea levels at specific sites allows for preventative action and contributes to raised awareness of the impacts of climate change to the Hawaiian Islands. Students will share results with the community and governmental agencies in hopes of inspiring action to minimize climate change. It will take collaboration between scientists and cultural communities to inspire future action on climate change.

Characterization of Equine Infectious Anemia Virus Integration in the Horse Genome.

PubMed

Liu, Qiang; Wang, Xue-Feng; Ma, Jian; He, Xi-Jun; Wang, Xiao-Jun; Zhou, Jian-Hua

2015-06-19

Human immunodeficiency virus (HIV)-1 has a unique integration profile in the human genome relative to murine and avian retroviruses. Equine infectious anemia virus (EIAV) is another well-studied lentivirus that can also be used as a promising retro-transfection vector, but its integration into its native host has not been characterized. In this study, we mapped 477 integration sites of the EIAV strain EIAVFDDV13 in fetal equine dermal (FED) cells during in vitro infection. Published integration sites of EIAV and HIV-1 in the human genome were also analyzed as references. Our results demonstrated that EIAVFDDV13 tended to integrate into genes and AT-rich regions, and it avoided integrating into transcription start sites (TSS), which is consistent with EIAV and HIV-1 integration in the human genome. Notably, the integration of EIAVFDDV13 favored long interspersed elements (LINEs) and DNA transposons in the horse genome, whereas the integration of HIV-1 favored short interspersed elements (SINEs) in the human genome. The chromosomal environment near LINEs or DNA transposons potentially influences viral transcription and may be related to the unique EIAV latency states in equids. The data on EIAV integration in its natural host will facilitate studies on lentiviral infection and lentivirus-based therapeutic vectors.

Landscape dynamics assessment of dry climatic zones on the Baikal-Gobi transect from NDVI time series and field investigations data

NASA Astrophysics Data System (ADS)

Sayapina, D. O.; Zharnikova, M. A.; Tsydypov, B. Z.; Sodnomov, B. V.; Garmaev, E. Zh

2016-11-01

Starting in the eighties of the 20th century, the scientists of the Baikal Institute of Nature Management (BINM SB RAS) have been conducting field observations of the Transbaikalia geosystems transformation due to the change of climate and nature management. An utmost importance is placed on the study of a negative response of the land geosystems. This is shown through their deterioration, degradation, and desertification in particular. Through the years of research (1985-2015) in dry areas of the north of Central Asia, the scientists of the BINM SB RAS established a network of key sites for contact monitoring of the status and dynamics of the geosystems and the negative natural-anthropogenic processes along the Baikal-Gobi meridional transect (51-44° N, 105-107° E). The monitoring of the status and dynamics of the vegetation cover of some key sites is conducted by processing and analysis of multitemporal and multispectral Landsat and MODIS Terra imagery. An automatic analysis of the time variation of NDVI and a comparison with the progress of the index in the previous seasons are performed. The landscape indication of the key sites is made on the basis of satellite imagery and complete geobotanical descriptions. Landscape profiles and facies maps with natural boundaries are created.

Characterization of Equine Infectious Anemia Virus Integration in the Horse Genome

PubMed Central

Liu, Qiang; Wang, Xue-Feng; Ma, Jian; He, Xi-Jun; Wang, Xiao-Jun; Zhou, Jian-Hua

2015-01-01

Human immunodeficiency virus (HIV)-1 has a unique integration profile in the human genome relative to murine and avian retroviruses. Equine infectious anemia virus (EIAV) is another well-studied lentivirus that can also be used as a promising retro-transfection vector, but its integration into its native host has not been characterized. In this study, we mapped 477 integration sites of the EIAV strain EIAVFDDV13 in fetal equine dermal (FED) cells during in vitro infection. Published integration sites of EIAV and HIV-1 in the human genome were also analyzed as references. Our results demonstrated that EIAVFDDV13 tended to integrate into genes and AT-rich regions, and it avoided integrating into transcription start sites (TSS), which is consistent with EIAV and HIV-1 integration in the human genome. Notably, the integration of EIAVFDDV13 favored long interspersed elements (LINEs) and DNA transposons in the horse genome, whereas the integration of HIV-1 favored short interspersed elements (SINEs) in the human genome. The chromosomal environment near LINEs or DNA transposons potentially influences viral transcription and may be related to the unique EIAV latency states in equids. The data on EIAV integration in its natural host will facilitate studies on lentiviral infection and lentivirus-based therapeutic vectors. PMID:26102582

Sure start: voices of the 'hard-to-reach'.

PubMed

Coe, C; Gibson, A; Spencer, N; Stuttaford, M

2008-07-01

This research aimed to look in depth at the factors affecting the ability of four Sure Start local programmes, based in a multicultural Midlands city, to engage with 'hard-to-reach' populations. A variety of research strategies and methods were employed. Geographical information systems, participatory research methods and interviews were used in order to understand the extent of the challenge, and hear first hand, why parents may not get involved with Sure Start. The mapping exercise involved collation and mapping of postcode data with respect to boundaries and potential and actual users of Sure Start services. This made possible the identification of any geographical patterning in the distribution of service users and non-users. Participatory research methods were used with parents, enabling them to conduct short interviews within their own communities and make sense of the data collected. Interviews were also conducted with 70 parents across the city, recruited through local schools. The results indicate that parental decisions regarding Sure Start are the product of a complex interaction between numerous factors which may act as either barriers or facilitators to service utilization. The results suggest that a multi-method approach to data collection is useful and appropriate in gaining access to those parents who are non-users of the Sure Start services and enabling their voices to be heard. These findings offer some explanations and insight into the apparent ambivalent attitudes of some families toward Sure Start services. Implications for future practice are discussed.

Histocompatibility antigen test

MedlinePlus

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Stress and your heart

MedlinePlus

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Premenstrual dysphoric disorder

MedlinePlus

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Learn to manage stress

MedlinePlus

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Site plan, map, and statement of significance Promontory Route ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

Site plan, map, and statement of significance - Promontory Route Railroad Trestles, S.P. Trestle 779.91, One mile southwest of junction of State Highway 83 and Blue Creek, Corinne, Box Elder County, UT

Models of chromatin spatial organisation in the cell nucleus

NASA Astrophysics Data System (ADS)

Nicodemi, Mario

2014-03-01

In the cell nucleus chromosomes have a complex architecture serving vital functional purposes. Recent experiments have started unveiling the interaction map of DNA sites genome-wide, revealing different levels of organisation at different scales. The principles, though, which orchestrate such a complex 3D structure remain still mysterious. I will overview the scenario emerging from some classical polymer physics models of the general aspect of chromatin spatial organisation. The available experimental data, which can be rationalised in a single framework, support a picture where chromatin is a complex mixture of differently folded regions, self-organised across spatial scales according to basic physical mechanisms. I will also discuss applications to specific DNA loci, e.g. the HoxB locus, where models informed with biological details, and tested against targeted experiments, can help identifying the determinants of folding.

Multiscale site-response mapping: A case study of Parkfield, California

USGS Publications Warehouse

Thompson, E.M.; Baise, L.G.; Kayen, R.E.; Morgan, E.C.; Kaklamanos, J.

2011-01-01

The scale of previously proposed methods for mapping site-response ranges from global coverage down to individual urban regions. Typically, spatial coverage and accuracy are inversely related.We use the densely spaced strong-motion stations in Parkfield, California, to estimate the accuracy of different site-response mapping methods and demonstrate a method for integrating multiple site-response estimates from the site to the global scale. This method is simply a weighted mean of a suite of different estimates, where the weights are the inverse of the variance of the individual estimates. Thus, the dominant site-response model varies in space as a function of the accuracy of the different models. For mapping applications, site-response models should be judged in terms of both spatial coverage and the degree of correlation with observed amplifications. Performance varies with period, but in general the Parkfield data show that: (1) where a velocity profile is available, the square-rootof- impedance (SRI) method outperforms the measured VS30 (30 m divided by the S-wave travel time to 30 m depth) and (2) where velocity profiles are unavailable, the topographic slope method outperforms surficial geology for short periods, but geology outperforms slope at longer periods. We develop new equations to estimate site response from topographic slope, derived from the Next Generation Attenuation (NGA) database.

Arabidopsis Microtubule-Associated Protein MAP65-3 Cross-Links Antiparallel Microtubules toward Their Plus Ends in the Phragmoplast via Its Distinct C-Terminal Microtubule Binding Domain[W

PubMed Central

Ho, Chin-Min Kimmy; Lee, Yuh-Ru Julie; Kiyama, Lindsay D.; Dinesh-Kumar, Savithramma P.; Liu, Bo

2012-01-01

Plant cytokinesis is brought about by the phragmoplast, which contains an antiparallel microtubule (MT) array. The MT-associated protein MAP65-3 acts as an MT-bundling factor that specifically cross-links antiparallel MTs near their plus ends. MAP65 family proteins contain an N-terminal dimerization domain and C-terminal MT interaction domain. Compared with other MAP65 isoforms, MAP65-3 contains an extended C terminus. A MT binding site was discovered in the region between amino acids 496 and 588 and found to be essential for the organization of phragmoplast MTs. The frequent cytokinetic failure caused by loss of MAP65-3 was not rescued by ectopic expression of MAP65-1 under the control of the MAP65-3 promoter, indicating nonoverlapping functions between the two isoforms. In the presence of MAP65-3, however, ectopic MAP65-1 appeared in the phragmoplast midline. We show that MAP65-1 could acquire the function of MAP65-3 when the C terminus of MAP65-3, which contains the MT binding site, was grafted to it. Our results also show that MAP65-1 and MAP65-3 may share redundant functions in MT stabilization. Such a stabilization effect was likely brought about by MT binding and bundling. We conclude that MAP65-3 contains a distinct C-terminal MT binding site with a specific role in cross-linking antiparallel MTs toward their plus ends in the phragmoplast. PMID:22570443

What Is the Role of Manual Preference in Hand-Digit Mapping During Finger Counting? A Study in a Large Sample of Right- and Left-Handers.

PubMed

Zago, Laure; Badets, Arnaud

2016-01-01

The goal of the present study was to test whether there is a relationship between manual preference and hand-digit mapping in 369 French adults with similar numbers of right- and left-handers. Manual laterality was evaluated with the finger tapping test to evaluate hand motor asymmetry, and the Edinburgh handedness inventory was used to assess manual preference strength (MPS) and direction. Participants were asked to spontaneously "count on their fingers from 1 to 10" without indications concerning the hand(s) to be used. The results indicated that both MPS and hand motor asymmetry affect the hand-starting preference for counting. Left-handers with a strong left-hand preference (sLH) or left-hand motor asymmetry largely started to count with their left hand (left-starter), while right-handers with a strong right-hand preference (sRH) or right-hand motor asymmetry largely started to count with their right hand (right-starter). Notably, individuals with weak MPS did not show a hand-starting preference. These findings demonstrated that manual laterality contributes to finger counting directionality. Lastly, the results showed a higher proportion of sLH left-starter individuals compared with sRH right-starters, indicating an asymmetric bias of MPS on hand-starting preference. We hypothesize that the higher proportion of sLH left-starters could be explained by the congruence between left-to-right hand-digit mapping and left-to-right mental number line representation that has been largely reported in the literature. Taken together, these results indicate that finger-counting habits integrate biological and cultural information. © The Author(s) 2015.

Astronaut Kevin Chilton displays map of Scandinavia on flight deck

NASA Technical Reports Server (NTRS)

1994-01-01

Astronaut Kevin P. Chilton, pilot, displays a map of Scandinavia on the Space Shuttle Endeavour's flight deck. Large scale maps such as this were used by the crew to locate specific sites of interest to the Space Radar Laboratory scientists. The crew then photographed the sites at the same time as the radar in the payload bay imaged them.

Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells.

PubMed

Pastor, William A; Pape, Utz J; Huang, Yun; Henderson, Hope R; Lister, Ryan; Ko, Myunggon; McLoughlin, Erin M; Brudno, Yevgeny; Mahapatra, Sahasransu; Kapranov, Philipp; Tahiliani, Mamta; Daley, George Q; Liu, X Shirley; Ecker, Joseph R; Milos, Patrice M; Agarwal, Suneet; Rao, Anjana

2011-05-19

5-hydroxymethylcytosine (5hmC) is a modified base present at low levels in diverse cell types in mammals. 5hmC is generated by the TET family of Fe(II) and 2-oxoglutarate-dependent enzymes through oxidation of 5-methylcytosine (5mC). 5hmC and TET proteins have been implicated in stem cell biology and cancer, but information on the genome-wide distribution of 5hmC is limited. Here we describe two novel and specific approaches to profile the genomic localization of 5hmC. The first approach, termed GLIB (glucosylation, periodate oxidation, biotinylation) uses a combination of enzymatic and chemical steps to isolate DNA fragments containing as few as a single 5hmC. The second approach involves conversion of 5hmC to cytosine 5-methylenesulphonate (CMS) by treatment of genomic DNA with sodium bisulphite, followed by immunoprecipitation of CMS-containing DNA with a specific antiserum to CMS. High-throughput sequencing of 5hmC-containing DNA from mouse embryonic stem (ES) cells showed strong enrichment within exons and near transcriptional start sites. 5hmC was especially enriched at the start sites of genes whose promoters bear dual histone 3 lysine 27 trimethylation (H3K27me3) and histone 3 lysine 4 trimethylation (H3K4me3) marks. Our results indicate that 5hmC has a probable role in transcriptional regulation, and suggest a model in which 5hmC contributes to the 'poised' chromatin signature found at developmentally-regulated genes in ES cells.

Spectral Mapping at Asteroid 101955 Bennu

NASA Astrophysics Data System (ADS)

Clark, Beth Ellen; Hamilton, Victoria E.; Emery, Joshua P.; Hawley, C. Luke; Howell, Ellen S.; Lauretta, Dante; Simon, Amy A.; Christensen, Philip R.; Reuter, Dennis

2017-10-01

The OSIRIS-REx Asteroid Sample Return mission was launched in September 2016. The main science surveys of asteroid 101955 Bennu start in March 2019. Science instruments include a Visible-InfraRed Spectrometer (OVIRS) and a Thermal Emission Spectrometer (OTES) that will produce observations that will be co-registered to the tessellated shape model of Bennu (the fundamental unit of which is a triangular facet). One task of the science team is to synthesize the results in real time during proximity operations to contribute to selection of the sampling site. Hence, we will be focused on quickly producing spectral maps for: (1) mineral abundances; (2) band strengths of minerals and chemicals (including a search for the subtle ~5% absorption feature produced by organics in meteorites); and (3) temperature and thermal inertia values. In sum, we will be producing on the order of ~60 spectral maps of Bennu’s surface composition and thermophysical properties. Due to overlapping surface spots, simulations of our spectral maps show there may be an opportunity to perform spectral super-resolution. We have a large parameter space of choices available in creating spectral maps of Bennu, including: (a) mean facet size (shape model resolution), (b) percentage of overlap between subsequent spot measurements, (c) the number of spectral spots measured per facet, and (d) the mathematical algorithm used to combine the overlapping spots (or bin them on a per-facet basis). Projection effects -- caused by irregular sampling of an irregularly shaped object with circular spectrometer fields-of-view and then mapping these circles onto triangular facets -- can be intense. To prepare for prox ops, we are simulating multiple mineralogical “truth worlds” of Bennu to study the projection effects that result from our planned methods of spectral mapping. This presentation addresses: Can we combine the three planned global surveys of the asteroid (to be obtained at different phase angles) to create a spectral map with higher spatial resolution than the native spectrometer field-of-view in order to increase our confidence in detection of a spatially small occurrence of organics on Bennu?

Where can cone penetrometer technology be applied? Development of a map of Europe regarding the soil penetrability.

PubMed

Fleischer, Matthias; van Ree, Derk; Leven, Carsten

2014-01-01

Over the past decades, significant efforts have been invested in the development of push-in technology for site characterization and monitoring for geotechnical and environmental purposes and have especially been undertaken in the Netherlands and Germany. These technologies provide the opportunity for faster, cheaper, and collection of more reliable subsurface data. However, to maximize the technology both from a development and implementation point of view, it is necessary to have an overview of the areas suitable for the application of this type of technology. Such an overview is missing and cannot simply be read from existing maps and material. This paper describes the development of a map showing the feasibility or applicability of Direct Push/Cone Penetrometer Technology (DPT/CPT) in Europe which depends on the subsurface and its extremely varying properties throughout Europe. Subsurface penetrability is dependent on a range of factors that have not been mapped directly or can easily be inferred from existing databases, especially the maximum depth reachable would be of interest. Among others, it mainly depends on the geology, the soil mechanical properties, the type of equipment used as well as soil-forming processes. This study starts by looking at different geological databases available at the European scale. Next, a scheme has been developed linking geological properties mapped to geotechnical properties to determine basic penetrability categories. From this, a map of soil penetrability is developed and presented. Validating the output by performing field tests was beyond the scope of this study, but for the country of the Netherlands, this map has been compared against a database containing actual cone penetrometer depth data to look for possible contradictory results that would negate the approach. The map for the largest part of Europe clearly shows that there is a much wider potential for the application of Direct Push Technology than is currently seen. The study also shows that there is a lack of large-scale databases that contain depth-resolved data as well as soil mechanical and physical properties that can be used for engineering purposes in relation to the subsurface.

Utilizing HDF4 File Content Maps for the Cloud

NASA Technical Reports Server (NTRS)

Lee, Hyokyung Joe

2016-01-01

We demonstrate a prototype study that HDF4 file content map can be used for efficiently organizing data in cloud object storage system to facilitate cloud computing. This approach can be extended to any binary data formats and to any existing big data analytics solution powered by cloud computing because HDF4 file content map project started as long term preservation of NASA data that doesn't require HDF4 APIs to access data.

USGS US topo maps for Alaska

USGS Publications Warehouse

Anderson, Becci; Fuller, Tracy

2014-01-01

In July 2013, the USGS National Geospatial Program began producing new topographic maps for Alaska, providing a new map series for the state known as US Topo. Prior to the start of US Topo map production in Alaska, the most detailed statewide USGS topographic maps were 15-minute 1:63,360-scale maps, with their original production often dating back nearly fifty years. The new 7.5-minute digital maps are created at 1:25,000 map scale, and show greatly increased topographic detail when compared to the older maps. The map scale and data specifications were selected based on significant outreach to various map user groups in Alaska. This multi-year mapping initiative will vastly enhance the base topographic maps for Alaska and is possible because of improvements to key digital map datasets in the state. The new maps and data are beneficial in high priority applications such as safety, planning, research and resource management. New mapping will support science applications throughout the state and provide updated maps for parks, recreation lands and villages.

Healthy habits for weight loss

MedlinePlus

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Regional Topographic Views of Mars from MOLA

NASA Technical Reports Server (NTRS)

2000-01-01

With one year of global mapping of the Mars Global Surveyor mission completed, the MOLA dataset has achieved excellent spatial and vertical resolution. The maps below (and above) have been produced from the altimetric observations collected during MOLA's first year of global mapping and provide a variety of regional topographic views of the Martian surface. The maps were compiled from a data base of 266.7 million laser altimetric measurements collected between March 1, 1999 and February 29, 2000. In each map the spatial resolution is approximately 1/16o by 1/32o (where 1o on Mars is about 59 km) and the vertical accuracy is approximately 1 meter. Note that the sizes of the regions vary. Click on image for to see full resolution (Warning! these are large files) [figure removed for brevity, see original site] Nirgal Vallis region: 23o to 33o S; 313 to 323o E.

[figure removed for brevity, see original site] Locras Valles region: 5o to 15o N; 45 to 55o E.

[figure removed for brevity, see original site] Syrtis Major: 5o to 15o S; 62 to 72o E.

[figure removed for brevity, see original site] Viking 1 landing site: 20o to 25o N; 310 to 315o E. The landing site is marked by the plus sign.

[figure removed for brevity, see original site] Nicholson crater: 5o S to 5o N; 190 to 200o E. [figure removed for brevity, see original site] Schiaparelli crater: 8o S to 2o N; 12 to 22o E.

Interstitial telomeric sequences in human chromosomes cluster with common fragile sites, mutagen sensitive sites, viral integration sites, cancer breakpoints, proto-oncogenes and breakpoints involved in primate evolution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Adekunle, S.S.A.; Wyandt, H.; Mark, H.F.L.

1994-09-01

Recently we mapped the telomeric repeat sequences to 111 interstitial sites in the human genome and to sites of gaps and breaks induced by aphidicolin and sister chromatid exchange sites detected by BrdU. Many of these sites correspond to conserved fragile sites in man, gorilla and chimpazee, to sites of conserved sister chromatid exchange in the mammalian X chromosome, to mutagenic sensitive sites, mapped locations of proto-oncogenes, breakpoints implicated in primate evolution and to breakpoints indicated as the sole anomaly in neoplasia. This observation prompted us to investigate if the interstitial telomeric sites cluster with these sites. An extensive literaturemore » search was carried out to find all the available published sites mentioned above. For comparison, we also carried out a statistical analysis of the clustering of the sites of the telomeric repeats with the gene locations where only nucleotide mutations have been observed as the only chromosomal abnormality. Our results indicate that the telomeric repeats cluster most with fragile sites, mutagenic sensitive sites and breakpoints implicated in primate evolution and least with cancer breakpoints, mapped locations of proto-oncogenes and other genes with nucleotide mutations.« less

Preliminary Estimation of Kappa Parameter in Croatia

NASA Astrophysics Data System (ADS)

Stanko, Davor; Markušić, Snježana; Ivančić, Ines; Mario, Gazdek; Gülerce, Zeynep

2017-12-01

Spectral parameter kappa κ is used to describe spectral amplitude decay “crash syndrome” at high frequencies. The purpose of this research is to estimate spectral parameter kappa for the first time in Croatia based on small and moderate earthquakes. Recordings of local earthquakes with magnitudes higher than 3, epicentre distances less than 150 km, and focal depths less than 30 km from seismological stations in Croatia are used. The value of kappa was estimated from the acceleration amplitude spectrum of shear waves from the slope of the high-frequency part where the spectrum starts to decay rapidly to a noise floor. Kappa models as a function of a site and distance were derived from a standard linear regression of kappa-distance dependence. Site kappa was determined from the extrapolation of the regression line to a zero distance. The preliminary results of site kappa across Croatia are promising. In this research, these results are compared with local site condition parameters for each station, e.g. shear wave velocity in the upper 30 m from geophysical measurements and with existing global shear wave velocity - site kappa values. Spatial distribution of individual kappa’s is compared with the azimuthal distribution of earthquake epicentres. These results are significant for a couple of reasons: to extend the knowledge of the attenuation of near-surface crust layers of the Dinarides and to provide additional information on the local earthquake parameters for updating seismic hazard maps of studied area. Site kappa can be used in the re-creation, and re-calibration of attenuation of peak horizontal and/or vertical acceleration in the Dinarides area since information on the local site conditions were not included in the previous studies.

Quantification of map similarity to magnetic pre-screening for heavy metal pollution assessment in top soil

NASA Astrophysics Data System (ADS)

Cao, L.; Appel, E.; Roesler, W.; Ojha, G.

2013-12-01

From numerous published results, the link between magnetic concentration and heavy metal (HM) concentrations is well established. However, bivariate correlation analysis does not imply causality, and if there are extreme values, which often appear in magnetic data, they can lead to seemingly excellent correlation. It seems clear that site selection for chemical sampling based on magnetic pre-screening can deliver a superior result for outlining HM pollution, but this conclusion has only been drawn from qualitative evaluation so far. In this study, we use map similarity comparison techniques to demonstrate the usefulness of a combined magnetic-chemical approach quantitatively. We chose available data around the 'Schwarze Pumpe', a large coal burning power plant complex located in eastern Germany. The site of 'Schwarze Pumpe' is suitable for a demonstration study as soil in its surrounding is heavy fly-ash polluted, the magnetic natural background is very low, and magnetic investigations can be done in undisturbed forest soil. Magnetic susceptibility (MS) of top soil was measured by a Bartington MS2D surface sensor at 180 locations and by a SM400 downhole device in ~0.5m deep vertical sections at 90 locations. Cores from the 90 downhole sites were also studied for HM analysis. From these results 85 sites could be used to determine a spatial distribution map of HM contents reflecting the 'True' situation of pollution. Different sets comprising 30 sites were chosen by arbitrarily selection from the above 85 sample sites (we refer to four such maps here: S1-4). Additionally, we determined a 'Targeted' map from 30 sites selected on the basis of the pre-screening MS results. The map comparison process is as follows: (1) categorization of all absolute values into five classes by the Natural Breaks classification method; (2) use Delaunay triangulation for connecting the sample locations in the x-y plane; (3) determination of a distribution map of triangular planes with classified values as the Z coordinate; (4) calculation of normal vectors for each individual triangular plane; (5)transformation to the TINs into raster data assigning the same normal vectors to all grid-points which are inside the same TIN; (6) calculation of the root-mean-square of angles between normal vectors of two maps at the same grid points. Additionally, we applied the kappa statistics method to assess map similarities, and moreover developed a Fuzzy set approach. Combining both methods using indices of Khisto, Klocation, Kappa, Kfuzzy obtains a broad comparison system, which allows determining the degree of similarity and also the spatial distribution of similarity between two maps. The results indicate that the similarity between the 'Targeted' and 'True' distribution map is higher than that between 'S1-4' and the 'True' map. It manifests that magnetic pre-screening can provide a reliable basis for targeted selection of chemical sampling sites demonstrating the superior efficiency of a combined magnetic-chemical site assessment in comparison to a traditional chemical-only approach.

NOVEL EPIGENETIC CHANGES IN CDKN2A ARE ASSOCIATED WITH PROGRESSION OF CERVICAL INTRAEPITHELIAL NEOPLASIA

PubMed Central

Wijetunga, N. Ari; Belbin, Thomas J.; Burk, Robert D.; Whitney, Kathleen; Abadi, Maria; Greally, John M.; Einstein, Mark H.; Schlecht, Nicolas F.

2016-01-01

Objective To conduct a comprehensive mapping of the genomic DNA methylation in CDKN2A, which codes for the p16INK4A and p14ARF proteins, and 14 of the most promising DNA methylation marker candidates previously reported to be associated with progression of low-grade cervical intraepithelial neoplasia (CIN1) to cervical cancer. Methods We analyzed DNA methylation in 68 HIV-seropositive and negative women with incident CIN1, CIN2, CIN3 and invasive cervical cancer, assaying 120 CpG dinucleotide sites spanning APC, CDH1, CDH13, CDKN2A, CDKN2B, DAPK1, FHIT, GSTP1, HIC1, MGMT, MLH1, RARB, RASSF1, TERT and TIMP3 using the Illumina Infinium array. Validation was performed using high resolution mapping of the target genes with HELP-tagging for 286 CpGs, followed by fine mapping of candidate genes with targeted bisulfite sequencing. We assessed for statistical differences in DNA methylation levels for each CpG loci assayed using univariate and multivariate methods correcting for multiple comparisons. Results In our discovery sample set, we identified dose dependent differences in DNA methylation with grade of disease in CDKN2A, APC, MGMT, MLH1 and HIC1, whereas single CpG locus differences between CIN2/3 and cancer groups were seen for CDH13, DAPK1 and TERT. Only those CpGs in the gene body of CDKN2A showed a monotonic increase in methylation between persistent CIN1, CIN2, CIN3 and cancers. Conclusion Our data suggests a novel link between early cervical disease progression and DNA methylation in a region downstream of the CDKN2A transcription start site that may lead to increased p16INK4A/p14ARF expression prior to development of malignant disease. PMID:27401842

Critical metals in manganese nodules from the Cook Islands EEZ, abundances and distributions

USGS Publications Warehouse

Hein, James R.; Spinardi, Francesca; Okamoto, Nobuyuki; Mizell, Kira; Thorburn, Darryl; Tawake, Akuila

2015-01-01

Compiled data from a series of four cruises by the Japan International Cooperation Agency and the Mining agency of Japan from 1985 to 2000 were used to generate a map that defines the statistical distribution of nodule abundance throughout the EEZ, except the Manihiki Plateau. The abundance distribution map shows a belt of high nodule abundance (19–45 kg/m2) that starts in the southeast corner of the EEZ, runs northwest, and also bifurcates into a SW trending branch. Small, isolated areas contain abundances of nodules of up to 58 kg/m2. Six ~ 20,000 km2 areas of particularly high abundance were chosen to represent potential exploration areas, and maps for metal concentration were generated to visualize metal distribution and to extrapolate estimated metal tonnages within the six sites and the EEZ as a whole. Grades for Mn, Cu, and Ni are low in CIs nodules in areas of high abundance; however, Ti, Co, and REY show high contents where nodule abundances are high. Of the six areas identified to represent a range of metal contents, one at the northern end of the N-S abundance main belt optimizes the most metals and would yield the highest dry metric tons for Mn (61,002,292), Ni (1,247,834), Mo (186,166), V (356,247), W (30,215), and Zr (195,323). When compared with the Clarion–Clipperton Zone, the CIs nodules show higher nodule abundances (> 25 kg/m2 over ~ 123,844 km2), and are more enriched in the green-tech, high-tech, and energy metals Co, Ti, Te, Nb, REY, Pt, and Zr. The CIs EEZ shows a significant resource potential for these critical metals due to their high prices, high demand, and the high nodule abundance, which will allow for a smaller footprint for a 20-year mine site and therefore smaller environmental impact.

Novel epigenetic changes in CDKN2A are associated with progression of cervical intraepithelial neoplasia.

PubMed

Wijetunga, N Ari; Belbin, Thomas J; Burk, Robert D; Whitney, Kathleen; Abadi, Maria; Greally, John M; Einstein, Mark H; Schlecht, Nicolas F

2016-09-01

To conduct a comprehensive mapping of the genomic DNA methylation in CDKN2A, which codes for the p16(INK4A) and p14(ARF) proteins, and 14 of the most promising DNA methylation marker candidates previously reported to be associated with progression of low-grade cervical intraepithelial neoplasia (CIN1) to cervical cancer. We analyzed DNA methylation in 68 HIV-seropositive and negative women with incident CIN1, CIN2, CIN3 and invasive cervical cancer, assaying 120 CpG dinucleotide sites spanning APC, CDH1, CDH13, CDKN2A, CDKN2B, DAPK1, FHIT, GSTP1, HIC1, MGMT, MLH1, RARB, RASSF1, TERT and TIMP3 using the Illumina Infinium array. Validation was performed using high resolution mapping of the target genes with HELP-tagging for 286 CpGs, followed by fine mapping of candidate genes with targeted bisulfite sequencing. We assessed for statistical differences in DNA methylation levels for each CpG loci assayed using univariate and multivariate methods correcting for multiple comparisons. In our discovery sample set, we identified dose dependent differences in DNA methylation with grade of disease in CDKN2A, APC, MGMT, MLH1 and HIC1, whereas single CpG locus differences between CIN2/3 and cancer groups were seen for CDH13, DAPK1 and TERT. Only those CpGs in the gene body of CDKN2A showed a monotonic increase in methylation between persistent CIN1, CIN2, CIN3 and cancers. Our data suggests a novel link between early cervical disease progression and DNA methylation in a region downstream of the CDKN2A transcription start site that may lead to increased p16(INK4A)/p14(ARF) expression prior to development of malignant disease. Copyright © 2016 Elsevier Inc. All rights reserved.

Structure-function analysis of the extracellular domain of the pneumococcal cell division site positioning protein MapZ

NASA Astrophysics Data System (ADS)

Manuse, Sylvie; Jean, Nicolas L.; Guinot, Mégane; Lavergne, Jean-Pierre; Laguri, Cédric; Bougault, Catherine M.; Vannieuwenhze, Michael S.; Grangeasse, Christophe; Simorre, Jean-Pierre

2016-06-01

Accurate placement of the bacterial division site is a prerequisite for the generation of two viable and identical daughter cells. In Streptococcus pneumoniae, the positive regulatory mechanism involving the membrane protein MapZ positions precisely the conserved cell division protein FtsZ at the cell centre. Here we characterize the structure of the extracellular domain of MapZ and show that it displays a bi-modular structure composed of two subdomains separated by a flexible serine-rich linker. We further demonstrate in vivo that the N-terminal subdomain serves as a pedestal for the C-terminal subdomain, which determines the ability of MapZ to mark the division site. The C-terminal subdomain displays a patch of conserved amino acids and we show that this patch defines a structural motif crucial for MapZ function. Altogether, this structure-function analysis of MapZ provides the first molecular characterization of a positive regulatory process of bacterial cell division.

Image Analysis for Facility Siting: a Comparison of Lowand High-altitude Image Interpretability for Land Use/land Cover Mapping

NASA Technical Reports Server (NTRS)

Borella, H. M.; Estes, J. E.; Ezra, C. E.; Scepan, J.; Tinney, L. R.

1982-01-01

For two test sites in Pennsylvania the interpretability of commercially acquired low-altitude and existing high-altitude aerial photography are documented in terms of time, costs, and accuracy for Anderson Level II land use/land cover mapping. Information extracted from the imagery is to be used in the evaluation process for siting energy facilities. Land use/land cover maps were drawn at 1:24,000 scale using commercially flown color infrared photography obtained from the United States Geological Surveys' EROS Data Center. Detailed accuracy assessment of the maps generated by manual image analysis was accomplished employing a stratified unaligned adequate class representation. Both 'area-weighted' and 'by-class' accuracies were documented and field-verified. A discrepancy map was also drawn to illustrate differences in classifications between the two map scales. Results show that the 1:24,000 scale map set was more accurate (99% to 94% area-weighted) than the 1:62,500 scale set, especially when sampled by class (96% to 66%). The 1:24,000 scale maps were also more time-consuming and costly to produce, due mainly to higher image acquisition costs.

National Park Service Vegetation Mapping Inventory Program: Appalachian National Scenic Trail vegetation mapping project

USGS Publications Warehouse

Hop, Kevin D.; Strassman, Andrew C.; Hall, Mark; Menard, Shannon; Largay, Ery; Sattler, Stephanie; Hoy, Erin E.; Ruhser, Janis; Hlavacek, Enrika; Dieck, Jennifer

2017-01-01

The National Park Service (NPS) Vegetation Mapping Inventory (VMI) Program classifies, describes, and maps existing vegetation of national park units for the NPS Natural Resource Inventory and Monitoring (I&M) Program. The NPS VMI Program is managed by the NPS I&M Division and provides baseline vegetation information to the NPS Natural Resource I&M Program. The U.S. Geological Survey Upper Midwest Environmental Sciences Center, NatureServe, NPS Northeast Temperate Network, and NPS Appalachian National Scenic Trail (APPA) have completed vegetation classification and mapping of APPA for the NPS VMI Program.Mappers, ecologists, and botanists collaborated to affirm vegetation types within the U.S. National Vegetation Classification (USNVC) of APPA and to determine how best to map the vegetation types by using aerial imagery. Analyses of data from 1,618 vegetation plots were used to describe USNVC associations of APPA. Data from 289 verification sites were collected to test the field key to vegetation associations and the application of vegetation associations to a sample set of map polygons. Data from 269 validation sites were collected to assess vegetation mapping prior to submitting the vegetation map for accuracy assessment (AA). Data from 3,265 AA sites were collected, of which 3,204 were used to test accuracy of the vegetation map layer. The collective of these datasets affirmed 280 USNVC associations for the APPA vegetation mapping project.To map the vegetation and land cover of APPA, 169 map classes were developed. The 169 map classes consist of 150 that represent natural (including ruderal) vegetation types in the USNVC, 11 that represent cultural (agricultural and developed) vegetation types in the USNVC, 5 that represent natural landscapes with catastrophic disturbance or some other modification to natural vegetation preventing accurate classification in the USNVC, and 3 that represent nonvegetated water (non-USNVC). Features were interpreted from viewing 4-band digital aerial imagery using digital onscreen three-dimensional stereoscopic workflow systems in geographic information systems (GIS). (Digital aerial imagery was collected each fall during 2009–11 to capture leaf-phenology change of hardwood trees across the latitudinal range of APPA.) The interpreted data were digitally and spatially referenced, thus making the spatial-database layers usable in GIS. Polygon units were mapped to either a 0.5-hectare (ha) or 0.25-ha minimum mapping unit, depending on vegetation type or scenario; however, polygon units were mapped to 0.1 ha for alpine vegetation.A geodatabase containing various feature-class layers and tables provide locations and support data to USNVC vegetation types (vegetation map layer), vegetation plots, verification sites, validation sites, AA sites, project boundary extent and zones, and aerial image centers and flight lines. The feature-class layer and related tables of the vegetation map layer provide 30,395 polygons of detailed attribute data covering 110,919.7 ha, with an average polygon size of 3.6 ha; the vegetation map coincides closely with the administrative boundary for APPA.Summary reports generated from the vegetation map layer of the map classes representing USNVC natural (including ruderal) vegetation types apply to 28,242 polygons (92.9% of polygons) and cover 106,413.0 ha (95.9%) of the map extent for APPA. The map layer indicates APPA to be 92.4% forest and woodland (102,480.8 ha), 1.7% shrubland (1866.3 ha), and 1.8% herbaceous cover (2,065.9 ha). Map classes representing park-special vegetation (undefined in the USNVC) apply to 58 polygons (0.2% of polygons) and cover 404.3 ha (0.4%) of the map extent. Map classes representing USNVC cultural types apply to 1,777 polygons (5.8% of polygons) and cover 2,516.3 ha (2.3%) of the map extent. Map classes representing nonvegetated water (non-USNVC) apply to 332 polygons (1.1% of polygons) and cover 1,586.2 ha (1.4%) of the map extent.

Geologic map of the MTM 25047 and 20047 quadrangles, central Chryse Planitia/Viking 1 Lander site, Mars

USGS Publications Warehouse

Crumpler, L.S.; Craddock, R.A.; Aubele, J.C.

2001-01-01

This map uses Viking Orbiter image data and Viking 1 Lander image data to evaluate the geologic history of a part of Chryse Planitia, Mars. The map area lies at the termini of the Maja and Kasei Valles outwash channels and includes the site of the Viking 1 Lander. The photomosaic base for these quadrangles was assembled from 98 Viking Orbiter frames comprising 1204 pixels per line and 1056 lines and ranging in resolution from 20 to 200 m/pixel. These orbital image data were supplemented with images of the surface as seen from the Viking 1 Lander, one of only three sites on the martian surface where planetary geologic mapping is assisted by ground truth.

Independent mapping methods reveal rotational activation near pulmonary veins where atrial fibrillation terminates before pulmonary vein isolation.

PubMed

Navara, Rachita; Leef, George; Shenasa, Fatemah; Kowalewski, Christopher; Rogers, Albert J; Meckler, Gabriela; Zaman, Junaid A B; Baykaner, Tina; Park, Shirley; Turakhia, Mintu P; Zei, Paul; Viswanathan, Mohan; Wang, Paul J; Narayan, Sanjiv M

2018-01-29

To investigate mechanisms by which atrial fibrillation (AF) may terminate during ablation near the pulmonary veins before the veins are isolated (PVI). It remains unstudied how AF may terminate during ablation before PVs are isolated, or how patients with PV reconnection can be arrhythmia-free. We studied patients in whom PV antral ablation terminated AF before PVI, using two independent mapping methods. We studied patients with AF referred for ablation, in whom biatrial contact basket electrograms were studied by both an activation/phase mapping method and by a second validated mapping method reported not to create false rotational activity. In 22 patients (age 60.1 ± 10.4, 36% persistent AF), ablation at sites near the PVs terminated AF (77% to sinus rhythm) prior to PVI. AF propagation revealed rotational (n  =  20) and focal (n  =  2) patterns at sites of termination by mapping method 1 and method 2. Both methods showed organized sites that were spatially concordant (P < 0.001) with similar stability (P < 0.001). Vagal slowing was not observed at sites of AF termination. PV antral regions where ablation terminated AF before PVI exhibited rotational and focal activation by two independent mapping methods. These data provide an alternative mechanism for the success of PVI, and may explain AF termination before PVI or lack of arrhythmias despite PV reconnection. Mapping such sites may enable targeted PV lesion sets and improved freedom from AF. © 2018 Wiley Periodicals, Inc.

Cancer--Living with Cancer: MedlinePlus Health Topic

MedlinePlus

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Selecting PPE for the Workplace (Personal Protective Equipment for the Eyes and Face)

MedlinePlus

... Additional References Site Map Credits Selecting Personal Protective Equipment (PPE) for the Workplace Impact Heat Chemicals Dust Optical Radiation OSHA Requirements Home | Selecting Personal Protective Equipment (PPE) for the Workplace | OSHA Requirements Site Map | ...

Detailed Geophysical Fault Characterization in Yucca Flat, Nevada Test Site, Nevada

USGS Publications Warehouse

Asch, Theodore H.; Sweetkind, Donald S.; Burton, Bethany L.; Wallin, Erin L.

2009-01-01

Yucca Flat is a topographic and structural basin in the northeastern part of the Nevada Test Site (NTS) in Nye County, Nevada. Between the years 1951 and 1992, 659 underground nuclear tests took place in Yucca Flat; most were conducted in large, vertical excavations that penetrated alluvium and the underlying Cenozoic volcanic rocks. Radioactive and other potential chemical contaminants at the NTS are the subject of a long-term program of investigation and remediation by the U.S. Department of Energy (DOE), National Nuclear Security Administration, Nevada Site Office, under its Environmental Restoration Program. As part of the program, the DOE seeks to assess the extent of contamination and to evaluate the potential risks to humans and the environment from byproducts of weapons testing. To accomplish this objective, the DOE Environmental Restoration Program is constructing and calibrating a ground-water flow model to predict hydrologic flow in Yucca Flat as part of an effort to quantify the subsurface hydrology of the Nevada Test Site. A necessary part of calibrating and evaluating a model of the flow system is an understanding of the location and characteristics of faults that may influence ground-water flow. In addition, knowledge of fault-zone architecture and physical properties is a fundamental component of the containment of the contamination from underground nuclear tests, should such testing ever resume at the Nevada Test Site. The goal of the present investigation is to develop a detailed understanding of the geometry and physical properties of fault zones in Yucca Flat. This study was designed to investigate faults in greater detail and to characterize fault geometry, the presence of fault splays, and the fault-zone width. Integrated geological and geophysical studies have been designed and implemented to work toward this goal. This report describes the geophysical surveys conducted near two drill holes in Yucca Flat, the data analyses performed, and the integrated interpretations developed from the suite of geophysical methodologies utilized in this investigation. Data collection for this activity started in the spring of 2005 and continued into 2006. A suite of electrical geophysical surveys were run in combination with ground magnetic surveys; these surveys resulted in high-resolution subsurface data that portray subsurface fault geometry at the two sites and have identified structures not readily apparent from surface geologic mapping, potential field geophysical data, or surface effects fracture maps.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kolonko, Nadine; Bannach, Oliver; Aschermann, Katja

Viroids are single-stranded, circular RNAs of 250 to 400 bases, that replicate autonomously in their host plants but do not code for a protein. Viroids of the family Pospiviroidae, of which potato spindle tuber viroid (PSTVd) is the type strain, are replicated by the host's DNA-dependent RNA polymerase II in the nucleus. To analyze the initiation site of transcription from the (+)-stranded circles into (-)-stranded replication intermediates, we used a nuclear extract from a non-infected cell culture of the host plant S. tuberosum. The (-)-strands, which were de novo-synthesized in the extract upon addition of circular (+)-PSTVd, were purified bymore » affinity chromatography. This purification avoided contamination by host nucleic acids that had resulted in a misassignment of the start site in an earlier study. Primer-extension analysis of the de novo-synthesized (-)-strands revealed a single start site located in the hairpin loop of the left terminal region in circular PSTVd's secondary structure. This start site is supported further by analysis of the infectivity and replication behavior of site-directed mutants in planta.« less

Epicardial-endocardial breakthrough during stable atrial macroreentry: Evidence from ultra-high-resolution 3-dimensional mapping.

PubMed

Pathik, Bhupesh; Lee, Geoffrey; Sacher, Frédéric; Haïssaguerre, Michel; Jaïs, Pierre; Massoullié, Grégoire; Derval, Nicolas; Sanders, Prashanthan; Kistler, Peter; Kalman, Jonathan M

2017-08-01

Evidence for epicardial-endocardial breakthrough (EEB) is derived from mapping inferences in patients with atrial fibrillation who may also have focal activations. The purpose of this study was to investigate whether EEB could be discerned during stable right atrial (RA) macroreentry using high-density high-spatial resolution 3-dimensional mapping. Macroreentry was diagnosed using 3-dimensional mapping and entrainment. Bipolar maps were reviewed for EEB defined as (1) presence of focal endocardial activation with radial spread unaccounted for by an endocardial wavefront and (2) present with the same timing on every tachycardia cycle. The EEB site was always in proximity to a line of endocardial conduction slowing or block. Distance and conduction velocity from the line of block to the EEB site was calculated. Electrograms at EEB sites were individually analyzed for morphology and to confirm direction of activation. Entrainment was performed at EEB sites. Twenty-six patients were studied. Fourteen examples of EEB were seen: 11 at the posterior RA (4 at the superior portion of the posterior wall and 7 at the inferior section) and 1 each at the cavotricuspid isthmus postablation, RA septum, and inferolateral RA. The mean area of the EEB site was 0.6 ± 0.2 cm 2 . A mean of 79.5% ± 18.6% of unipolar electrograms at the EEB site demonstrated an rS morphology. The mean distance and conduction velocity from the line of endocardial block to the EEB site at the posterior RA was 13.6 ± 2.3 mm and 59.3 ± 12.3 cm/s, respectively. In 4 patients, entrainment demonstrated that EEB sites were within the circuit and in 1 of these patients critical to arrhythmia maintenance. Activation maps during tachycardia and coronary sinus pacing demonstrated EEB at the same anatomic site. EEB sites were demonstrated in stable atrial macroreentry supported by systematic entrainment confirmation and demonstration of the same phenomenon during pacing. Copyright © 2017 Heart Rhythm Society. Published by Elsevier Inc. All rights reserved.

Feynman diagrams and rooted maps

NASA Astrophysics Data System (ADS)

Prunotto, Andrea; Alberico, Wanda Maria; Czerski, Piotr

2018-04-01

The rooted maps theory, a branch of the theory of homology, is shown to be a powerful tool for investigating the topological properties of Feynman diagrams, related to the single particle propagator in the quantum many-body systems. The numerical correspondence between the number of this class of Feynman diagrams as a function of perturbative order and the number of rooted maps as a function of the number of edges is studied. A graphical procedure to associate Feynman diagrams and rooted maps is then stated. Finally, starting from rooted maps principles, an original definition of the genus of a Feynman diagram, which totally differs from the usual one, is given.

The Design and Product of National 1:1000000 Cartographic Data of Topographic Map

NASA Astrophysics Data System (ADS)

Wang, Guizhi

2016-06-01

National administration of surveying, mapping and geoinformation started to launch the project of national fundamental geographic information database dynamic update in 2012. Among them, the 1:50000 database was updated once a year, furthermore the 1:250000 database was downsized and linkage-updated on the basis. In 2014, using the latest achievements of 1:250000 database, comprehensively update the 1:1000000 digital line graph database. At the same time, generate cartographic data of topographic map and digital elevation model data. This article mainly introduce national 1:1000000 cartographic data of topographic map, include feature content, database structure, Database-driven Mapping technology, workflow and so on.

Development of Tools and Techniques to Survey, Assess, Stabilise, Monitor and Preserve Underwater Archaeological Sites: SASMAP

NASA Astrophysics Data System (ADS)

Gregory, D. J.

2015-08-01

SASMAP's purpose is to develop new technologies and best practices in order to locate, assess and manage Europe's underwater cultural heritage in a more effective way than is possible today. SASMAP has taken an holistic- and process- based approach to investigating underwater environments and the archaeological sites contained therein. End user of the results of SASMAP are severalfold; i) to benefiet the SMEs involved in the project and development of their products for the offshore industry (not just for archaeological purposes) ii) a better understanding of the marine environment and its effect on archaeological materials iii) the collation of the results from the project into guidelines that can be used by cultural resource managers to better administer and optimise developer lead underwater archaeological project within Europe in accordance with European legislation (Treaty of Valetta (1992). Summarily the project has utilised a down scaling approach to localise archaeological sites at a large scale regional level. This has involved using innovative satellite imagery to obtain seamless topography maps over coastal areas and the seabed (accurate to a depth of 6m) as well as the development of a 3D sub bottom profiler to look within the seabed. Results obtained from the downscaling approach at the study areas in the project (Greece and Denmark) have enabled geological models to be developed inorder to work towards predictive modelling of where submerged prehistoric sites may be encountered. Once sites have been located an upscaling approach has been taken to assessing an individual site and the materials on and within it in order to better understand the state of preservation and dynamic conditions of a site and how it can best be preserved through in situ preservation or excavation. This has involved the development of equipment to monitor the seabed environment (open water and in sediments), equipment for sampling sediments and assessing the state of preservation of wood, once of the common materials on archaeological sites. The guidelines and all information and experiences obtained during the course of the project will be utilised to enhance and develop existing legislation and best practice for mapping and preserving Europe's underwater and coastal heritage. The project started in September 2012 and finished at the end of August 2015 and the aim of the paper is to give a brief introduction to the results of the project. Further information on the project is available at www.sasmap.eu

Examining the Use of Curriculum to Support Early Literacy Instruction: A Multiple Case Study of Head Start Teachers

ERIC Educational Resources Information Center

Mihai, Alina; Butera, Gretchen; Friesen, Amber

2017-01-01

Research Findings: This qualitative study examined how Head Start teachers thought about children's early literacy and how they enacted their thinking in a year-long curriculum reform effort. Data collected included interviews, observations, questionnaires, concept maps, and teachers' reflections on implementation. The results indicated that as…

Science as the Center of a Coherent, Integrated Early Childhood Curriculum

ERIC Educational Resources Information Center

French, Lucia

2004-01-01

This article describes the ScienceStart! Curriculum, an early childhood curriculum that takes coherently organized science content as the hub of an integrated approach. ScienceStart! maps onto the typical preschool day and may be adapted for use in full-day or half-day preschool programs. It is designed to support the important developmental…

Mapping the petroleum system - An investigative technique to explore the hydrocarbon fluid system

USGS Publications Warehouse

Magoon, L.B.; Dow, W.G.

2000-01-01

Creating a petroleum system map includes a series of logical steps that require specific information to explain the origin in time and space of discovered hydrocarbon occurrences. If used creatively, this map provides a basis on which to develop complementary plays and prospects. The logical steps include the characterization of a petroleum system (that is, to identify, map, and name the hydrocarbon fluid system) and the summary of these results on a folio sheet. A petroleum system map is based on the understanding that there are several levels of certainty from "guessing" to "knowing" that specific oil and gas accumulations emanated from a particular pod of active source rock. Levels of certainty start with the close geographic proximity of two or more accumulations, continues with the close stratigraphic proximity, followed by the similarities in bulk properties, and then detailed geochemical properties. The highest level of certainty includes the positive geochemical correlation of the hydrocarbon fluid in the accumulations to the extract of the active source rock. A petroleum system map is created when the following logic is implemented. Implementation starts when the oil and gas accumulations of a petroleum province are grouped stratigraphically and geographically. Bulk and geochemical properties are used to further refine the groups through the determination of genetically related oil and gas types. To this basic map, surface seeps and well shows are added. Similarly, the active source rock responsible for these hydrocarbon occurrences are mapped to further define the extent of the system. A folio sheet constructed for a hypothetical case study of the Deer-Boar(.) petroleum system illustrates this methodology.

GIS integration of the 1:2880 Stabile cadastre map sheets from Bukovina

NASA Astrophysics Data System (ADS)

Crǎciunescu, Vasile; Niè›U, Constantin; Timár, Gábor; Boicu, Alin; Rus, Ioan

2010-05-01

Starting with 1975, the North-West part of the Moldavia Principality was occupied by the Habsburg Monarchy and become known as Duchy of Bukovina. During the 143 years of Austrian rule (1775 - 1918), this territory was the subject of several topographic and cadastral surveys. The paper will focus on the cadastral maps produced under the Stabile cadaster (also known as Franciscan cadastre). In the Habsburg Empire, this cadastral survey was started in 1817, at an order of the Emperor Francis I of Austria, as a base for his land taxation reform. In Bukovina, the land registration system was introduced in 1832. The base maps, known as Katastralmappe or Parzellenplan, were drawn under the 1:2880 scale, using Viennese Klafter (fathom) as length unit (1 Viennese Klafter = 1.89648 meters). Each taxation parish (usually centered on the most important cities/villages) was surveyed and mapped individually. The map sheets were accompanied by several registers (e.g. register of building plots, register of land plots) with informations regarding the cadastral parcels. Today, such documents represent a valuable resource in reconstructing the natural and built environment. The study presents the way this maps can be georeferenced and integrated into modern GIS applications, for precise digitization, spatial analysis and 3D reconstruction. The base of the georeference is the knowledge of the projection and datum parameters of the survey in Bukovina as well as the sheet labeling system.

Quantifying the uncertainty in site amplification modeling and its effects on site-specific seismic-hazard estimation in the upper Mississippi embayment and adjacent areas

USGS Publications Warehouse

Cramer, C.H.

2006-01-01

The Mississippi embayment, located in the central United States, and its thick deposits of sediments (over 1 km in places) have a large effect on earthquake ground motions. Several previous studies have addressed how these thick sediments might modify probabilistic seismic-hazard maps. The high seismic hazard associated with the New Madrid seismic zone makes it particularly important to quantify the uncertainty in modeling site amplification to better represent earthquake hazard in seismic-hazard maps. The methodology of the Memphis urban seismic-hazard-mapping project (Cramer et al., 2004) is combined with the reference profile approach of Toro and Silva (2001) to better estimate seismic hazard in the Mississippi embayment. Improvements over previous approaches include using the 2002 national seismic-hazard model, fully probabilistic hazard calculations, calibration of site amplification with improved nonlinear soil-response estimates, and estimates of uncertainty. Comparisons are made with the results of several previous studies, and estimates of uncertainty inherent in site-amplification modeling for the upper Mississippi embayment are developed. I present new seismic-hazard maps for the upper Mississippi embayment with the effects of site geology incorporating these uncertainties.

The EM SSAB Annual Work Plan Process: Focusing Board Efforts and Resources - 13667

DOE Office of Scientific and Technical Information (OSTI.GOV)

Young, Ralph

One of the most daunting tasks for any new member of a local board of the Environmental Management Site Specific Advisory Board (EM SSAB) is to try to understand the scope of the clean-up activities going on at the site. In most cases, there are at least two or three major cleanup activities in progress as well as monitoring of past projects. When planning for future projects is added to the mix, the list of projects can be long. With the clean-up activities involving all major environmental media - air, water, soils, and groundwater, new EM SSAB members can findmore » themselves totally overwhelmed and ineffective. Helping new members get over this initial hurdle is a major objective of EM and all local boards of the EM SSAB. Even as members start to understand the size and scope of the projects at a site, they can still be frustrated at the length of time it takes to see results and get projects completed. Many project and clean-up timelines for most of the sites go beyond 10 years, so it's not unusual for an EM SSAB member to see the completion of only 1 or 2 projects over the course of their 6-year term on the board. This paper explores the annual work planning process of the EM SSAB local boards, one tool that can be used to educate EM SSAB members into seeing the broader picture for the site. EM SSAB local work plans divide the site into projects focused on a specific environmental issue or media such as groundwater and/or waste disposal options. Projects are further broken down into smaller segments by highlighting major milestones. Using these metrics, local boards of the EM SSAB can start to quantify the effectiveness of the project in achieving the ultimate goal of site clean-up. These metrics can also trigger board advice and recommendations for EM. At the beginning of each fiscal year, the EM SSAB work plan provides a road map with quantifiable checkpoints for activities throughout the year. When the work plans are integrated with site-specific, enforceable regulatory milestones, they can provide a comprehensive work plan for not only the board, but also regulators, site contractors, and DOE. Because the work plans are reviewed and approved by DOE, they carry some weight in holding local boards of the EM SSAB accountable. This structure provides the basis for local boards to achieve their primary function, to provide DOE with information, advice, and recommendations concerning issues affecting the EM program at the site. (authors)« less

Reported consent processes and demographics: a substudy of the INSIGHT Strategic Timing of AntiRetroviral Treatment trial

PubMed Central

Denning, Eileen; Sharma, Shweta; Smolskis, Mary; Touloumi, Giota; Walker, Sarah; Babiker, Abdel; Clewett, Megan; Emanuel, Ezekiel; Florence, Eric; Papadopoulos, Antonios; Sánchez, Adriana; Tavel, Jorge; Grady, Christine

2014-01-01

Objectives Efforts are needed to improve informed consent of participants in research. The Strategic Timing of AntiRetroviral Therapy (START) study provides a unique opportunity to study the effect of length and complexity of informed consent documents on understanding and satisfaction among geographically diverse participants. Methods Interested START sites were randomised to use either the standard consent form or the concise consent form for all of the site’s participants. Results A total of 4473 HIV-positive participants at 154 sites worldwide took part in the Informed Consent Substudy, with consent given in 11 primary languages. Most sites sent written information to potential participants in advance of clinic visits, usually including the consent form. At about half the sites, staff reported spending less than an hour per participant in the consent process. The vast majority of sites assessed participant understanding using informal nonspecific questions or clinical judgment. Conclusions These data reflect the interest of START research staff in evaluating the consent process and improving informed consent. The START Informed Consent Substudy is by far the largest study of informed consent intervention ever conducted. Its results have the potential to impact how consent forms are written around the world. PMID:25711320

MedlinePlus - Health Information from the National Library of Medicine

MedlinePlus

... MedlinePlus GO GO About MedlinePlus Site Map FAQs Customer Support Health Topics Drugs & Supplements Videos & Tools Español ... Connect for EHRs About MedlinePlus Site Map FAQs Customer Support Get email updates Subscribe to RSS Follow ...

Maps | Geospatial Data Science | NREL

Science.gov Websites

Maps Maps NREL develops an array of maps to support renewable energy development and generation resource in the United States by county Geothermal Maps of geothermal power plants, resources for enhanced geothermal systems, and hydrothermal sites in the United States Hydrogen Maps of hydrogen production

Digital geologic map database of the Nevada Test Site area, Nevada

USGS Publications Warehouse

Wahl, R.R.; Sawyer, D.A.; Minor, S.A.; Carr, M.D.; Cole, J.C.; Swadley, W.C.; Laczniak, R.J.; Warren, R.G.; Green, K.S.; Engle, C.M.

1997-01-01

Forty years of geologic investigations at the Nevada Test Site (NTS) have been digitized. These data include all geologic information that: (1) has been collected, and (2) can be represented on a map within the map borders at the map scale is included in the map digital coverages. The following coverages are included with this dataset: Coverage Type Description geolpoly Polygon Geologic outcrops geolflts line Fault traces geolatts Point Bedding attitudes, etc. geolcald line Caldera boundaries geollins line Interpreted lineaments geolmeta line Metamorphic gradients The above coverages are attributed with numeric values and interpreted information. The entity files documented below show the data associated with each coverage.

Head-started Kemp’s ridley turtle (Lepidochelys kempii) nest recorded in Florida: Possible implications

USGS Publications Warehouse

Shaver, Donna J.; Lamont, Margaret M.; Maxwell, Sharon; Walker, Jennifer Shelby; Dillingham, Ted

2016-01-01

A head-started Kemp’s ridley sea turtle (Lepidochelys kempii) was documented nesting on South Walton Beach, Florida on 25 May 2015. This record supports the possibility that exposure to Florida waters after being held in captivity through 1–3 yrs of age during the head-starting process may have influenced future nest site selection of this and perhaps other Kemp’s ridley turtles. Such findings could have important ramifications for marine water experimentation and release site selection for turtles that have been reared in captivity.

Application of remote sensor data to geologic analysis of the Bonanza Test Site Colorado

NASA Technical Reports Server (NTRS)

Lee, K. (Compiler)

1973-01-01

A geologic map of the Bonanza Test Site is nearing completion. Using published large scale geologic maps from various sources, the geology of the area is being compiled on a base scaled at 1:250,000. Sources of previously published geologic mapping include: (1) USGS Bulletins; (2) professional papers and geologic quadrangle maps; (3) Bureau of Mines reports; (4) Colorado School of Mines quarterlies; and (5) Rocky Mountain Association of Geologist Guidebooks. This compilation will be used to evaluate ERTS, Skylab, and remote sensing underflight data.

Evaluation of Story Maps to Enhance Public Engagement and Communication at Legacy Management Sites – 17334

DOE Office of Scientific and Technical Information (OSTI.GOV)

Castillo, Darina; Carpenter, Cliff; Linard, Joshua

Story Maps are being used in both public and private sectors to convey information to stakeholders, create enterprise platforms, and assist in decision making. Story Maps are web applications that combine maps, narrative text, images, and multimedia content to provide information. These applications provide a user-friendly platform to share the remarkable history of our sites, the complexity of their contamination and remediation, successes we achieve in our LTS&M activities, and even the challenges we face as we aim to fulfill our mission.

Satellite Power System (SPS) mapping of exclusion areas for rectenna sites

NASA Technical Reports Server (NTRS)

Blackburn, J. B., Jr.; Bavinger, B. A.

1978-01-01

The areas of the United States that were not available as potential sites for receiving antennas that are an integral part of the Satellite Power System concept are presented. Thirty-six variables with the potential to exclude the rectenna were mapped and coded in a computer. Some of these variables exclude a rectenna from locating within the area of its spatial influence, and other variables potentially exclude the rectenna. These maps of variables were assembled from existing data and were mapped on a grid system.

D Modelling and Mapping for Virtual Exploration of Underwater Archaeology Assets

NASA Astrophysics Data System (ADS)

Liarokapis, F.; Kouřil, P.; Agrafiotis, P.; Demesticha, S.; Chmelík, J.; Skarlatos, D.

2017-02-01

This paper investigates immersive technologies to increase exploration time in an underwater archaeological site, both for the public, as well as, for researchers and scholars. Focus is on the Mazotos shipwreck site in Cyprus, which is located 44 meters underwater. The aim of this work is two-fold: (a) realistic modelling and mapping of the site and (b) an immersive virtual reality visit. For 3D modelling and mapping optical data were used. The underwater exploration is composed of a variety of sea elements including: plants, fish, stones, and artefacts, which are randomly positioned. Users can experience an immersive virtual underwater visit in Mazotos shipwreck site and get some information about the shipwreck and its contents for raising their archaeological knowledge and cultural awareness.

Shear-wave velocity characterization of the USGS Hawaiian strong-motion network on the Island of Hawaii and development of an NEHRP site-class map

USGS Publications Warehouse

Wong, Ivan G.; Stokoe, Kenneth; Cox, Brady R.; Yuan, Jiabei; Knudsen, Keith L.; Terra, Fabia; Okubo, Paul G.; Lin, Yin-Cheng

2011-01-01

To assess the level and nature of ground shaking in Hawaii for the purposes of earthquake hazard mitigation and seismic design, empirical ground-motion prediction models are desired. To develop such empirical relationships, knowledge of the subsurface site conditions beneath strong-motion stations is critical. Thus, as a first step to develop ground-motion prediction models for Hawaii, spectral-analysis-of-surface-waves (SASW) profiling was performed at the 22 free-field U.S. Geological Survey (USGS) strong-motion sites on the Big Island to obtain shear-wave velocity (VS) data. Nineteen of these stations recorded the 2006 Kiholo Bay moment magnitude (M) 6.7 earthquake, and 17 stations recorded the triggered M 6.0 Mahukona earthquake. VS profiling was performed to reach depths of more than 100 ft. Most of the USGS stations are situated on sites underlain by basalt, based on surficial geologic maps. However, the sites have varying degrees of weathering and soil development. The remaining strong-motion stations are located on alluvium or volcanic ash. VS30 (average VS in the top 30 m) values for the stations on basalt ranged from 906 to 1908 ft/s [National Earthquake Hazards Reduction Program (NEHRP) site classes C and D], because most sites were covered with soil of variable thickness. Based on these data, an NEHRP site-class map was developed for the Big Island. These new VS data will be a significant input into an update of the USGS statewide hazard maps and to the operation of ShakeMap on the island of Hawaii.

Maximal Aerobic Power in Aging Men: Insights From a Record of 1-Hour Unaccompanied Cycling.

PubMed

Capelli, Carlo

2018-01-01

To analyze best 1-h unaccompanied performances of master athletes in ages ranging from 35 to 105 y to estimate the decay of maximal aerobic power (MAP) across the spectrum of age. MAP at the various ages was estimated by computing the metabolic power ([Formula: see text]) maintained to cover the distances during best 1-h unaccompanied performances established by master athletes of different classes of age and by assuming that they were able to maintain an [Formula: see text] equal to 88% of their MAP during 1 h of exhaustive exercise. MAP started monotonically decreasing at 47 y of age. Thereafter, it showed an average rate of decrease of ∼14% for the decades up to 105 y of age, similar to other classes of master athletes. The results confirm, by extending the analysis to centennial subjects, that MAP seems to start declining from the middle of the 5th decade of age, with an average percentage decay that is faster than that traditionally reported, even when one maintains a very active lifestyle. The proposed approach may be applied to other types of human locomotion for which the relationship between speed and [Formula: see text] is known.

Concept mapping as an approach for expert-guided model building: The example of health literacy.

PubMed

Soellner, Renate; Lenartz, Norbert; Rudinger, Georg

2017-02-01

Concept mapping served as the starting point for the aim of capturing the comprehensive structure of the construct of 'health literacy.' Ideas about health literacy were generated by 99 experts and resulted in 105 statements that were subsequently organized by 27 experts in an unstructured card sorting. Multidimensional scaling was applied to the sorting data and a two and three-dimensional solution was computed. The three dimensional solution was used in subsequent cluster analysis and resulted in a concept map of nine "clusters": (1) self-regulation, (2) self-perception, (3) proactive approach to health, (4) basic literacy and numeracy skills, (5) information appraisal, (6) information search, (7) health care system knowledge and acting, (8) communication and cooperation, and (9) beneficial personality traits. Subsequently, this concept map served as a starting point for developing a "qualitative" structural model of health literacy and a questionnaire for the measurement of health literacy. On the basis of questionnaire data, a "quantitative" structural model was created by first applying exploratory factor analyses (EFA) and then cross-validating the model with confirmatory factor analyses (CFA). Concept mapping proved to be a highly valuable tool for the process of model building up to translational research in the "real world". Copyright © 2016 Elsevier Ltd. All rights reserved.

Hydroxymethyl cytosine marks in the human mitochondrial genome are dynamic in nature.

PubMed

Ghosh, Sourav; Sengupta, Shantanu; Scaria, Vinod

2016-03-01

Apart from DNA methylation, hydroxymethylation has increasingly been studied as an important epigenetic mark. 5- hydroxymethylcytosines, though initially were thought to be an intermediary product of demethylation, recent studies suggest this to be a highly regulated process and modulated by the TET family of enzymes. Recent genome wide studies have shown that hydroxymethylcytosine marks are closely associated with the regulation of important biological processes like transcription and embryonic development. It is also known that aberrant hydroxymethylation marks have been associated with diseases like cancer. The presence of hydroxymethylcytosines in the mitochondrial genome has been earlier suggested, though the genome-scale map has not been laid out. In this present study, we have mapped and analyzed the hydroxymethylcytosine marks in the mitochondrial genome using 23 different publicly available datasets. We cross validated our data by checking for consistency across a subset of genomic regions previously annotated to hydroxymethylcytosines and show good consistency. We observe a dynamic distribution of hydroxymethylation marks in the mitochondrial genome. Unlike the methylcytosine marks, hydroxymethylcytosine marks are characterized by the lack of conservation across the samples considered, though similar cell types shared the pattern. We additionally observed that the hydroxymethylation marks are enriched in the upstream of GSS (gene start site) regions and in gene body as similar as nuclear genes. To the best of our knowledge, this is the first genome-scale map of hydroxymethyl cytosines in the human mitochondrial genome. Copyright © 2016 Elsevier B.V. and Mitochondria Research Society. All rights reserved.

Gamma-sky.net: Portal to the gamma-ray sky

NASA Astrophysics Data System (ADS)

Voruganti, Arjun; Deil, Christoph; Donath, Axel; King, Johannes

2017-01-01

http://gamma-sky.net is a novel interactive website designed for exploring the gamma-ray sky. The Map View portion of the site is powered by the Aladin Lite sky atlas, providing a scalable survey image tesselated onto a three-dimensional sphere. The map allows for interactive pan and zoom navigation as well as search queries by sky position or object name. The default image overlay shows the gamma-ray sky observed by the Fermi-LAT gamma-ray space telescope. Other survey images (e.g. Planck microwave images in low/high frequency bands, ROSAT X-ray image) are available for comparison with the gamma-ray data. Sources from major gamma-ray source catalogs of interest (Fermi-LAT 2FHL, 3FGL and a TeV source catalog) are overlaid over the sky map as markers. Clicking on a given source shows basic information in a popup, and detailed pages for every source are available via the Catalog View component of the website, including information such as source classification, spectrum and light-curve plots, and literature references. We intend for gamma-sky.net to be applicable for both professional astronomers as well as the general public. The website started in early June 2016 and is being developed as an open-source, open data project on GitHub (https://github.com/gammapy/gamma-sky). We plan to extend it to display more gamma-ray and multi-wavelength data. Feedback and contributions are very welcome!

Utilizing inventory information to calibrate a landscape simulation model

Treesearch

Steven R. Shifley; Frank R., III Thompson; David R. Larsen; David J. Mladenoff; Eric J. Gustafson

2000-01-01

LANDIS is a spatially explicit model that uses mapped landscape conditions as a starting point and projects the patterns in forest vegetation that will result from alternative harvest practices, alternative fire regimes, and wind events. LANDIS was originally developed for Lake States forests, but it is capable of handling the input, output, bookkeeping, and mapping...

NREL: Renewable Resource Data Center - Geothermal Resource Information

Science.gov Websites

Energy's Office of Energy Efficiency and Renewable Energy Geothermal Technologies Program. Its collection , and thermal springs. View NREL's Geothermal resource maps as well as maps for other renewable energy Geothermal Resource Information Geothermal Prospector Start exploring U.S. geothermal resources

Physical signals for protein-DNA recognition

NASA Astrophysics Data System (ADS)

Cao, Xiao-Qin; Zeng, Jia; Yan, Hong

2009-09-01

This paper discovers consensus physical signals around eukaryotic splice sites, transcription start sites, and replication origin start and end sites on a genome-wide scale based on their DNA flexibility profiles calculated by three different flexibility models. These salient physical signals are localized highly rigid and flexible DNAs, which may play important roles in protein-DNA recognition by the sliding search mechanism. The found physical signals lead us to a detailed hypothetical view of the search process in which a DNA-binding protein first finds a genomic region close to the target site from an arbitrary starting location by three-dimensional (3D) hopping and intersegment transfer mechanisms for long distances, and subsequently uses the one-dimensional (1D) sliding mechanism facilitated by the localized highly rigid DNAs to accurately locate the target flexible binding site within 30 bp (base pair) short distances. Guided by these physical signals, DNA-binding proteins rapidly search the entire genome to recognize a specific target site from the 3D to 1D pathway. Our findings also show that current promoter prediction programs (PPPs) based on DNA physical properties may suffer from lots of false positives because other functional sites such as splice sites and replication origins have similar physical signals as promoters do.

SITE-SPECIFIC MEASUREMENTS OF RESIDENTIAL RADON PROTECTION CATEGORY

EPA Science Inventory

The report describes a series of benchmark measurements of soil radon potential at seven Florida sites and compares the measurements with regional estimates of radon potential from the Florida radon protection map. The measurements and map were developed under the Florida Radon R...

CIDR

Science.gov Websites

Completed Projects Publications Contact Information NIH Contacts CIDR Contacts ___________________ -Contact Us -Privacy Policy -Site Map Search You are here: CIDR>Contact Information> CIDR Contacts CIDR 1812 Ashland Ave Suite 200 Baltimore, MD 21205 Contact Us | Privacy Policy | Site Map | Get Adobe

A hyper-temporal remote sensing protocol for high-resolution mapping of ecological sites

PubMed Central

Karl, Jason W.

2017-01-01

Ecological site classification has emerged as a highly effective land management framework, but its utility at a regional scale has been limited due to the spatial ambiguity of ecological site locations in the U.S. or the absence of ecological site maps in other regions of the world. In response to these shortcomings, this study evaluated the use of hyper-temporal remote sensing (i.e., hundreds of images) for high spatial resolution mapping of ecological sites. We posit that hyper-temporal remote sensing can provide novel insights into the spatial variability of ecological sites by quantifying the temporal response of land surface spectral properties. This temporal response provides a spectral ‘fingerprint’ of the soil-vegetation-climate relationship which is central to the concept of ecological sites. Consequently, the main objective of this study was to predict the spatial distribution of ecological sites in a semi-arid rangeland using a 28-year time series of normalized difference vegetation index from Landsat TM 5 data and modeled using support vector machine classification. Results from this study show that support vector machine classification using hyper-temporal remote sensing imagery was effective in modeling ecological site classes, with a 62% correct classification. These results were compared to Gridded Soil Survey Geographic database and expert delineated maps of ecological sites which had a 51 and 89% correct classification, respectively. An analysis of the effects of ecological state on ecological site misclassifications revealed that sites in degraded states (e.g., shrub-dominated/shrubland and bare/annuals) had a higher rate of misclassification due to their close spectral similarity with other ecological sites. This study identified three important factors that need to be addressed to improve future model predictions: 1) sampling designs need to fully represent the range of both within class (i.e., states) and between class (i.e., ecological sites) spectral variability through time, 2) field sampling protocols that accurately characterize key soil properties (e.g., texture, depth) need to be adopted, and 3) additional environmental covariates (e.g. terrain attributes) need to be evaluated that may help further differentiate sites with similar spectral signals. Finally, the proposed hyper-temporal remote sensing framework may provide a standardized approach to evaluate and test our ecological site concepts through examining differences in vegetation dynamics in response to climatic variability and other drivers of land-use change. Results from this study demonstrate the efficacy of the hyper-temporal remote sensing approach for high resolution mapping of ecological sites, and highlights its utility in terms of reduced cost and time investment relative to traditional manual mapping approaches. PMID:28414731

A hyper-temporal remote sensing protocol for high-resolution mapping of ecological sites.

PubMed

Maynard, Jonathan J; Karl, Jason W

2017-01-01

Ecological site classification has emerged as a highly effective land management framework, but its utility at a regional scale has been limited due to the spatial ambiguity of ecological site locations in the U.S. or the absence of ecological site maps in other regions of the world. In response to these shortcomings, this study evaluated the use of hyper-temporal remote sensing (i.e., hundreds of images) for high spatial resolution mapping of ecological sites. We posit that hyper-temporal remote sensing can provide novel insights into the spatial variability of ecological sites by quantifying the temporal response of land surface spectral properties. This temporal response provides a spectral 'fingerprint' of the soil-vegetation-climate relationship which is central to the concept of ecological sites. Consequently, the main objective of this study was to predict the spatial distribution of ecological sites in a semi-arid rangeland using a 28-year time series of normalized difference vegetation index from Landsat TM 5 data and modeled using support vector machine classification. Results from this study show that support vector machine classification using hyper-temporal remote sensing imagery was effective in modeling ecological site classes, with a 62% correct classification. These results were compared to Gridded Soil Survey Geographic database and expert delineated maps of ecological sites which had a 51 and 89% correct classification, respectively. An analysis of the effects of ecological state on ecological site misclassifications revealed that sites in degraded states (e.g., shrub-dominated/shrubland and bare/annuals) had a higher rate of misclassification due to their close spectral similarity with other ecological sites. This study identified three important factors that need to be addressed to improve future model predictions: 1) sampling designs need to fully represent the range of both within class (i.e., states) and between class (i.e., ecological sites) spectral variability through time, 2) field sampling protocols that accurately characterize key soil properties (e.g., texture, depth) need to be adopted, and 3) additional environmental covariates (e.g. terrain attributes) need to be evaluated that may help further differentiate sites with similar spectral signals. Finally, the proposed hyper-temporal remote sensing framework may provide a standardized approach to evaluate and test our ecological site concepts through examining differences in vegetation dynamics in response to climatic variability and other drivers of land-use change. Results from this study demonstrate the efficacy of the hyper-temporal remote sensing approach for high resolution mapping of ecological sites, and highlights its utility in terms of reduced cost and time investment relative to traditional manual mapping approaches.

Drivers of drift sand dynamics; a reconstruction for the Wekeromse Zand, the Netherlands

NASA Astrophysics Data System (ADS)

Hendriks, Chantal; Sonneveld, Marthijn; Wallinga, Jakob

2013-04-01

Inland active drift sand landscapes are regarded as unique ecosystems of great historical and geomorphological value. Recent studies have highlighted the role of multiple factors in the initiation and stabilization of drift sand landscapes. To unravel the importance of different forcings (e.g. agricultural practices, climate) and their interplay, insight in the chronology of drift sand dynamics is essential. In this study, we aimed to reconstruct the dynamics of the drift sand landscape of the Wekeromse Zand (central Netherlands) and to develop a conceptual model to understand the processes involved. The Wekeromse Zand study area (370 ha) is located on the border of a central push moraine and is characterised by open active drift sands (14 ha) and vegetated hills and valleys. The surroundings are dominated by modern agricultural practices, and remnants from ancient iron age Celtic Field systems showing that the area has been in agricultural use since at least the Iron Age. For the study area we: i) analysed historical maps going back to the early 19th century, ii) performed a field survey to map the palaeolandscape (before drift sand activation) and iii) employed optically stimulated luminescence (OSL) dating of drift sand deposits on 11 samples from two locations to determine the timing of drift sand deposition. Analysis of the available topographic maps showed no substantial aeolean activity of the area outside its morphological boundaries. OSL dating revealed that two drift sand layers were deposited between 1373 and 1462 AD and between 1680 and 1780 AD. A layer with a higher organic matter content was found at one of the sites. This suggests that the Wekeromse Zand has known three relatively stable periods: i) a period between the start of the Holocene to the Late Medieval Period, ii) in between the Medieval climatic optimum and the climatic Maunder minimum, and iii) current situation. Despite the fact that agricultural activities occurred in this area from the Iron Age onwards, drift sand activity only started in the mid- to late 14th century. The two active phases appear to correspond with active phases in the coastal dune systems and are probably the combined result of anthropogenic land use and climatic changes.

Geological and technological assessment of artificial reef sites, Louisiana outer continental shelf

USGS Publications Warehouse

Pope, D.L.; Moslow, T.F.; Wagner, J.B.

1993-01-01

This paper describes the general procedures used to select sites for obsolete oil and gas platforms as artificial reefs on the Louisiana outer continental shelf (OCS). The methods employed incorporate six basic steps designed to resolve multiple-use conflicts that might otherwise arise with daily industry and commercial fishery operations, and to identify and assess both geological and technological constraints that could affect placement of the structures. These steps include: (1) exclusion mapping; (2) establishment of artificial reef planning areas; (3) database compilation; (4) assessment and interpretation of database; (5) mapping of geological and man-made features within each proposed reef site; and (6) site selection. Nautical charts, bathymetric maps, and offshore oil and gas maps were used for exclusion mapping, and to select nine regional planning areas. Pipeline maps were acquired from federal agencies and private industry to determine their general locations within each planning area, and to establish exclusion fairways along each pipeline route. Approximately 1600 line kilometers of high-resolution geophysical data collected by federal agencies and private industry was acquired for the nine planning areas. These data were interpreted to determine the nature and extent of near-surface geologic features that could affect placement of the structures. Seismic reflection patterns were also characterized to evaluate near-bottom sedimentation processes in the vicinity of each reef site. Geotechnical borings were used to determine the lithological and physical properties of the sediment, and for correlation with the geophysical data. Since 1987, five sites containing 10 obsolete production platforms have been selected on the Louisiana OCS using these procedures. Industry participants have realized a total savings of approximately US $1 500 000 in salvaging costs by converting these structures into artificial reefs. ?? 1993.

13. "CIVIL, SITE PLAN AND VICINITY MAP, AREA LOCATIONS." Test ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

13. "CIVIL, SITE PLAN AND VICINITY MAP, AREA LOCATIONS." Test Area 1-125. Specifications No. ENG (NASA)-04-35363-1; Drawing No. 60-09-34; sheet 11. Ref. No. C-l. D.O. SERIES 1597/1. Approved for siting on 24 April 1962. - Edwards Air Force Base, Air Force Rocket Propulsion Laboratory, Leuhman Ridge near Highways 58 & 395, Boron, Kern County, CA

Reconnaissance surficial geologic map of the Taylor Mountains quadrangle, southwestern Alaska

USGS Publications Warehouse

Wilson, Frederic H.

2015-09-28

I used the Platt and Muller 1950s-era aerial photographic interpretation map as the starting point for the surficial geology; their unpublished data were produced using a reconnaissance quality topographic base map. In addition to transferring their data to a modern base to use as a guide, all of the photographs were re-examined. As result, in a number of areas, the features have been reinterpreted and the linework revised. A major difference between the maps is the recognition of much more extensive glacially dammed lake deposits and reassignment of some glacial deposits to different glacial events.

Scanner qualification with IntenCD based reticle error correction

NASA Astrophysics Data System (ADS)

Elblinger, Yair; Finders, Jo; Demarteau, Marcel; Wismans, Onno; Minnaert Janssen, Ingrid; Duray, Frank; Ben Yishai, Michael; Mangan, Shmoolik; Cohen, Yaron; Parizat, Ziv; Attal, Shay; Polonsky, Netanel; Englard, Ilan

2010-03-01

Scanner introduction into the fab production environment is a challenging task. An efficient evaluation of scanner performance matrices during factory acceptance test (FAT) and later on during site acceptance test (SAT) is crucial for minimizing the cycle time for pre and post production-start activities. If done effectively, the matrices of base line performance established during the SAT are used as a reference for scanner performance and fleet matching monitoring and maintenance in the fab environment. Key elements which can influence the cycle time of the SAT, FAT and maintenance cycles are the imaging, process and mask characterizations involved with those cycles. Discrete mask measurement techniques are currently in use to create across-mask CDU maps. By subtracting these maps from their final wafer measurement CDU map counterparts, it is possible to assess the real scanner induced printed errors within certain limitations. The current discrete measurement methods are time consuming and some techniques also overlook mask based effects other than line width variations, such as transmission and phase variations, all of which influence the final printed CD variability. Applied Materials Aera2TM mask inspection tool with IntenCDTM technology can scan the mask at high speed, offer full mask coverage and accurate assessment of all masks induced source of errors simultaneously, making it beneficial for scanner qualifications and performance monitoring. In this paper we report on a study that was done to improve a scanner introduction and qualification process using the IntenCD application to map the mask induced CD non uniformity. We will present the results of six scanners in production and discuss the benefits of the new method.

Effects of Nickel Treatment on H3K4 Trimethylation and Gene Expression

PubMed Central

Tchou-Wong, Kam-Meng; Kluz, Thomas; Arita, Adriana; Smith, Phillip R.; Brown, Stuart; Costa, Max

2011-01-01

Occupational exposure to nickel compounds has been associated with lung and nasal cancers. We have previously shown that exposure of the human lung adenocarcinoma A549 cells to NiCl2 for 24 hr significantly increased global levels of trimethylated H3K4 (H3K4me3), a transcriptional activating mark that maps to the promoters of transcribed genes. To further understand the potential epigenetic mechanism(s) underlying nickel carcinogenesis, we performed genome-wide mapping of H3K4me3 by chromatin immunoprecipitation and direct genome sequencing (ChIP-seq) and correlated with transcriptome genome-wide mapping of RNA transcripts by massive parallel sequencing of cDNA (RNA-seq). The effect of NiCl2 treatment on H3K4me3 peaks within 5,000 bp of transcription start sites (TSSs) on a set of genes highly induced by nickel in both A549 cells and human peripheral blood mononuclear cells were analyzed. Nickel exposure increased the level of H3K4 trimethylation in both the promoters and coding regions of several genes including CA9 and NDRG1 that were increased in expression in A549 cells. We have also compared the extent of the H3K4 trimethylation in the absence and presence of formaldehyde crosslinking and observed that crosslinking of chromatin was required to observe H3K4 trimethylation in the coding regions immediately downstream of TSSs of some nickel-induced genes including ADM and IGFBP3. This is the first genome-wide mapping of trimethylated H3K4 in the promoter and coding regions of genes induced after exposure to NiCl2. This study may provide insights into the epigenetic mechanism(s) underlying the carcinogenicity of nickel compounds. PMID:21455298

Eulusmap: An international land resources map utilizing satellite imagery

NASA Technical Reports Server (NTRS)

Paludan, T.; Csati, E.

1978-01-01

In 1972, the International Geographical Union's Commission on World Land Use Survey adopted a project for a land-use map of Europe. Such a map, under the name Eulusmap was started earlier under sponsorship of several government offices in Hungary. Although there was great response from a number of contributors in many countries, it became evident by mid-1974 that the map would contain gaps and some inaccuracies unless additional data sources were utilized. By then, the satellite Landsat-1 had obtained imagery of most of Europe. Using theme extraction techniques, the map was completed in draft form and portions of it displayed at the 23d International Geographical Congress in Moscow during July 1976. Printing of the completed map was accomplished in May 1978.

Techniques, problems and uses of mega-geomorphological mapping

NASA Technical Reports Server (NTRS)

Embleton, C.

1985-01-01

A plea for a program of global geomorphological mapping based on remote sensing data is presented. It is argued that the program is a necessary step in bringing together the rapidly evolving concepts of plate tectonics with the science of geomorphology. Geomorphologists are urged to bring temporal scales into their subject and to abandon their recent isolation from tectonics and geological history. It is suggested that a start be made with a new geomorphological map of Europe, utilizing the latest space technology.

How to Start, Build and Sustain a Multi-Credit Integrated Curriculum Package

ERIC Educational Resources Information Center

Wilson, Andrew Kerr

2011-01-01

Over the last 17 years, the author has been asked many times for help starting Integrated Curriculum Programs (ICPs). Visiting teachers are instantly engaged and enthused by the possibilities they see in his program. In this article, he provides a step-by-step road map to a full ICP continuum. By distilling the lessons of almost 20 years of…

Washington State Even Start 1993-1994: Final Evaluation. A Report to the Office of Adult Literacy.

ERIC Educational Resources Information Center

Iglitzin, Lynne; Wandschneider, Mary

All 18 Washington State Even Start sites participated in the program's evaluation. Site coordinators administered the assessment and evaluation measures to the adults served by the program and to teachers working with children at both entry and exit from the program. An indepth study was conducted of 134 families for whom there were complete sets…

Considerations for applying digital soil mapping to ecological sites

USDA-ARS?s Scientific Manuscript database

Recent advancements in the spatial prediction of soil properties are not currently being fully utilized for ecological studies. Linking digital soil mapping (DSM) with ecological sites (ES) has the potential to better land management decisions by improving spatial resolution and precision as well as...

WE-AB-209-10: Optimizing the Delivery of Sequential Fluence Maps for Efficient VMAT Delivery

DOE Office of Scientific and Technical Information (OSTI.GOV)

Craft, D; Balvert, M

2016-06-15

Purpose: To develop an optimization model and solution approach for computing MLC leaf trajectories and dose rates for high quality matching of a set of optimized fluence maps to be delivered sequentially around a patient in a VMAT treatment. Methods: We formulate the fluence map matching problem as a nonlinear optimization problem where time is discretized but dose rates and leaf positions are continuous variables. For a given allotted time, which is allocated across the fluence maps based on the complexity of each fluence map, the optimization problem searches for the best leaf trajectories and dose rates such that themore » original fluence maps are closely recreated. Constraints include maximum leaf speed, maximum dose rate, and leaf collision avoidance, as well as the constraint that the ending leaf positions for one map are the starting leaf positions for the next map. The resulting model is non-convex but smooth, and therefore we solve it by local searches from a variety of starting positions. We improve solution time by a custom decomposition approach which allows us to decouple the rows of the fluence maps and solve each leaf pair individually. This decomposition also makes the problem easily parallelized. Results: We demonstrate method on a prostate case and a head-and-neck case and show that one can recreate fluence maps to high degree of fidelity in modest total delivery time (minutes). Conclusion: We present a VMAT sequencing method that reproduces optimal fluence maps by searching over a vast number of possible leaf trajectories. By varying the total allotted time given, this approach is the first of its kind to allow users to produce VMAT solutions that span the range of wide-field coarse VMAT deliveries to narrow-field high-MU sliding window-like approaches.« less

Promoter analysis of the membrane protein gp64 gene of the cellular slime mold Polysphondylium pallidum.

PubMed

Takaoka, N; Fukuzawa, M; Saito, T; Sakaitani, T; Ochiai, H

1999-10-28

We cloned a genomic fragment of the membrane protein gp64 gene of the cellular slime mold Polysphondylium pallidum by inverse PCR. Primer extension analysis identified a major transcription start site 65 bp upstream of the translation start codon. The promoter region of the gp64 gene contains sequences homologous to a TATA box at position -47 to -37 and to an initiator (Inr, PyPyCAPyPyPyPy) at position -3 to +5 from the transcription start site. Successively truncated segments of the promoter were tested for their ability to drive expression of the beta-galactosidase reporter gene in transformed cells; also the difference in activity between growth conditions was compared. The results indicated that there are two positive vegetative regulatory elements extending between -187 and -62 bp from the transcription start site of the gp64 promoter; also their activity was two to three times higher in the cells grown with bacteria in shaken suspension than in the cells grown in an axenic medium.

The archives of the glacier survey of the Austrian Alpine Club

NASA Astrophysics Data System (ADS)

Fischer, Andrea; Bendler, Gebhard

2016-04-01

The archive of the Austrian Alpine Club holds masses of material on glaciers and their former extent. The material includes descriptions and sketches of the summits conquered by early mountaineers, mapping campaigns and data from early scientific expeditions as well as data on glacier length change. To date a large proportion of the glaciological information in the material has not been catalogued or analysed. As cold ice, containing relevant climate information, might still exist at the highest peaks of Austria, a pilot project was started to collect some of the data of two test sites in Tyrol, in Silvretta and Ötztal Alps, to reveal former summit shapes and glacier tongue positions. Additional information on the number and position of crevasses as well as firn extent is often evident from the material. Challenging tasks not yet tackled are compiling a catalogue of the material and defining an analysis scheme.

High-energy anomalies in covalent high-Tc cuprates with large Hubbard Ud on copper

NASA Astrophysics Data System (ADS)

Barišić, O. S.; Barišić, S.

2015-03-01

A large Ud theory is constructed for the metallic state of high-Tc cuprates. The Emery three-band model, extended with Ox-Oy hopping tpp, and with Ud → ∞, is mapped on slave fermions. The Dyson time-dependent diagrammatic theory in terms of the Cu-O hopping tpd, starting from the nondegenerate unperturbed ground state, is translationally and asymptotically locally gauge invariant. The small parameter of the theory is the average hole occupation of Cu sites nd. The lowest order of the theory generates the single particle propagators of the hybridized pdp- and dpd-fermions with the exact covalent three band structure. The leading many-body effect is band narrowing, accompanied by Landau-like damping of the single particle propagation, due to incoherent local charge Cu-O fluctuations. The corresponding continuum is found below and above the Fermi level.

Human Promoters Are Intrinsically Directional

PubMed Central

Duttke, Sascha H.C.; Lacadie, Scott A.; Ibrahim, Mahmoud M.; Glass, Christopher K.; Corcoran, David L.; Benner, Christopher; Heinz, Sven; Kadonaga, James T.; Ohler, Uwe

2015-01-01

Divergent transcription, in which reverse-oriented transcripts occur upstream of eukaryotic promoters in regions devoid of annotated genes, has been suggested to be a general property of active promoters. Here we show that the human basal RNA polymerase II transcriptional machinery and core promoter are inherently unidirectional, and that reverse-oriented transcripts originate from their own cognate reverse-directed core promoters. In vitro transcription analysis and mapping of nascent transcripts in cells revealed that sequences at reverse start sites are similar to those of their forward counterparts. The use of DNase I accessibility to define proximal promoter borders revealed that up to half of promoters are unidirectional and that unidirectional promoters are depleted at their upstream edges of reverse core promoter sequences and their associated chromatin features. Divergent transcription is thus not an inherent property of the transcription process, but rather the consequence of the presence of both forward- and reverse-directed core promoters. PMID:25639469

Improving a Synechocystis-based photoautotrophic chassis through systematic genome mapping and validation of neutral sites

PubMed Central

Pinto, Filipe; Pacheco, Catarina C.; Oliveira, Paulo; Montagud, Arnau; Landels, Andrew; Couto, Narciso; Wright, Phillip C.; Urchueguía, Javier F.; Tamagnini, Paula

2015-01-01

The use of microorganisms as cell factories frequently requires extensive molecular manipulation. Therefore, the identification of genomic neutral sites for the stable integration of ectopic DNA is required to ensure a successful outcome. Here we describe the genome mapping and validation of five neutral sites in the chromosome of Synechocystis sp. PCC 6803, foreseeing the use of this cyanobacterium as a photoautotrophic chassis. To evaluate the neutrality of these loci, insertion/deletion mutants were produced, and to assess their functionality, a synthetic green fluorescent reporter module was introduced. The constructed integrative vectors include a BioBrick-compatible multiple cloning site insulated by transcription terminators, constituting robust cloning interfaces for synthetic biology approaches. Moreover, Synechocystis mutants (chassis) ready to receive purpose-built synthetic modules/circuits are also available. This work presents a systematic approach to map and validate chromosomal neutral sites in cyanobacteria, and that can be extended to other organisms. PMID:26490728

Mapping of Arithmetic Processing by Navigated Repetitive Transcranial Magnetic Stimulation in Patients with Parietal Brain Tumors and Correlation with Postoperative Outcome.

PubMed

Ille, Sebastian; Drummer, Katharina; Giglhuber, Katrin; Conway, Neal; Maurer, Stefanie; Meyer, Bernhard; Krieg, Sandro M

2018-06-01

Preserving functionality is important during neurosurgical resection of brain tumors. Specialized centers also map further brain functions apart from motor and language functions, such as arithmetic processing (AP). The mapping of AP by navigated repetitive transcranial magnetic stimulation (nrTMS) in healthy volunteers has been reported. The present study aimed to correlate the results of mapping AP with functional patient outcomes. We included 26 patients with parietal brain tumors. Because of preoperative impairment of AP, mapping was not possible in 8 patients (31%). We stimulated 52 cortical sites by nrTMS while patients performed a calculation task. Preoperatively and postoperatively, patients underwent a standardized number-processing and calculation test (NPCT). Tumor resection was blinded to nrTMS results, and the change in NPCT performance was correlated to resected AP-positive spots as identified by nrTMS. The resection of AP-positive sites correlated with a worsening of the postoperative NPCT result in 12 cases. In 3 cases, no AP-positive sites were resected and the postoperative NPCT result was similar to or better than preoperatively. Also, in 3 cases, the postoperative NPCT result was better than preoperatively, although AP-positive sites were resected. Despite presenting only a few cases, nrTMS might be a useful tool for preoperative mapping of AP. However, the reliability of the present results has to be evaluated in a larger series and by intraoperative mapping data. Copyright © 2018 Elsevier Inc. All rights reserved.

Annualized earthquake loss estimates for California and their sensitivity to site amplification

USGS Publications Warehouse

Chen, Rui; Jaiswal, Kishor; Bausch, D; Seligson, H; Wills, C.J.

2016-01-01

Input datasets for annualized earthquake loss (AEL) estimation for California were updated recently by the scientific community, and include the National Seismic Hazard Model (NSHM), site‐response model, and estimates of shear‐wave velocity. Additionally, the Federal Emergency Management Agency’s loss estimation tool, Hazus, was updated to include the most recent census and economic exposure data. These enhancements necessitated a revisit to our previous AEL estimates and a study of the sensitivity of AEL estimates subjected to alternate inputs for site amplification. The NSHM ground motions for a uniform site condition are modified to account for the effect of local near‐surface geology. The site conditions are approximated in three ways: (1) by VS30 (time‐averaged shear‐wave velocity in the upper 30 m) value obtained from a geology‐ and topography‐based map consisting of 15 VS30 groups, (2) by site classes categorized according to National Earthquake Hazards Reduction Program (NEHRP) site classification, and (3) by a uniform NEHRP site class D. In case 1, ground motions are amplified using the Seyhan and Stewart (2014) semiempirical nonlinear amplification model. In cases 2 and 3, ground motions are amplified using the 2014 version of the NEHRP site amplification factors, which are also based on the Seyhan and Stewart model but are approximated to facilitate their use for building code applications. Estimated AELs are presented at multiple resolutions, starting with the state level assessment and followed by detailed assessments for counties, metropolitan statistical areas (MSAs), and cities. AEL estimate at the state level is ∼$3.7  billion, 70% of which is contributed from Los Angeles–Long Beach–Santa Ana, San Francisco–Oakland–Fremont, and Riverside–San Bernardino–Ontario MSAs. The statewide AEL estimate is insensitive to alternate assumptions of site amplification. However, we note significant differences in AEL estimates among the three sensitivity cases for smaller geographic units.

Testing maternal depression and attachment style as moderators of Early Head Start's effects on parenting.

PubMed

Berlin, Lisa J; Whiteside-Mansell, Leanne; Roggman, Lori A; Green, Beth L; Robinson, JoAnn; Spieker, Susan

2011-01-01

This study examined maternal depression, attachment avoidance, and attachment anxiety as moderators of Early Head Start's effects on four parenting outcomes assessed at age three. Participants (N = 947) were drawn from six sites of the Early Head Start National Research and Evaluation Project, a multi-site randomized trial. Findings suggest more positive program effects for mothers with less initial attachment avoidance or attachment anxiety. First, baseline attachment avoidance moderated Early Head Start program effects on observed maternal supportiveness, such that program mothers with lower baseline attachment avoidance were rated as more supportive of their three-year-olds than program mothers with higher baseline attachment avoidance. Second, program effects on spanking varied depending on mothers' baseline attachment anxiety.

Differential transcriptional control of the two tRNA(fMet) genes of Escherichia coli K-12.

PubMed

Nagase, T; Ishii, S; Imamoto, F

1988-07-15

The metZ gene of Escherichia coli, which encodes the tRNA(f1Met), was cloned. Using the nucleotide sequence, in vitro transcription, and S1 nuclease mapping analyses, we identified the promoter region, transcriptional start point, the two tandem tRNA(f1Met) structural genes separated by an intergenic space of 33 bp, and the two Rho-independent transcriptional termination sites, in that order. We compared the promoter region of the metZ gene with that of the metY gene, which encodes the tRNA(f2Met) and is located in the promoter-proximal portion of the nusA operon. A G + C-rich sequence (5'-GCGCATCCAC-3'), similar to the corresponding sequence of the rrn promoters that are under stringent control, was found between the Pribnow box and the transcriptional start point of the metZ promoter, but not in the metY promoter region. We therefore examined the effect of guanosine 3'-diphosphate, 5'-diphosphate (ppGpp), the chemical mediator of stringent control, and found that ppGpp inhibited the transcription of the metZ gene, but not that of the metY gene. These data suggested that the promoters for metZ and metY have different physiological functions and are regulated by different mechanisms.

Genome-Wide DNA Methylation Analysis of Human Pancreatic Islets from Type 2 Diabetic and Non-Diabetic Donors Identifies Candidate Genes That Influence Insulin Secretion

PubMed Central

Dayeh, Tasnim; Volkov, Petr; Salö, Sofia; Hall, Elin; Nilsson, Emma; Olsson, Anders H.; Kirkpatrick, Clare L.; Wollheim, Claes B.; Eliasson, Lena; Rönn, Tina; Bacos, Karl; Ling, Charlotte

2014-01-01

Impaired insulin secretion is a hallmark of type 2 diabetes (T2D). Epigenetics may affect disease susceptibility. To describe the human methylome in pancreatic islets and determine the epigenetic basis of T2D, we analyzed DNA methylation of 479,927 CpG sites and the transcriptome in pancreatic islets from T2D and non-diabetic donors. We provide a detailed map of the global DNA methylation pattern in human islets, β- and α-cells. Genomic regions close to the transcription start site showed low degrees of methylation and regions further away from the transcription start site such as the gene body, 3′UTR and intergenic regions showed a higher degree of methylation. While CpG islands were hypomethylated, the surrounding 2 kb shores showed an intermediate degree of methylation, whereas regions further away (shelves and open sea) were hypermethylated in human islets, β- and α-cells. We identified 1,649 CpG sites and 853 genes, including TCF7L2, FTO and KCNQ1, with differential DNA methylation in T2D islets after correction for multiple testing. The majority of the differentially methylated CpG sites had an intermediate degree of methylation and were underrepresented in CpG islands (∼7%) and overrepresented in the open sea (∼60%). 102 of the differentially methylated genes, including CDKN1A, PDE7B, SEPT9 and EXOC3L2, were differentially expressed in T2D islets. Methylation of CDKN1A and PDE7B promoters in vitro suppressed their transcriptional activity. Functional analyses demonstrated that identified candidate genes affect pancreatic β- and α-cells as Exoc3l silencing reduced exocytosis and overexpression of Cdkn1a, Pde7b and Sept9 perturbed insulin and glucagon secretion in clonal β- and α-cells, respectively. Together, our data can serve as a reference methylome in human islets. We provide new target genes with altered DNA methylation and expression in human T2D islets that contribute to perturbed insulin and glucagon secretion. These results highlight the importance of epigenetics in the pathogenesis of T2D. PMID:24603685

Probing the dynamic nature of water molecules and their influences on ligand binding in a model binding site.

PubMed

Cappel, Daniel; Wahlström, Rickard; Brenk, Ruth; Sotriffer, Christoph A

2011-10-24

The model binding site of the cytochrome c peroxidase (CCP) W191G mutant is used to investigate the structural and dynamic properties of the water network at the buried cavity using computational methods supported by crystallographic analysis. In particular, the differences of the hydration pattern between the uncomplexed state and various complexed forms are analyzed as well as the differences between five complexes of CCP W191G with structurally closely related ligands. The ability of docking programs to correctly handle the water molecules in these systems is studied in detail. It is found that fully automated prediction of water replacement or retention upon docking works well if some additional preselection is carried out but not necessarily if the entire water network in the cavity is used as input. On the other hand, molecular interaction fields for water calculated from static crystal structures and hydration density maps obtained from molecular dynamics simulations agree very well with crystallographically observed water positions. For one complex, the docking and MD results sensitively depend on the quality of the starting structure, and agreement is obtained only after redetermination of the crystal structure and refinement at higher resolution.

Geology of the U12n. 02 (Midi Mist) drift, and postshot observations, Rainier Mesa, Area 12, Nevada Test Site

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ege, J R; Danilchik, W; Feazel, C T

1980-05-01

Mining of the Ul2n.02 drift for the Midi Mist event started on December 31, 1965, in Rainier Mesa, Nevada Test Site, and was completed on December 30, 1966. The drift was mined along a bearing of S. 65/sup 0/ W. at an altitude of 1,850.2 m (6,070.2 ft) to a length of 643 m (2,109 ft). The drift lies in tunnel bed 4 and penetrates stratigraphically up the section through sub-units 4AB, 4CD, 4E, 4F, 4G, 4H, and 4J, all of Tertiary age. Two faults mapped at the surface of the mesa were identified as having cut the complex atmore » drift level. No engineering construction or support problems greater than minor rock slabbing, ravelly ground, or water inflow along fractures were uncountered. Visual inspection showed that shot-induced effects in the rock medium at drift level extended for 237.7 m (780 ft) from the working point in the form of fractures and small shear displacements along bedding planes.« less

Current Status of the Nuclear Waste Management Programme in Finland - 13441

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lehto, Kimmo; Vuorio, Petteri

2013-07-01

Pursuant to the Decision-in-Principle of 2001 the Finnish programme for geologic disposal of spent fuel has now moved to the phase of applying for construction licence to build up the encapsulation plant and underground repository. The main objective of former programme phase, underground characterisation phase, was to confirm - or refute - the suitability of the Olkiluoto site by investigations conducted underground at the actual depth of the repository. The construction work of the access tunnel to the rock characterisation facility (ONKALO) started in the late summer of 2004. The site research and investigations work aimed at the maturity neededmore » for submission of the application for construction license of the actual repository in end of 2012. This requires, however, that also the technology has reached the maturity needed. The design and technical plans form the necessary platform for the development of the safety case for spent fuel disposal. A plan, 'road map', has been produced for the portfolio of reports that demonstrates the safety of disposal as required by the criteria set by the government and further detailed by the safety authority, STUK. (authors)« less

CPC - Monitoring & Data: Regional Climate Maps

Science.gov Websites

Weather Service NWS logo - Click to go to the NWS home page Climate Prediction Center Site Map News Information CPC Web Team HOME > Monitoring and Data > Global Climate Data & Maps > Global Regional Climate Maps Regional Climate Maps Banner The Monthly regional analyses products are usually

Integrating Radar Image Data with Google Maps

NASA Technical Reports Server (NTRS)

Chapman, Bruce D.; Gibas, Sarah

2010-01-01

A public Web site has been developed as a method for displaying the multitude of radar imagery collected by NASA s Airborne Synthetic Aperture Radar (AIRSAR) instrument during its 16-year mission. Utilizing NASA s internal AIRSAR site, the new Web site features more sophisticated visualization tools that enable the general public to have access to these images. The site was originally maintained at NASA on six computers: one that held the Oracle database, two that took care of the software for the interactive map, and three that were for the Web site itself. Several tasks were involved in moving this complicated setup to just one computer. First, the AIRSAR database was migrated from Oracle to MySQL. Then the back-end of the AIRSAR Web site was updated in order to access the MySQL database. To do this, a few of the scripts needed to be modified; specifically three Perl scripts that query that database. The database connections were then updated from Oracle to MySQL, numerous syntax errors were corrected, and a query was implemented that replaced one of the stored Oracle procedures. Lastly, the interactive map was designed, implemented, and tested so that users could easily browse and access the radar imagery through the Google Maps interface.

Electrocorticographic high gamma activity versus electrical cortical stimulation mapping of naming.

PubMed

Sinai, Alon; Bowers, Christopher W; Crainiceanu, Ciprian M; Boatman, Dana; Gordon, Barry; Lesser, Ronald P; Lenz, Frederick A; Crone, Nathan E

2005-07-01

Subdural electrocorticographic (ECoG) recordings in patients undergoing epilepsy surgery have shown that functional activation is associated with event-related broadband gamma activity in a higher frequency range (>70 Hz) than previously studied in human scalp EEG. To investigate the utility of this high gamma activity (HGA) for mapping language cortex, we compared its neuroanatomical distribution with functional maps derived from electrical cortical stimulation (ECS), which remains the gold standard for predicting functional impairment after surgery for epilepsy, tumours or vascular malformations. Thirteen patients had undergone subdural electrode implantation for the surgical management of intractable epilepsy. Subdural ECoG signals were recorded while each patient verbally named sequentially presented line drawings of objects, and estimates of event-related HGA (80-100 Hz) were made at each recording site. Routine clinical ECS mapping used a subset of the same naming stimuli at each cortical site. If ECS disrupted mouth-related motor function, i.e. if it affected the mouth, lips or tongue, naming could not be tested with ECS at the same cortical site. Because naming during ECoG involved these muscles of articulation, the sensitivity and specificity of ECoG HGA were estimated relative to both ECS-induced impairments of naming and ECS disruption of mouth-related motor function. When these estimates were made separately for 12 electrode sites per patient (the average number with significant HGA), the specificity of ECoG HGA with respect to ECS was 78% for naming and 81% for mouth-related motor function, and equivalent sensitivities were 38% and 46%, respectively. When ECS maps of naming and mouth-related motor function were combined, the specificity and sensitivity of ECoG HGA with respect to ECS were 84% and 43%, respectively. This study indicates that event-related ECoG HGA during confrontation naming predicts ECS interference with naming and mouth-related motor function with good specificity but relatively low sensitivity. Its favourable specificity suggests that ECoG HGA can be used to construct a preliminary functional map that may help identify cortical sites of lower priority for ECS mapping. Passive recordings of ECoG gamma activity may be done simultaneously at all electrode sites without the risk of after-discharges associated with ECS mapping, which must be done sequentially at pairs of electrodes. We discuss the relative merits of these two functional mapping techniques.

Identifying Interactions that Determine Fragment Binding at Protein Hotspots.

PubMed

Radoux, Chris J; Olsson, Tjelvar S G; Pitt, Will R; Groom, Colin R; Blundell, Tom L

2016-05-12

Locating a ligand-binding site is an important first step in structure-guided drug discovery, but current methods do little to suggest which interactions within a pocket are the most important for binding. Here we illustrate a method that samples atomic hotspots with simple molecular probes to produce fragment hotspot maps. These maps specifically highlight fragment-binding sites and their corresponding pharmacophores. For ligand-bound structures, they provide an intuitive visual guide within the binding site, directing medicinal chemists where to grow the molecule and alerting them to suboptimal interactions within the original hit. The fragment hotspot map calculation is validated using experimental binding positions of 21 fragments and subsequent lead molecules. The ligands are found in high scoring areas of the fragment hotspot maps, with fragment atoms having a median percentage rank of 97%. Protein kinase B and pantothenate synthetase are examined in detail. In each case, the fragment hotspot maps are able to rationalize a Free-Wilson analysis of SAR data from a fragment-based drug design project.

Increased /sup 3/H-spiperone binding sites in mesolimbic area related to methamphetamine-induced behavioral hypersensitivity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Akiyama, K.; Sato, M.; Otsuki, S.

1982-02-01

The specific /sup 3/H-spiperone binding to membrane homogenates of the striatum, mesolimbic area, and frontal cortex was examined in two groups of rats pretreated once daily with saline or 4 mg/kg of methamphetamine (MAP) for 14 days. At 7 days following cessation of chronic pretreatment, all rats received an injection of 4 mg/kg of MAP and were decapitated 1 hr after the injection. In the chronic saline-pretreatment group, the single administration of MAP induced significant changes in the number (Bmax) of specific /sup 3/H-spiperone binding sites (a decrease in the striatum and an increase in the mesolimbic area and frontalmore » cortex), but no significant changes in the affinity (KD) in any brain area. The chronic MAP pretreatment markedly augmented the changes in Bmax in the striatum and mesolimbic area. The increase in specific /sup 3/H-spiperone binding sites in the mesolimbic area is discussed in relation to MAP-induced behavioral hypersensitivity.« less

Preliminary Geologic Map of the Laredo, Crystal City-Eagle Pass, San Antonio, and Del Rio 1 x 2 Quadrangles, Texas, and the Nuevo Laredo, Ciudad Acuna, Piedras Negras, and Nueva Rosita 1 x 2 Quadrangles, Mexico

USGS Publications Warehouse

Page, William R.; Berry, Margaret E.; VanSistine, D. Paco; Snyders, Scott R.

2009-01-01

The purpose of this map is to provide an integrated, bi-national geologic map dataset for display and analyses on an Arc Internet Map Service (IMS) dedicated to environmental health studies in the United States-Mexico border region. The IMS web site was designed by the US-Mexico Border Environmental Health Initiative project and collaborators, and the IMS and project web site address is http://borderhealth.cr.usgs.gov/. The objective of the project is to acquire, evaluate, analyze, and provide earth, biologic, and human health resources data within a GIS framework (IMS) to further our understanding of possible linkages between the physical environment and public health issues. The geologic map dataset is just one of many datasets included in the web site; other datasets include biologic, hydrologic, geographic, and human health themes.

Cruise report, RV ocean alert cruise A1-98-HW; January 30 through February 23, 1998, Honolulu to Honolulu, Hawaii

USGS Publications Warehouse

Gardner, James V.; Hughes-Clarke, John E.

1998-01-01

The major objective of cruise A1-98 was to map portions of the insular slopes of Oahu, Kauai, Maui, Molokai, and Hawaii and to survey in detail US Environmental Protection Agency (USEPA) ocean dumping sites using a Simrad EM300 high-resolution multibeam mapping system. The cruise was a jointly funded project between the US Army Corps of Engineers (USCOE), USEPA, and the US Geological Survey (USGS). The USACOE and EPA are interested in these areas because of a series of ocean dump sites off Oahu, Kauai, Maui, and Hawaii (Fig. 1) that require high-resolution base maps for site monitoring purposes. The USGS Coastal and Marine Geology Program has several on-going projects off Oahu and Maui that lack high-precision base maps for a variety of ongoing geological studies. The cruise was conducted under a Cooperative Agreement between the USGS and the Ocean Mapping Group, University of New Brunswick, Canada.

A Time, and a Place, to Gather Stones Together

ERIC Educational Resources Information Center

Biemiller, Lawrence

2009-01-01

Lenka Clayton, a British artist and documentary filmmaker, did not leave London and cross the Atlantic Ocean intending to paint tiny, precise numbers on 7,000 loose stones--that idea didn't come to her until later. By the time she began numbering, she had already started a class of freshmen at Alfred University mapping hard-to-map things (like…

Schematizing and Processing Informational Texts with Mind Maps in Fifth and Sixth Grade

ERIC Educational Resources Information Center

Merchie, Emmelien; Van Keer, Hilde

2013-01-01

From the age of 11-13, children start to spend increasingly more time on learning from texts. The need arises to support them in dealing with this text information and engaging them in self-regulated learning (SRL). This study is embedded within the cognitive component of SRL and focuses on mind mapping as a promising organizational learning…

Bladder cancer mapping in Libya based on standardized morbidity ratio and log-normal model

NASA Astrophysics Data System (ADS)

Alhdiri, Maryam Ahmed; Samat, Nor Azah; Mohamed, Zulkifley

2017-05-01

Disease mapping contains a set of statistical techniques that detail maps of rates based on estimated mortality, morbidity, and prevalence. A traditional approach to measure the relative risk of the disease is called Standardized Morbidity Ratio (SMR). It is the ratio of an observed and expected number of accounts in an area, which has the greatest uncertainty if the disease is rare or if geographical area is small. Therefore, Bayesian models or statistical smoothing based on Log-normal model are introduced which might solve SMR problem. This study estimates the relative risk for bladder cancer incidence in Libya from 2006 to 2007 based on the SMR and log-normal model, which were fitted to data using WinBUGS software. This study starts with a brief review of these models, starting with the SMR method and followed by the log-normal model, which is then applied to bladder cancer incidence in Libya. All results are compared using maps and tables. The study concludes that the log-normal model gives better relative risk estimates compared to the classical method. The log-normal model has can overcome the SMR problem when there is no observed bladder cancer in an area.

Oregon Magnetic and Gravity Maps and Data: A Web Site for Distribution of Data

USGS Publications Warehouse

Roberts, Carter W.; Kucks, Robert P.; Hill, Patricia L.

2008-01-01

This web site gives the results of a USGS project to acquire the best available, public-domain, aeromagnetic and gravity data in the United States and merge these data into uniform, composite grids for each State. The results for the State of Oregon are presented here on this site. Files of aeromagnetic and gravity grids and images are available for these States for downloading. In Oregon, 49 magnetic surveys have been knit together to form a single digital grid and map. Also, a complete Bouguer gravity anomaly grid and map was generated from 40,665 gravity station measurements in and adjacent to Oregon. In addition, a map shows the location of the aeromagnetic surveys, color-coded to the survey flight-line spacing. This project was supported by the Mineral Resource Program of the USGS.

VS30 – A site-characterization parameter for use in building Codes, simplified earthquake resistant design, GMPEs, and ShakeMaps

USGS Publications Warehouse

Borcherdt, Roger D.

2012-01-01

VS30, defined as the average seismic shear-wave velocity from the surface to a depth of 30 meters, has found wide-spread use as a parameter to characterize site response for simplified earthquake resistant design as implemented in building codes worldwide. VS30 , as initially introduced by the author for the US 1994 NEHRP Building Code, provides unambiguous definitions of site classes and site coefficients for site-dependent response spectra based on correlations derived from extensive borehole logging and comparative ground-motion measurement programs in California. Subsequent use of VS30 for development of strong ground motion prediction equations (GMPEs) and measurement of extensive sets of VS borehole data have confirmed the previous empirical correlations and established correlations of SVS30 with VSZ at other depths. These correlations provide closed form expressions to predict S30 V at a large number of additional sites and further justify S30 V as a parameter to characterize site response for simplified building codes, GMPEs, ShakeMap, and seismic hazard mapping.

Concealed Accessory Pathways with a Single Ventricular and Two Discrete Atrial Insertion Sites.

PubMed

Kipp, Ryan T; Abu Sham'a, Raed; Hiroyuki, Ito; Han, Frederick T; Refaat, Marwan; Hsu, Jonathan C; Field, Michael E; Kopp, Douglas E; Marcus, Gregory M; Scheinman, Melvin M; Hoffmayer, Kurt S

2017-03-01

Atrioventricular reciprocating tachycardia (AVRT) utilizing a concealed accessory pathway is common. It is well appreciated that some patients may have multiple accessory pathways with separate atrial and ventricular insertion sites. We present three cases of AVRT utilizing concealed pathways with evidence that each utilizing a single ventricular insertion and two discrete atrial insertion sites. In case one, two discrete atrial insertion sites were mapped in two separate procedures, and only during the second ablation was the Kent potential identified. Ablation of the Kent potential at this site remote from the two atrial insertion sites resulted in the termination of the retrograde conduction in both pathways. Case two presented with supraventricular tachycardia (SVT) with alternating eccentric atrial activation patterns without alteration in the tachycardia cycle length. The two distinct atrial insertion sites during orthodromic AVRT and ventricular pacing were targeted and each of the two atrial insertion sites were successfully mapped and ablated. In case three, retrograde decremental conduction utilizing both atrial insertion sites was identified prior to ablation. After mapping and ablation of the first discrete atrial insertion site, tachycardia persisted utilizing the second atrial insertion site. Only after ablation of the second atrial insertion site was SVT noninducible, and VA conduction was no longer present. Concealed retrograde accessory pathways with discrete atrial insertion sites may have a common ventricular insertion site. Identification and ablation of the ventricular insertion site or the separate discrete atrial insertion sites result in successful treatment. © 2017 Wiley Periodicals, Inc.

LenVarDB: database of length-variant protein domains.

PubMed

Mutt, Eshita; Mathew, Oommen K; Sowdhamini, Ramanathan

2014-01-01

Protein domains are functionally and structurally independent modules, which add to the functional variety of proteins. This array of functional diversity has been enabled by evolutionary changes, such as amino acid substitutions or insertions or deletions, occurring in these protein domains. Length variations (indels) can introduce changes at structural, functional and interaction levels. LenVarDB (freely available at http://caps.ncbs.res.in/lenvardb/) traces these length variations, starting from structure-based sequence alignments in our Protein Alignments organized as Structural Superfamilies (PASS2) database, across 731 structural classification of proteins (SCOP)-based protein domain superfamilies connected to 2 730 625 sequence homologues. Alignment of sequence homologues corresponding to a structural domain is available, starting from a structure-based sequence alignment of the superfamily. Orientation of the length-variant (indel) regions in protein domains can be visualized by mapping them on the structure and on the alignment. Knowledge about location of length variations within protein domains and their visual representation will be useful in predicting changes within structurally or functionally relevant sites, which may ultimately regulate protein function. Non-technical summary: Evolutionary changes bring about natural changes to proteins that may be found in many organisms. Such changes could be reflected as amino acid substitutions or insertions-deletions (indels) in protein sequences. LenVarDB is a database that provides an early overview of observed length variations that were set among 731 protein families and after examining >2 million sequences. Indels are followed up to observe if they are close to the active site such that they can affect the activity of proteins. Inclusion of such information can aid the design of bioengineering experiments.

Human-Specific Histone Methylation Signatures at Transcription Start Sites in Prefrontal Neurons

PubMed Central

Cheung, Iris; Bharadwaj, Rahul; Chou, Hsin-Jung; Houston, Isaac B.; Peter, Cyril J.; Mitchell, Amanda C.; Yao, Wei-Dong; Myers, Richard H.; Chen, Jiang-fan; Preuss, Todd M.; Rogaev, Evgeny I.; Jensen, Jeffrey D.; Weng, Zhiping; Akbarian, Schahram

2012-01-01

Cognitive abilities and disorders unique to humans are thought to result from adaptively driven changes in brain transcriptomes, but little is known about the role of cis-regulatory changes affecting transcription start sites (TSS). Here, we mapped in human, chimpanzee, and macaque prefrontal cortex the genome-wide distribution of histone H3 trimethylated at lysine 4 (H3K4me3), an epigenetic mark sharply regulated at TSS, and identified 471 sequences with human-specific enrichment or depletion. Among these were 33 loci selectively methylated in neuronal but not non-neuronal chromatin from children and adults, including TSS at DPP10 (2q14.1), CNTN4 and CHL1 (3p26.3), and other neuropsychiatric susceptibility genes. Regulatory sequences at DPP10 and additional loci carried a strong footprint of hominid adaptation, including elevated nucleotide substitution rates and regulatory motifs absent in other primates (including archaic hominins), with evidence for selective pressures during more recent evolution and adaptive fixations in modern populations. Chromosome conformation capture at two neurodevelopmental disease loci, 2q14.1 and 16p11.2, revealed higher order chromatin structures resulting in physical contact of multiple human-specific H3K4me3 peaks spaced 0.5–1 Mb apart, in conjunction with a novel cis-bound antisense RNA linked to Polycomb repressor proteins and downregulated DPP10 expression. Therefore, coordinated epigenetic regulation via newly derived TSS chromatin could play an important role in the emergence of human-specific gene expression networks in brain that contribute to cognitive functions and neurological disease susceptibility in modern day humans. PMID:23185133

Joint explorative analysis of neuroreceptor subsystems in the human brain: application to receptor-transporter correlation using PET data.

PubMed

Cselényi, Zsolt; Lundberg, Johan; Halldin, Christer; Farde, Lars; Gulyás, Balázs

2004-10-01

Positron emission tomography (PET) has proved to be a highly successful technique in the qualitative and quantitative exploration of the human brain's neurotransmitter-receptor systems. In recent years, the number of PET radioligands, targeted to different neuroreceptor systems of the human brain, has increased considerably. This development paves the way for a simultaneous analysis of different receptor systems and subsystems in the same individual. The detailed exploration of the versatility of neuroreceptor systems requires novel technical approaches, capable of operating on huge parametric image datasets. An initial step of such explorative data processing and analysis should be the development of novel exploratory data-mining tools to gain insight into the "structure" of complex multi-individual, multi-receptor data sets. For practical reasons, a possible and feasible starting point of multi-receptor research can be the analysis of the pre- and post-synaptic binding sites of the same neurotransmitter. In the present study, we propose an unsupervised, unbiased data-mining tool for this task and demonstrate its usefulness by using quantitative receptor maps, obtained with positron emission tomography, from five healthy subjects on (pre-synaptic) serotonin transporters (5-HTT or SERT) and (post-synaptic) 5-HT(1A) receptors. Major components of the proposed technique include the projection of the input receptor maps to a feature space, the quasi-clustering and classification of projected data (neighbourhood formation), trans-individual analysis of neighbourhood properties (trajectory analysis), and the back-projection of the results of trajectory analysis to normal space (creation of multi-receptor maps). The resulting multi-receptor maps suggest that complex relationships and tendencies in the relationship between pre- and post-synaptic transporter-receptor systems can be revealed and classified by using this method. As an example, we demonstrate the regional correlation of the serotonin transporter-receptor systems. These parameter-specific multi-receptor maps can usefully guide the researchers in their endeavour to formulate models of multi-receptor interactions and changes in the human brain.

Mapping areas invaded by Prosopis juliflora in Somaliland on Landsat 8 imagery

NASA Astrophysics Data System (ADS)

Rembold, Felix; Leonardi, Ugo; Ng, Wai-Tim; Gadain, Hussein; Meroni, Michele; Atzberger, Clement

2015-10-01

Prosopis juliflora is a fast growing tree species originating from South and Central America with a high invasion potential in semi-arid areas around the globe. It was introduced to East Africa for the stabilization of dune systems and for providing fuel wood after prolonged droughts and deforestation in the 1970s and 1980s. In many dry lands in East Africa the species has expanded rapidly and has become challenging to control. The species generally starts its colonization on deep soils with high water availability while in later stages or on poorer soils, its thorny thickets expand into drier grasslands and rangelands. Abandoned or low input farmland is also highly susceptible for invasion as P. juliflora has competitive advantages to native species and is extremely drought tolerant. In this work we describe a rapid approach to detect and map P. juliflora invasion at country level for the whole of Somaliland. Field observations were used to delineate training sites for a supervised classification of Landsat 8 imagery collected during the driest period of the year (i.e., from late February to early April). The choice of such a period allowed to maximise the spectral differences between P. juliflora and other species present in the area, as P. juliflora tends to maintain a higher vigour and canopy water content than native vegetation, when exposed to water stress. The results of our classification map the current status of invasion of Prosopis in Somaliland showing where the plant is invading natural vegetation or agricultural areas. These results have been verified for two spatial subsets of the whole study area with very high resolution (VHR) imagery, proving that Landsat 8 imagery is highly adequate to map P. juliflora. The produced map represents a baseline for understanding spatial distribution of P. juliflora across Somaliland but also for change detection and monitoring of long term dynamics in support to P. juliflora management and control activities.

Longitudinal structure of the equatorial ionosphere: Time evolution of the four-peaked EIA structure

NASA Astrophysics Data System (ADS)

Lin, C. H.; Hsiao, C. C.; Liu, J. Y.; Liu, C. H.

2007-12-01

Longitudinal structure of the equatorial ionosphere during the 24 h local time period is observed by the FORMOSAT-3/COSMIC (F3/C) satellite constellation. By binning the F3/C radio occultation observations during September and October 2006, global ionospheric total electron content (TEC) maps at a constant local time map (local time TEC map, referred as LT map) can be obtained to monitor the development and subsidence of the four-peaked longitudinal structure of the equatorial ionosphere. From LT maps, the four-peaked structure starts to develop at 0800-1000 LT and becomes most prominent at 1200-1600 LT. The longitudinal structure starts to subside after 2200-2400 LT and becomes indiscernible after 0400-0600 LT. In addition to TEC, ionospheric peak altitude also shows a four-peaked longitudinal structure with variation very similar to TEC during daytime. The four-peaked structure of the ionospheric peak altitude is indiscernible at night. With global local time maps of ionospheric TEC and peak altitude, we compare temporal variations of the longitudinal structure with variations of E × B drift from the empirical model. Our results indicate that the observations are consistent with the hypothesis that the four-peaked longitudinal structure is caused by the equatorial plasma fountain modulated by the E3 nonmigrating tide. Additionally, the four maximum regions show a tendency of moving eastward with propagation velocity of several 10 s m/s.

Key Principles in Providing Integrated Behavioral Health Services for Young Children and Their Families: The "Starting Early Starting Smart" Experience.

ERIC Educational Resources Information Center

Hanson, Lori, Comp.; Deere, David, Comp.; Lee, Carol Amundson, Comp.; Lewin, Amy, Comp.; Seval, Carolyn, Comp.

This paper describes the Starting Early Starting Smart (SESS) project, an early intervention program that has been developed in the context of the national, multi-site program and evaluation. The emphasis in SESS is on the integration of behavioral health services into easily accessible, non-threatening settings where caregivers naturally and…

Topographic mapping of the Apollo 16 landing site

NASA Technical Reports Server (NTRS)

Hill, R. O.; Bender, M. J.

1972-01-01

The techniques are described for obtaining high resolution photographs from the Apollo 14 lunar orbiter for topographic mapping of the Descartes landing site for use in planning Apollo 16. The Apollo 16 spacecraft landed approximately 250 m from the selected target point, and few topographic surprises were encountered.

CIDR

Science.gov Websites

Completed Projects Publications Contact Information NIH Contacts CIDR Contacts ___________________ -Contact Us -Privacy Policy -Site Map Search You are here: CIDR>Contact Us Contact Us The CIDR facility is Contact Us | Privacy Policy | Site Map | Get Adobe Reader Subscribe to CIDR News photo of 1812 Ashland

Lean principles optimize on-time vascular surgery operating room starts and decrease resident work hours.

PubMed

Warner, Courtney J; Walsh, Daniel B; Horvath, Alexander J; Walsh, Teri R; Herrick, Daniel P; Prentiss, Steven J; Powell, Richard J

2013-11-01

Lean process improvement techniques are used in industry to improve efficiency and quality while controlling costs. These techniques are less commonly applied in health care. This study assessed the effectiveness of Lean principles on first case on-time operating room starts and quantified effects on resident work hours. Standard process improvement techniques (DMAIC methodology: define, measure, analyze, improve, control) were used to identify causes of delayed vascular surgery first case starts. Value stream maps and process flow diagrams were created. Process data were analyzed with Pareto and control charts. High-yield changes were identified and simulated in computer and live settings prior to implementation. The primary outcome measure was the proportion of on-time first case starts; secondary outcomes included hospital costs, resident rounding time, and work hours. Data were compared with existing benchmarks. Prior to implementation, 39% of first cases started on time. Process mapping identified late resident arrival in preoperative holding as a cause of delayed first case starts. Resident rounding process inefficiencies were identified and changed through the use of checklists, standardization, and elimination of nonvalue-added activity. Following implementation of process improvements, first case on-time starts improved to 71% at 6 weeks (P = .002). Improvement was sustained with an 86% on-time rate at 1 year (P < .001). Resident rounding time was reduced by 33% (from 70 to 47 minutes). At 9 weeks following implementation, these changes generated an opportunity cost potential of $12,582. Use of Lean principles allowed rapid identification and implementation of perioperative process changes that improved efficiency and resulted in significant cost savings. This improvement was sustained at 1 year. Downstream effects included improved resident efficiency with decreased work hours. Copyright © 2013 Society for Vascular Surgery. Published by Mosby, Inc. All rights reserved.

Methods of analysis and resources available for genetic trait mapping.

PubMed

Ott, J

1999-01-01

Methods of genetic linkage analysis are reviewed and put in context with other mapping techniques. Sources of information are outlined (books, web sites, computer programs). Special consideration is given to statistical problems in canine genetic mapping (heterozygosity, inbreeding, marker maps).

Identification and Characterization of Sites Where Persistent Atrial Fibrillation Is Terminated by Localized Ablation.

PubMed

Zaman, Junaid A B; Sauer, William H; Alhusseini, Mahmood I; Baykaner, Tina; Borne, Ryan T; Kowalewski, Christopher A B; Busch, Sonia; Zei, Paul C; Park, Shirley; Viswanathan, Mohan N; Wang, Paul J; Brachmann, Johannes; Krummen, David E; Miller, John M; Rappel, Wouter Jan; Narayan, Sanjiv M; Peters, Nicholas S

2018-01-01

The mechanisms by which persistent atrial fibrillation (AF) terminates via localized ablation are not well understood. To address the hypothesis that sites where localized ablation terminates persistent AF have characteristics identifiable with activation mapping during AF, we systematically examined activation patterns acquired only in cases of unequivocal termination by ablation. We recruited 57 patients with persistent AF undergoing ablation, in whom localized ablation terminated AF to sinus rhythm or organized tachycardia. For each site, we performed an offline analysis of unprocessed unipolar electrograms collected during AF from multipolar basket catheters using the maximum -dV/dt assignment to construct isochronal activation maps for multiple cycles. Additional computational modeling and phase analysis were used to study mechanisms of map variability. At all sites of AF termination, localized repetitive activation patterns were observed. Partial rotational circuits were observed in 26 of 57 (46%) cases, focal patterns in 19 of 57 (33%), and complete rotational activity in 12 of 57 (21%) cases. In computer simulations, incomplete segments of partial rotations coincided with areas of slow conduction characterized by complex, multicomponent electrograms, and variations in assigning activation times at such sites substantially altered mapped mechanisms. Local activation mapping at sites of termination of persistent AF showed repetitive patterns of rotational or focal activity. In computer simulations, complete rotational activation sequence was observed but was sensitive to assignment of activation timing particularly in segments of slow conduction. The observed phenomena of repetitive localized activation and the mechanism by which local ablation terminates putative AF drivers require further investigation. © 2018 American Heart Association, Inc.

High-throughput detection of RNA processing in bacteria.

PubMed

Gill, Erin E; Chan, Luisa S; Winsor, Geoffrey L; Dobson, Neil; Lo, Raymond; Ho Sui, Shannan J; Dhillon, Bhavjinder K; Taylor, Patrick K; Shrestha, Raunak; Spencer, Cory; Hancock, Robert E W; Unrau, Peter J; Brinkman, Fiona S L

2018-03-27

Understanding the RNA processing of an organism's transcriptome is an essential but challenging step in understanding its biology. Here we investigate with unprecedented detail the transcriptome of Pseudomonas aeruginosa PAO1, a medically important and innately multi-drug resistant bacterium. We systematically mapped RNA cleavage and dephosphorylation sites that result in 5'-monophosphate terminated RNA (pRNA) using monophosphate RNA-Seq (pRNA-Seq). Transcriptional start sites (TSS) were also mapped using differential RNA-Seq (dRNA-Seq) and both datasets were compared to conventional RNA-Seq performed in a variety of growth conditions. The pRNA-Seq library revealed known tRNA, rRNA and transfer-messenger RNA (tmRNA) processing sites, together with previously uncharacterized RNA cleavage events that were found disproportionately near the 5' ends of transcripts associated with basic bacterial functions such as oxidative phosphorylation and purine metabolism. The majority (97%) of the processed mRNAs were cleaved at precise codon positions within defined sequence motifs indicative of distinct endonucleolytic activities. The most abundant of these motifs corresponded closely to an E. coli RNase E site previously established in vitro. Using the dRNA-Seq library, we performed an operon analysis and predicted 3159 potential TSS. A correlation analysis uncovered 105 antiparallel pairs of TSS that were separated by 18 bp from each other and were centered on single palindromic TAT(A/T)ATA motifs (likely - 10 promoter elements), suggesting that, consistent with previous in vitro experimentation, these sites can initiate transcription bi-directionally and may thus provide a novel form of transcriptional regulation. TSS and RNA-Seq analysis allowed us to confirm expression of small non-coding RNAs (ncRNAs), many of which are differentially expressed in swarming and biofilm formation conditions. This study uses pRNA-Seq, a method that provides a genome-wide survey of RNA processing, to study the bacterium Pseudomonas aeruginosa and discover extensive transcript processing not previously appreciated. We have also gained novel insight into RNA maturation and turnover as well as a potential novel form of transcription regulation. NOTE: All sequence data has been submitted to the NCBI sequence read archive. Accession numbers are as follows: [NCBI sequence read archive: SRX156386, SRX157659, SRX157660, SRX157661, SRX157683 and SRX158075]. The sequence data is viewable using Jbrowse on www.pseudomonas.com .

Six Landing Sites on Mars

NASA Technical Reports Server (NTRS)

2008-01-01

The landing site chosen for NASA's Phoenix Mars Lander, at about 68 degrees north latitude, is much farther north than the sites where previous spacecraft have landed on Mars.

Color coding on this map indicates relative elevations based on data from the Mars Orbiter Laser Altimeter on NASA's Mars Global Surveyor. Red is higher elevation; blue is lower elevation. In longitude, the map extends from 70 degrees (north) to minus 70 degrees (south).

183. Photocopy of map (Twin Falls Canal Company). TOPOGRAPHICAL MAP ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

183. Photocopy of map (Twin Falls Canal Company). TOPOGRAPHICAL MAP OF MILNER DAM SITE, TWIN FALLS COUNTY, MILNER, IDAHO; MAP, LEFT SIDE ONLY. CROSS REFERENCE: ID-15-192. - Milner Dam & Main Canal: Twin Falls Canal Company, On Snake River, 11 miles West of city of Burley, Idaho, Twin Falls, Twin Falls County, ID

BOREAS Hardcopy Maps

NASA Technical Reports Server (NTRS)

Hall, Forrest G. (Editor); Nelson, Elizabeth; Newcomer, Jeffrey A.

2000-01-01

Boreal Ecosystem-Atmospheric Study (BOREAS) hardcopy maps are a collection of approximately 1,000 hardcopy maps representing the physical, climatological, and historical attributes of areas covering primarily the Manitoba and Saskatchewan provinces of Canada. These maps were collected by BOREAS Information System (BORIS) and Canada for Remote Sensing (CCRS) staff to provide basic information about site positions, manmade features, topography, geology, hydrology, land cover types, fire history, climate, and soils of the BOREAS study region. These maps are not available for distribution through the BOREAS project but may be used as an on-site resource. Information is provided within this document for individuals who want to order copies of these maps from the original map source. Note that the maps are not contained on the BOREAS CD-ROM set. An inventory listing file is supplied on the CD-ROM to inform users of the maps that are available. This inventory listing is available from the Earth Observing System Data and Information System (EOSDIS) Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC). For hardcopies of the individual maps, contact the sources provided.

Catalog of known hot springs and thermal place names for Honduras

DOE Office of Scientific and Technical Information (OSTI.GOV)

Finch, R.C.

Thermal place names were compiled from all 1:50,000 topographic quadrangle maps for the Republic of Honduras as of July 1986, from other published maps, and from several sources of unpublished data. Known hot spring sites include those visited by Empresa Nacional de Energia Electrica (Honduras) geologists, sites visited by Los Alamos geologists in 1985, and other sites known to R.C. Finch. The number of known hot spring sites in Honduras with temperatures >30/sup 0/C is 125. In addition, 56 thermal sites are suspected on the basis of thermal place names. The total number of geothermal sites, known and suspected, ismore » 181.« less

Vegetation database for land-cover mapping, Clark and Lincoln Counties, Nevada

USGS Publications Warehouse

Charlet, David A.; Damar, Nancy A.; Leary, Patrick J.

2014-01-01

Floristic and other vegetation data were collected at 3,175 sample sites to support land-cover mapping projects in Clark and Lincoln Counties, Nevada, from 2007 to 2013. Data were collected at sample sites that were selected to fulfill mapping priorities by one of two different plot sampling approaches. Samples were described at the stand level and classified into the National Vegetation Classification hierarchy at the alliance level and above. The vegetation database is presented in geospatial and tabular formats.

Global Land Survey Impervious Mapping Project Web Site

NASA Technical Reports Server (NTRS)

DeColstoun, Eric Brown; Phillips, Jacqueline

2014-01-01

The Global Land Survey Impervious Mapping Project (GLS-IMP) aims to produce the first global maps of impervious cover at the 30m spatial resolution of Landsat. The project uses Global Land Survey (GLS) Landsat data as its base but incorporates training data generated from very high resolution commercial satellite data and using a Hierarchical segmentation program called Hseg. The web site contains general project information, a high level description of the science, examples of input and output data, as well as links to other relevant projects.

24 CFR 200.1545 - Appeals of MAP Lender Review Board decisions.

Code of Federal Regulations, 2011 CFR

2011-04-01

...): MAP Lender Quality Assurance Enforcement § 200.1545 Appeals of MAP Lender Review Board decisions. (a... information included in the administrative record and any new information presented at the appeal conference... to overturn will be posted on HUD's MAP Web site. ...

24 CFR 200.1545 - Appeals of MAP Lender Review Board decisions.

Code of Federal Regulations, 2012 CFR

2012-04-01

...): MAP Lender Quality Assurance Enforcement § 200.1545 Appeals of MAP Lender Review Board decisions. (a... information included in the administrative record and any new information presented at the appeal conference... to overturn will be posted on HUD's MAP Web site. ...

24 CFR 200.1545 - Appeals of MAP Lender Review Board decisions.

Code of Federal Regulations, 2014 CFR

2014-04-01

...): MAP Lender Quality Assurance Enforcement § 200.1545 Appeals of MAP Lender Review Board decisions. (a... information included in the administrative record and any new information presented at the appeal conference... to overturn will be posted on HUD's MAP Web site. ...

24 CFR 200.1545 - Appeals of MAP Lender Review Board decisions.

Code of Federal Regulations, 2013 CFR

2013-04-01

...): MAP Lender Quality Assurance Enforcement § 200.1545 Appeals of MAP Lender Review Board decisions. (a... information included in the administrative record and any new information presented at the appeal conference... to overturn will be posted on HUD's MAP Web site. ...

Arizona land use experiment

NASA Technical Reports Server (NTRS)

Winikka, C. C.; Schumann, H. H.

1975-01-01

Utilization of new sources of statewide remote sensing data, taken from high-altitude aircraft and from spacecraft is discussed along with incorporation of information extracted from these sources into on-going land and resources management programs in Arizona. Statewide cartographic applications of remote sensor data taken by NASA high-altitude aircraft include the development of a statewide semi-analytic control network, the production of nearly 1900 orthophotoquads (image maps) that are coincident in scale and area with the U.S. Geological Survey (USGS) 7. 5 minute topographic quadrangle map series, and satellite image maps of Arizona produced from LANDSAt multispectral scanner imagery. These cartographic products are utilized for a wide variety of experimental and operational earth resources applications. Applications of the imagery, image maps, and derived information discussed include: soils and geologic mapping projects, water resources investigations, land use inventories, environmental impact studies, highway route locations and mapping, vegetation cover mapping, wildlife habitat studies, power plant siting studies, statewide delineation of irrigation cropland, position determination of drilling sites, pictorial geographic bases for thematic mapping, and court exhibits.

Census Cities experiment in urban change detection. [mapping of land use changes in San Francisco, Washington D.C., Phoenix, Tucson, Boston, New Haven, Cedar Rapids, and Pontiac

NASA Technical Reports Server (NTRS)

Wray, J. R. (Principal Investigator); Milazzo, V. A.

1974-01-01

The author has identified the following significant results. Mapping of 1970 and 1972 land use from high-flight photography has been completed for all test sites: San Francisco, Washington, Phoenix, Tucson, Boston, New Haven, Cedar Rapids, and Pontiac. Area analysis of 1970 and 1972 land use has been completed for each of the mandatory urban areas. All 44 sections of the 1970 land use maps of the San Francisco test site have been officially released through USGS Open File at 1:62,500. Five thousand copies of the Washington one-sheet color 1970 land use map, census tract map, and point line identification map are being printed by USGS Publication Division. ERTS-1 imagery for each of the eight test sites is being received and analyzed. Color infrared photo enlargements at 1:100,000 of ERTS-1 MSS images of Phoenix taken on October 16, 1972 and May 2, 1973 are being analyzed to determine to what level land use and land use changes can be identified and to what extent the ERTS-1 imagery can be used in updating the 1970 aircraft photo-derived land use data base. Work is proceeding on the analysis of ERTS-1 imagery by computer manipulation of ERTS-1 MSS data in digital format. ERTS-1 CCT maps at 1:24,000 are being analyzed for two dates over Washington and Phoenix. Anniversary tape sets have been received at Purdue LARS for some additional urban test sites.

Integration Of 3D Geographic Information System (GIS) For Effective Waste Management Practice

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rood, G.J.; Hecox, G.R.

2006-07-01

Soil remediation in response to the presence of residual radioactivity resulting from past MED/AEC activities is currently in progress under the Formerly Utilized Sites Remedial Action Program near the St. Louis, MO airport. During GY05, approximately 92,000 cubic meters (120,000 cubic yards) of radioactive soil was excavated, packaged and transported via rail for disposal at U.S. Ecology or Envirocare of Utah, LLC. To facilitate the management of excavation/transportation/disposal activities, a 3D GIS was developed for the site that was used to estimate the in-situ radionuclide activities, activities in excavation block areas, and shipping activities using a sum-of ratio (SOR) methodmore » for combining various radionuclide compounds into applicable transportation and disposal SOR values. The 3D GIS was developed starting with the SOR values for the approximately 900 samples from 90 borings. These values were processed into a three-dimensional (3D) point grid using kriging with nominal grid spacing of 1.5 by 1.5 meter horizontal by 0.3 meter vertical. The final grid, clipped to the area and soil interval above the planned base of excavation, consisted of 210,000 individual points. Standard GIS volumetric and spatial join procedures were used to calculate the volume of soil represented by each grid point, the base of excavation, depth below ground surface, elevation, surface elevation and SOR values for each point in the final grid. To create the maps needed for management, the point grid results were spatially joined to each excavation area in 0.9 meter (3 foot) depth intervals and the average SOR and total volumes were calculations. The final maps were color-coded for easy identification of areas above the specific transportation or disposal criteria. (authors)« less

Rapid detection and characterization of surface CO2 leakage through the real-time measurement of δ13C signatures in CO2 flux from the ground

NASA Astrophysics Data System (ADS)

Krevor, S.; Perrin, J.; Esposito, A.; Rella, C.; Benson, S. M.

2009-12-01

A portable stable carbon isotope ratio analyzer for carbon dioxide, based on wavelength scanned cavity ringdown spectroscopy, has been used to detect and characterize an intentional leakage of CO2 from an underground pipeline at the ZERT experimental facility in Bozeman, Montana. Rapid (~1 hour) walking surveys of the entire 100m x 100m site were collected using this mobile, real-time instrument. The resulting concentration and 13C isotopic abundance maps were processed using simple yet powerful analysis techniques, permitting not only the identification of specific leakage locations, but providing the ability to distinguish petrogenic sources of CO2 from biogenic sources. At the site an approximately 100-meter horizontal well has been drilled below an alfalfa field at a depth between 1-3 meters below the surface. The well has perforations along the central 70 meters of the well. The overlying strata are highly permeable sand, silt, and topsoil. The flora consists generally of long grasses and was cut to a height of less than 6 inches before the start of the experiment. For 30 days starting July 15, 2009, CO2 was injected at a rate of 0.2 tonnes per day. The injection rate is designed to simulate leakage from a mature storage reservoir at an annual rate of between .001 and .01%. The isotopic composition of the gas from the tank is at δ13C signature of approximately -52‰, far more negative than either atmospheric (approx. -8‰) or CO2 from soil respiration (approx. -26‰) at the site. The CO2 isotopic and concentration measurements were taken with a Picarro WS-CRDS analyzer with 1/8” tubing connected to a sampling inlet. Simultaneous with CO2 concentrations (including 13C), position data was logged using a GPS receiver. Datapoints are taken around every second. The analyzer was powered using batteries and housed in a conventional garden cart. The surveys consisted of traverses of the site along the length of the pipeline and extending out 100 meters on either side of the pipeline with the end of the gas inlet tube approximate 9 cm above the ground at a walking speed of 1-2m/sec. This simulates the type of survey that could be easily performed if the actual or potential site of a leak was known to within an area on the order of 100 square kilometers or less, the scale of expected industrial CO2 sequestration operations. The surveys were performed both during the day and during the evening when CO2 flux due to respiration from the soil is markedly different. Keeling plots were used to characterize the spatially varying 13C composition of ground source CO2 across the site. A map constructed from this data shows that CO2 flux from sources of leakage was characterized by a δ 13C of -40‰ or less whereas locations away from the leakage spots had much higher δ 13C signatures, -25‰ or higher. The distinct isotopic signature allows for a clear discernment between leakage of petrogenic CO2 and that of natural CO2 fluxes from soil respiration. This is particularly valuable in the circumstance where the leak is slow enough that it could not be identified from CO2 concentration or flux changes above the natural background signal alone.

The association between implementation strategy use and the uptake of hepatitis C treatment in a national sample.

PubMed

Rogal, Shari S; Yakovchenko, Vera; Waltz, Thomas J; Powell, Byron J; Kirchner, JoAnn E; Proctor, Enola K; Gonzalez, Rachel; Park, Angela; Ross, David; Morgan, Timothy R; Chartier, Maggie; Chinman, Matthew J

2017-05-11

Hepatitis C virus (HCV) is a common and highly morbid illness. New medications that have much higher cure rates have become the new evidence-based practice in the field. Understanding the implementation of these new medications nationally provides an opportunity to advance the understanding of the role of implementation strategies in clinical outcomes on a large scale. The Expert Recommendations for Implementing Change (ERIC) study defined discrete implementation strategies and clustered these strategies into groups. The present evaluation assessed the use of these strategies and clusters in the context of HCV treatment across the US Department of Veterans Affairs (VA), Veterans Health Administration, the largest provider of HCV care nationally. A 73-item survey was developed and sent to all VA sites treating HCV via electronic survey, to assess whether or not a site used each ERIC-defined implementation strategy related to employing the new HCV medication in 2014. VA national data regarding the number of Veterans starting on the new HCV medications at each site were collected. The associations between treatment starts and number and type of implementation strategies were assessed. A total of 80 (62%) sites responded. Respondents endorsed an average of 25 ± 14 strategies. The number of treatment starts was positively correlated with the total number of strategies endorsed (r = 0.43, p < 0.001). Quartile of treatment starts was significantly associated with the number of strategies endorsed (p < 0.01), with the top quartile endorsing a median of 33 strategies, compared to 15 strategies in the lowest quartile. There were significant differences in the types of strategies endorsed by sites in the highest and lowest quartiles of treatment starts. Four of the 10 top strategies for sites in the top quartile had significant correlations with treatment starts compared to only 1 of the 10 top strategies in the bottom quartile sites. Overall, only 3 of the top 15 most frequently used strategies were associated with treatment. These results suggest that sites that used a greater number of implementation strategies were able to deliver more evidence-based treatment in HCV. The current assessment also demonstrates the feasibility of electronic self-reporting to evaluate ERIC strategies on a large scale. These results provide initial evidence for the clinical relevance of the ERIC strategies in a real-world implementation setting on a large scale. This is an initial step in identifying which strategies are associated with the uptake of evidence-based practices in nationwide healthcare systems.

43 CFR 3271.10 - What do I need to start preparing a site and building and testing a utilization facility on...

Code of Federal Regulations, 2012 CFR

2012-10-01

... 43 Public Lands: Interior 2 2012-10-01 2012-10-01 false What do I need to start preparing a site and building and testing a utilization facility on Federal land leased for geothermal resources? 3271.10 Section 3271.10 Public Lands: Interior Regulations Relating to Public Lands (Continued) BUREAU OF LAND MANAGEMENT, DEPARTMENT OF THE INTERIOR...

43 CFR 3271.10 - What do I need to start preparing a site and building and testing a utilization facility on...

Code of Federal Regulations, 2014 CFR

2014-10-01

... 43 Public Lands: Interior 2 2014-10-01 2014-10-01 false What do I need to start preparing a site and building and testing a utilization facility on Federal land leased for geothermal resources? 3271.10 Section 3271.10 Public Lands: Interior Regulations Relating to Public Lands (Continued) BUREAU OF LAND MANAGEMENT, DEPARTMENT OF THE INTERIOR...

43 CFR 3271.10 - What do I need to start preparing a site and building and testing a utilization facility on...

Code of Federal Regulations, 2013 CFR

2013-10-01

... 43 Public Lands: Interior 2 2013-10-01 2013-10-01 false What do I need to start preparing a site and building and testing a utilization facility on Federal land leased for geothermal resources? 3271.10 Section 3271.10 Public Lands: Interior Regulations Relating to Public Lands (Continued) BUREAU OF LAND MANAGEMENT, DEPARTMENT OF THE INTERIOR...

43 CFR 3271.10 - What do I need to start preparing a site and building and testing a utilization facility on...

Code of Federal Regulations, 2011 CFR

2011-10-01

... 43 Public Lands: Interior 2 2011-10-01 2011-10-01 false What do I need to start preparing a site and building and testing a utilization facility on Federal land leased for geothermal resources? 3271.10 Section 3271.10 Public Lands: Interior Regulations Relating to Public Lands (Continued) BUREAU OF LAND MANAGEMENT, DEPARTMENT OF THE INTERIOR...

Flood characteristics of streams in Owyhee County, Idaho

USGS Publications Warehouse

Riggs, H.C.; Harenberg, W.A.

1976-01-01

Channel-width measurements were used to estimate annual peaks with a recurrence interval of 10 years at 79 sites in Owyhee County, Idaho, and adjacent areas. These discharges and those from 33 gaging stations are plotted on a map of the area. The map will allow the user to interpolate between sites. (Woodard-USGS)

Photocopy: Composite Map of Crossing Site by Daniel J. Mordell ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

Photocopy: Composite Map of Crossing Site by Daniel J. Mordell from Canal Society of New York State. Bottoming Out: Useful and Interesting Notes Collected for Members of the Canal Society of New York State. Vol. 18-19. Syracuse, 1962. - Erie Canal (Enlarged), Schoharie Creek Aqueduct, Spanning Schoharie Creek, Fort Hunter, Montgomery County, NY

Construction of a high-density genetic map for grape using next generation restriction-site associated DNA sequencing

PubMed Central

2012-01-01

Background Genetic mapping and QTL detection are powerful methodologies in plant improvement and breeding. Construction of a high-density and high-quality genetic map would be of great benefit in the production of superior grapes to meet human demand. High throughput and low cost of the recently developed next generation sequencing (NGS) technology have resulted in its wide application in genome research. Sequencing restriction-site associated DNA (RAD) might be an efficient strategy to simplify genotyping. Combining NGS with RAD has proven to be powerful for single nucleotide polymorphism (SNP) marker development. Results An F1 population of 100 individual plants was developed. In-silico digestion-site prediction was used to select an appropriate restriction enzyme for construction of a RAD sequencing library. Next generation RAD sequencing was applied to genotype the F1 population and its parents. Applying a cluster strategy for SNP modulation, a total of 1,814 high-quality SNP markers were developed: 1,121 of these were mapped to the female genetic map, 759 to the male map, and 1,646 to the integrated map. A comparison of the genetic maps to the published Vitis vinifera genome revealed both conservation and variations. Conclusions The applicability of next generation RAD sequencing for genotyping a grape F1 population was demonstrated, leading to the successful development of a genetic map with high density and quality using our designed SNP markers. Detailed analysis revealed that this newly developed genetic map can be used for a variety of genome investigations, such as QTL detection, sequence assembly and genome comparison. PMID:22908993

Search for Mars lander/rover/sample-return sites: A status review

NASA Technical Reports Server (NTRS)

Masursky, Harold; Dial, A. L., Jr.; Morris, E. C.; Strobell, M. E.; Applebee, D. J.; Chapman, M. G.

1988-01-01

Ten Mars sites were studied in the USA for four years. The sites are the Chasma Boreale (North Pole), Planum Australe (South Pole), Olympus Rupes, Mangala Valles, Memnonia Sulci, Candor Chasma, Kasel Valles, Nilosyrtis Mensae, Elysium Montes, and Apollinaris Patera. Seven sites are being studied by the USSR; their prime sites are located at the east mouth of Kasel Valles and near Uranius Patera. Thirteen geological maps of the first six USA sites are compiled and in review. Maps of the Mangala East and West sites at 1:1/2 million scale and a 1:2 million scale map show evidence of three episodes of small-channel formation interspersed with episodes of volcanism and tectonism that span the period from 3.5 to 0.6 b.y. ago. The tectonic and geological history of Mars, both ancient and modern, can be elucidated by sampling volcanic and fluvial geologic units at equatorial sites and layered deposits at polar sites. The evidence appears clear for multiple episodes of fluvial channeling, including some that are quite recent; this evidence contrasts with the theses of Baker and Partridge (1986) and many others that all channels are ancient. Verification of this hypothesis by Mars Observer will be an important step forward in the perception of the history of Mars.

Optimizing Travel Time to Outpatient Interventional Radiology Procedures in a Multi-Site Hospital System Using a Google Maps Application.

PubMed

Mandel, Jacob E; Morel-Ovalle, Louis; Boas, Franz E; Ziv, Etay; Yarmohammadi, Hooman; Deipolyi, Amy; Mohabir, Heeralall R; Erinjeri, Joseph P

2018-02-20

The purpose of this study is to determine whether a custom Google Maps application can optimize site selection when scheduling outpatient interventional radiology (IR) procedures within a multi-site hospital system. The Google Maps for Business Application Programming Interface (API) was used to develop an internal web application that uses real-time traffic data to determine estimated travel time (ETT; minutes) and estimated travel distance (ETD; miles) from a patient's home to each a nearby IR facility in our hospital system. Hypothetical patient home addresses based on the 33 cities comprising our institution's catchment area were used to determine the optimal IR site for hypothetical patients traveling from each city based on real-time traffic conditions. For 10/33 (30%) cities, there was discordance between the optimal IR site based on ETT and the optimal IR site based on ETD at non-rush hour time or rush hour time. By choosing to travel to an IR site based on ETT rather than ETD, patients from discordant cities were predicted to save an average of 7.29 min during non-rush hour (p = 0.03), and 28.80 min during rush hour (p < 0.001). Using a custom Google Maps application to schedule outpatients for IR procedures can effectively reduce patient travel time when more than one location providing IR procedures is available within the same hospital system.

Linking in situ LAI and fine resolution remote sensing data to map reference LAI over cropland and grassland using geostatistical regression method

NASA Astrophysics Data System (ADS)

He, Yaqian; Bo, Yanchen; Chai, Leilei; Liu, Xiaolong; Li, Aihua

2016-08-01

Leaf Area Index (LAI) is an important parameter of vegetation structure. A number of moderate resolution LAI products have been produced in urgent need of large scale vegetation monitoring. High resolution LAI reference maps are necessary to validate these LAI products. This study used a geostatistical regression (GR) method to estimate LAI reference maps by linking in situ LAI and Landsat TM/ETM+ and SPOT-HRV data over two cropland and two grassland sites. To explore the discrepancies of employing different vegetation indices (VIs) on estimating LAI reference maps, this study established the GR models for different VIs, including difference vegetation index (DVI), normalized difference vegetation index (NDVI), and ratio vegetation index (RVI). To further assess the performance of the GR model, the results from the GR and Reduced Major Axis (RMA) models were compared. The results show that the performance of the GR model varies between the cropland and grassland sites. At the cropland sites, the GR model based on DVI provides the best estimation, while at the grassland sites, the GR model based on DVI performs poorly. Compared to the RMA model, the GR model improves the accuracy of reference LAI maps in terms of root mean square errors (RMSE) and bias.

Mapping structural landmarks, ligand binding sites and missense mutations to the collagen IV heterotrimers predicts major functional domains, novel interactions and variation in phenotypes in inherited diseases affecting basement membranes

PubMed Central

Des Parkin, J.; San Antonio, James D.; Pedchenko, Vadim; Hudson, Billy; Jensen, Shane T.; Savige, Judy

2016-01-01

Collagen IV is the major protein found in basement membranes. It comprises 3 heterotrimers (α1α1α2, α3α4α5, and α5α5α6) that form distinct networks, and are responsible for membrane strength and integrity. We constructed linear maps of the collagen IV heterotrimers (‘interactomes’) that indicated major structural landmarks, known and predicted ligand-binding sites, and missense mutations, in order to identify functional and disease-associated domains, potential interactions between ligands, and genotype-phenotype relationships. The maps documented more than 30 known ligand-binding sites as well as motifs for integrins, heparin, von Willebrand factor (VWF), decorin and bone morphogenetic protein (BMP). They predicted functional domains for angiogenesis and haemostasis, and disease domains for autoimmunity, tumor growth and inhibition, infection and glycation. Cooperative ligand interactions were indicated by binding site proximity, for example, between integrins, matrix metalloproteinases and heparin. The maps indicated that mutations affecting major ligand-binding sites, for example for Von Hippel Lindau (VHL) protein in the α1 chain or integrins in the α5 chain, resulted in distinctive phenotypes (Hereditary Angiopathy, Nephropathy, Aneurysms and muscle Cramps (HANAC) syndrome, and early onset Alport syndrome respectively). These maps further our understanding of basement membrane biology and disease, and suggest novel membrane interactions, functions, and therapeutic targets. PMID:21280145

Where to Go Next? Identifying Target Areas in the North Atlantic for Future Seafloor Mapping Initiatives

NASA Astrophysics Data System (ADS)

Woelfl, A. C.; Jencks, J.; Johnston, G.; Varner, J. D.; Devey, C. W.

2017-12-01

Human activities are rapidly expanding into the oceans, yet detailed bathymetric maps do not exist for most of the seafloor that would permit governments to formulate sensible usage rules. Changing this situation will require an enormous international mapping effort. To ensure that this effort is directed towards the regions most in need of mapping, we need to know which areas have already been mapped and which areas are potentially most interesting. Despite various mapping efforts in recent years, large parts of the Atlantic still lack detailed bathymetric information. To successfully plan for future mapping efforts to fill these gaps, knowledge of current data coverage is imperative to avoid duplication of effort. While certain datasets are publically available online (e.g. NOAA's NCEI, EMODnet, IHO-DCDB, LDEO's GMRT), many are not. However, with the limited information we do have at hand, the question remains, where should we map next? And what criteria should we take into account? In 2016, a study was taken on as part of the efforts of the International Atlantic Seabed Mapping Working Group (ASMIWG). The ASMIWG, established by the Tri-Partite Galway Statement Implementation Committee, was tasked to develop a cohesive seabed mapping strategy for the Atlantic Ocean. The aim of our study was to develop a reproducible process for identifying and evaluating potential target areas within the North Atlantic that represent suitable sites for future bathymetric surveys. The sites were selected by applying a GIS-based suitability analysis that included specific user group-based parameters of the marine environment. Furthermore, information regarding current data coverage were gathered to take into account in the selection process. The results reveal the suitability of sites within the North Atlantic based on the selected criteria. Three potential target sites should be seen as flexible suggestions for future mapping initiatives rather than a rigid, defined set of areas. This methodology can be adjusted to other areas of interest and can include a variety of parameters based on stakeholder interest. Further this work only included accessible and displayable information about multibeam data coverage and would certainly benefit from more easily available and discoverable data sets or at least from location information.

Vegetation inventory, mapping, and classification report, Fort Bowie National Historic Site

USGS Publications Warehouse

Studd, Sarah; Fallon, Elizabeth; Crumbacher, Laura; Drake, Sam; Villarreal, Miguel

2013-01-01

A vegetation mapping and characterization effort was conducted at Fort Bowie National Historic Site in 2008-10 by the Sonoran Desert Network office in collaboration with researchers from the Office of Arid lands studies, Remote Sensing Center at the University of Arizona. This vegetation mapping effort was completed under the National Park Service Vegetation Inventory program which aims to complete baseline mapping inventories at over 270 national park units. The vegetation map data was collected to provide park managers with a digital map product that met national standards of spatial and thematic accuracy, while also placing the vegetation into a regional and even national context. Work comprised of three major field phases 1) concurrent field-based classification data collection and mapping (map unit delineation), 2) development of vegetation community types at the National Vegetation Classification alliance or association level and 3) map accuracy assessment. Phase 1 was completed in late 2008 and early 2009. Community type descriptions were drafted to meet the then-current hierarchy (version 1) of the National Vegetation Classification System (NVCS) and these were applied to each of the mapped areas. This classification was developed from both plot level data and censused polygon data (map units) as this project was conducted as a concurrent mapping and classification effort. The third stage of accuracy assessment completed in the fall of 2010 consisted of a complete census of each map unit and was conducted almost entirely by park staff. Following accuracy assessment the map was amended where needed and final products were developed including this report, a digital map and full vegetation descriptions. Fort Bowie National Historic Site covers only 1000 acres yet has a relatively complex landscape, topography and geology. A total of 16 distinct communities were described and mapped at Fort Bowie NHS. These ranged from lush riparian woodlands lining the ephemeral washes dominated by Ash (Fraxinus), Walnut (Juglans) and Hackberry (Celtis) to drier upland sites typical of desert scrub and semi-desert grassland communities. These shrublands boast a diverse mixture of shrubs, succulents and perennial grasses. In many places the vegetation could be seen to echo the history of the fort site, with management of shrub encroachment apparent in the grasslands and the paucity of trees evidence of historic cutting for timber and fire wood. Seven of the 16 vegetation types were ‘accepted’ types within the NVC while the others have been described here as specific to FOBO and have proposed status within the NVC. The map was designed to facilitate ecologically-based natural resources management and research. The map is in digital format within a geodatabase structure that allows for complex relationships to be established between spatial and tabular data, and makes accessing the product easy and seamless. The GIS format allows user flexibility and will also enable updates to be made as new information becomes available (such as revised NVC codes or vegetation type names) or in the event of major disturbance events that could impact the vegetation.

Improving a Synechocystis-based photoautotrophic chassis through systematic genome mapping and validation of neutral sites.

PubMed

Pinto, Filipe; Pacheco, Catarina C; Oliveira, Paulo; Montagud, Arnau; Landels, Andrew; Couto, Narciso; Wright, Phillip C; Urchueguía, Javier F; Tamagnini, Paula

2015-12-01

The use of microorganisms as cell factories frequently requires extensive molecular manipulation. Therefore, the identification of genomic neutral sites for the stable integration of ectopic DNA is required to ensure a successful outcome. Here we describe the genome mapping and validation of five neutral sites in the chromosome of Synechocystis sp. PCC 6803, foreseeing the use of this cyanobacterium as a photoautotrophic chassis. To evaluate the neutrality of these loci, insertion/deletion mutants were produced, and to assess their functionality, a synthetic green fluorescent reporter module was introduced. The constructed integrative vectors include a BioBrick-compatible multiple cloning site insulated by transcription terminators, constituting robust cloning interfaces for synthetic biology approaches. Moreover, Synechocystis mutants (chassis) ready to receive purpose-built synthetic modules/circuits are also available. This work presents a systematic approach to map and validate chromosomal neutral sites in cyanobacteria, and that can be extended to other organisms. © The Author 2015. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

NHS-Esters As Versatile Reactivity-Based Probes for Mapping Proteome-Wide Ligandable Hotspots.

PubMed

Ward, Carl C; Kleinman, Jordan I; Nomura, Daniel K

2017-06-16

Most of the proteome is considered undruggable, oftentimes hindering translational efforts for drug discovery. Identifying previously unknown druggable hotspots in proteins would enable strategies for pharmacologically interrogating these sites with small molecules. Activity-based protein profiling (ABPP) has arisen as a powerful chemoproteomic strategy that uses reactivity-based chemical probes to map reactive, functional, and ligandable hotspots in complex proteomes, which has enabled inhibitor discovery against various therapeutic protein targets. Here, we report an alkyne-functionalized N-hydroxysuccinimide-ester (NHS-ester) as a versatile reactivity-based probe for mapping the reactivity of a wide range of nucleophilic ligandable hotspots, including lysines, serines, threonines, and tyrosines, encompassing active sites, allosteric sites, post-translational modification sites, protein interaction sites, and previously uncharacterized potential binding sites. Surprisingly, we also show that fragment-based NHS-ester ligands can be made to confer selectivity for specific lysine hotspots on specific targets including Dpyd, Aldh2, and Gstt1. We thus put forth NHS-esters as promising reactivity-based probes and chemical scaffolds for covalent ligand discovery.

Insights into earthquake hazard map performance from shaking history simulations

NASA Astrophysics Data System (ADS)

Stein, S.; Vanneste, K.; Camelbeeck, T.; Vleminckx, B.

2017-12-01

Why recent large earthquakes caused shaking stronger than predicted by earthquake hazard maps is under debate. This issue has two parts. Verification involves how well maps implement probabilistic seismic hazard analysis (PSHA) ("have we built the map right?"). Validation asks how well maps forecast shaking ("have we built the right map?"). We explore how well a map can ideally perform by simulating an area's shaking history and comparing "observed" shaking to that predicted by a map generated for the same parameters. The simulations yield shaking distributions whose mean is consistent with the map, but individual shaking histories show large scatter. Infrequent large earthquakes cause shaking much stronger than mapped, as observed. Hence, PSHA seems internally consistent and can be regarded as verified. Validation is harder because an earthquake history can yield shaking higher or lower than that predicted while being consistent with the hazard map. The scatter decreases for longer observation times because the largest earthquakes and resulting shaking are increasingly likely to have occurred. For the same reason, scatter is much less for the more active plate boundary than for a continental interior. For a continental interior, where the mapped hazard is low, even an M4 event produces exceedances at some sites. Larger earthquakes produce exceedances at more sites. Thus many exceedances result from small earthquakes, but infrequent large ones may cause very large exceedances. However, for a plate boundary, an M6 event produces exceedance at only a few sites, and an M7 produces them in a larger, but still relatively small, portion of the study area. As reality gives only one history, and a real map involves assumptions about more complicated source geometries and occurrence rates, which are unlikely to be exactly correct and thus will contribute additional scatter, it is hard to assess whether misfit between actual shaking and a map — notably higher-than-mapped shaking — arises by chance or reflects biases in the map. Due to this problem, there are limits to how well we can expect hazard maps to predict future shaking, as well as to our ability to test the performance of a hazard map based on available observations.

Project of Near-Real-Time Generation of ShakeMaps and a New Hazard Map in Austria

NASA Astrophysics Data System (ADS)

Jia, Yan; Weginger, Stefan; Horn, Nikolaus; Hausmann, Helmut; Lenhardt, Wolfgang

2016-04-01

Target-orientated prevention and effective crisis management can reduce or avoid damage and save lives in case of a strong earthquake. To achieve this goal, a project for automatic generated ShakeMaps (maps of ground motion and shaking intensity) and updating the Austrian hazard map was started at ZAMG (Zentralanstalt für Meteorologie und Geodynamik) in 2015. The first goal of the project is set for a near-real-time generation of ShakeMaps following strong earthquakes in Austria to provide rapid, accurate and official information to support the governmental crisis management. Using newly developed methods and software by SHARE (Seismic Hazard Harmonization in Europe) and GEM (Global Earthquake Model), which allows a transnational analysis at European level, a new generation of Austrian hazard maps will be ultimately calculated. More information and a status of our project will be given by this presentation.

A Non-Canonical Initiation Site Is Required for Efficient Translation of the Dendritically Localized Shank1 mRNA

PubMed Central

Studtmann, Katrin; Ölschläger-Schütt, Janin; Buck, Friedrich; Richter, Dietmar; Sala, Carlo; Bockmann, Jürgen; Kindler, Stefan; Kreienkamp, Hans-Jürgen

2014-01-01

Local protein synthesis in dendrites enables neurons to selectively change the protein complement of individual postsynaptic sites. Though it is generally assumed that this mechanism requires tight translational control of dendritically transported mRNAs, it is unclear how translation of dendritic mRNAs is regulated. We have analyzed here translational control elements of the dendritically localized mRNA coding for the postsynaptic scaffold protein Shank1. In its 5′ region, the human Shank1 mRNA exhibits two alternative translation initiation sites (AUG+1 and AUG+214), three canonical upstream open reading frames (uORFs1-3) and a high GC content. In reporter assays, fragments of the 5′UTR with high GC content inhibit translation, suggesting a contribution of secondary structures. uORF3 is most relevant to translation control as it overlaps with the first in frame start codon (AUG+1), directing translation initiation to the second in frame start codon (AUG+214). Surprisingly, our analysis points to an additional uORF initiated at a non-canonical ACG start codon. Mutation of this start site leads to an almost complete loss of translation initiation at AUG+1, demonstrating that this unconventional uORF is required for Shank1 synthesis. Our data identify a novel mechanism whereby initiation at a non-canonical site allows for translation of the main Shank1 ORF despite a highly structured 5′UTR. PMID:24533096

The Supraclavicular Artery Perforator Flap: A Comparative Study of Imaging Techniques Used in Preoperative Mapping.

PubMed

Sheriff, Hemin Oathman; Mahmood, Kawa Abdullah; Hamawandi, Nzar; Mirza, Aram Jamal; Hawas, Jawad; Moreno, Esther Granell; Clavero, Juan Antonio; Hankins, Christopher; Masia, Jaume

2018-05-18

 The supraclavicular artery flap is an excellent flap for head and neck reconstruction. The aim of this study is to assess imaging techniques to define the precise vascular boundaries of this flap.  Six imaging techniques were used for supraclavicular artery mapping in 65 cases; handheld Doppler, triplex ultrasound, computed tomography angiography, magnetic resonance angiography, digital subtraction angiography, and indocyanine green angiography. We checked the site of the perforators, the course of a supraclavicular artery, and anatomical mapping of the supraclavicular artery.  Handheld Doppler identified perforators' sites in 80% of the cases but showed no results for the course of the vessel. Triplex ultrasound identified the site of perforators in 52.9%, and partial mapping of the course of a supraclavicular artery in 64.7% of the cases. Computerized tomography angiography showed the site of perforators in 60%, and the course of supraclavicular artery completely in 45%, and partially in an additional 30%of the cases examined. Magnetic resonance angiography showed negative results for all parameters. Digital subtraction angiography showed the partial course of a supraclavicular artery in 62.5%, but showed no perforators. Indocyanine green angiography showed the site of perforators in 60% and a partial course of supraclavicular artery distal to perforators in 60%.Anatomical mapping of the vessel was possible with computerized tomography angiogram completely in 45%, and partially in 30%, and was also possible with indocyanine green angiography partially in 60%.  Computerized tomography angiography showed best results in the mapping of the supraclavicular artery, but with an inability to define the perforator perfusion territories, and also with risks of irradiation, while indocyanine green angiography is a good alternative as it could precisely map the superficial course of the artery and angiosomes, with no radiation exposure. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

GIS walking maps to promote physical activity in low-income public housing communities: a qualitative examination.

PubMed

McNeill, Lorna H; Emmons, Karen

2012-01-01

Walking is the most commonly reported leisure-time activity. Members of racial/ethnic minority groups and people of low socioeconomic status disproportionately live in urban environments that are perceived to be unsafe, thereby reducing opportunities for engaging in walking. We examined the use of walking maps for increasing physical activity (PA) among low-income residents of public housing sites in Boston, Massachusetts. PA facilities, local businesses, and destinations in a walkable half-mile radius of the housing community were identified and plotted on maps by using geographic information systems technology. Four focus groups (n = 24) were conducted to learn how the walking maps were used by the residents and to understand map features that promoted use. Maps were used by participants to increase their PA, and use of the maps increased participants' awareness of community resources. Maps changed participants' perception of distances and were discussed as a means of fostering a sense of community. Use of the maps also increased participants' awareness of neighborhood incivilities. Barriers to map use were difficulty in interpreting the maps and lack of access to the maps. Walking maps that display PA opportunities and resources may be useful in increasing walking among residents of public housing sites.

A Multi-Sensor Approach to Enhance the Prediction of Mangrove Biophysical Characteristics in Chilika Lagoon and Bhitarkanika Wildlife Sanctuary, Odisha, India

NASA Astrophysics Data System (ADS)

Kumar, A.; Bledsoe, R.; Mishra, D. R.; Cameron, C.; Dahal, S.; Remillard, C.; Stone, A.; Stupp, P.

2017-12-01

Mangroves, one of the most productive ecosystems on Earth, play a major role in coastal ecosystem processes from mitigating erosion to acting as a barrier against tidal and storm surges associated with tropical cyclones. India has about 5 % of the world's mangrove vegetation, and over half of which is found along the east coast of the country. Chilika Lagoon and Bhitarkanika Wildlife Sanctuary are Ramsar sites of international wetland importance, situated in the state of Odisha along the east coast of India. Chilika Lagoon holds three small, but distinct mangrove patches, while Bhitarkanika Wildlife Sanctuary has several large, dense patches of mangroves. There is growing concern for the effective management and conservation of these mangrove forests. This study demonstrated the use of a suite of satellite data (Terra, Landsat, and Sentinel-1) for meeting the following objectives: 1. Derive a long-term spatio-temporal phenological maps of the biophysical parameters (chlorophyll, leaf area index, gross primary productivity, and evapotranspiration); 2. Analyze long-term spatio-temporal variability of physical and meteorological parameters; 3. Document decadal changes in mangroves area estimates starting from 1995 to 2017 using Landsat and radar data. The time series developed in this study revealed a phenological pattern for mangrove biophysical characteristics. Historical analysis of land cover maps indicated decrease in dense mangrove area and increase in open mangrove area and fragmentation. The results of this study will be used as an efficient biophysical mapping and monitoring protocol for mangrove forests in restoration decision-making.

Open data for water-related operational services, the SWITCH-ON approach

NASA Astrophysics Data System (ADS)

Mazzoli, Paolo; Bagli, Stefano; Valerio, Luzzi; Broccoli, Davide; Piccinini, Francesca

2017-04-01

Recently, a collaborative project started called SWITCH-ON (EU FP7 project No 603587) coordinated by SMHI (http://water-switch-on.eu/) as part of the contemporary European movement imposed by the INSPIRE directive and the Open Data Strategy. Among It's R&D activities GECOsistema develops and expands inside SWITCH-ON a set of online services to tackle major water related issues, from reservoir and irrigation supply, to hydrological change adaptation and hydropower potential mapping. Here we present major releases of APRIL, HyCAW and High-resolution European HydroPower Atlas; all of which make intense use of open data. APRIL is a tool for seasonal run-off forecasts, that takes advantage of open datasets or low-cost data and performs forecasts through calibrated machine learning algorithms. HyCAW is a wizard that supports the assessment of adaptation options to cope with change in the temporal distribution of water availability as well as in the total water quantity. EU HPA provides all relevant information necessary to appraise the feasibility of a micro-hydropower plant at a specific site, taking into account hydrological as well as technical and economic factors. All the tools share a common vision of the project to address water concerns and currently untapped potential of open data for improved water management across the EU. Users are guided through a Web GIS interface, created using open source Web Mapping Applications, Open-Layers and Map Server, to explore available hydrological information in the area of interest, plot available data, perform analysis, and get reports and statistics.

Mapping Ecosystem Services in the Jordan Valley, Jordan

NASA Astrophysics Data System (ADS)

Luz, Ana; Marques, Ana; Ribeiro, Inês; Alho, Maria; Catarina Afonso, Ana; Almeida, Erika; Branquinho, Cristina; Talozi, Samer; Pinho, Pedro

2016-04-01

In the last decade researchers started using ecosystem services as a new framework to understand the relationships between environment and society. Habitat quality and water quality are related with ecosystem services regulation and maintenance, or even provision. According to the Common International Classification of Ecosystem Services (CICES) both habitat quality and water quality are associated with lifecycle maintenance, habitat and gene pool protection, and water conditions, among others. As there is increased pressure on habitats and rivers especially for agricultural development, mapping and evaluating habitat and water quality has important implications for resource management and conservation, as well as for rural development. Here, we model and map habitat and water quality in the Jordan Valley, Jordan. In this study, we aim to identify and analyse ecosystem services both through 1) habitat quality and 2) water quality modelling using InVest, an integrated valuation of ecosystem services and tradeoffs. The data used in this study mainly includes the LULC, Jordan River watershed and main threats and pollutants in the study area, such as agriculture, industry, fish farms and urbanization. Results suggest a higher pressure on natural habitats in the Northern region of the Jordan Valley, where industry is dominant. Agriculture is present along the Jordan Valley and limits the few natural forested areas. Further, water pollution is mainly concentrated in disposal sites due to the low flow of the Jordan River. Our results can help to identify areas where natural resources and water resource management is most needed in the Jordan Valley. Acknowledgements: Transbasin FP7 project

Mapping polycyclic aromatic hydrocarbon and total toxicity equivalent soil concentrations by visible and near-infrared spectroscopy.

PubMed

Okparanma, Reuben N; Coulon, Frederic; Mayr, Thomas; Mouazen, Abdul M

2014-09-01

In this study, we used data from spectroscopic models based on visible and near-infrared (vis-NIR; 350-2500 nm) diffuse reflectance spectroscopy to develop soil maps of polycyclic aromatic hydrocarbons (PAHs) and total toxicity equivalent concentrations (TTEC) of the PAH mixture. The TTEC maps were then used for hazard assessment of three petroleum release sites in the Niger Delta province of Nigeria (5.317°N, 6.467°E). As the paired t-test revealed, there were non-significant (p > 0.05) differences between soil maps of PAH and TTEC developed with chemically measured and vis-NIR-predicted data. Comparison maps of PAH showed a slight to moderate agreement between measured and predicted data (Kappa coefficient = 0.19-0.56). Using proposed generic assessment criteria, hazard assessment showed that the degree of action for site-specific risk assessment and/or remediation is similar for both measurement methods. This demonstrates that the vis-NIR method may be useful for monitoring hydrocarbon contamination in a petroleum release site. Copyright © 2014 Elsevier Ltd. All rights reserved.

Flood-inundation maps for the Scioto River at La Rue, Ohio

USGS Publications Warehouse

Whitehead, Matthew

2015-08-26

Digital flood-inundation maps for a 3-mile (mi) reach of the Scioto River that extends about 1/2 mi upstream and 1/2 mi downstream of the corporate boundary for La Rue, Ohio, were created by the U.S. Geological Survey (USGS) in cooperation with the Village of La Rue, Marion County Commissioners, Montgomery Township, and Marion County Scioto River Conservancy. The flood-inundation maps show estimates of the areal extent and depth of flooding correspond ing to selected water levels (stages) at the USGS streamgage on the Scioto River at La Rue (station number 03217500). The maps can be accessed through the USGS Flood Inundation Mapping Science Web site at http://water.usgs.gov/osw/flood_ inundation/ . Near-real-time stages at this streamgage can be obtained from the USGS National Water Information System at http://waterdata.usgs.gov/oh/nwis/uv/?site_no=03217500 or the National Weather Service (NWS) Advanced Hydro - logic Prediction Service at http://water.weather.gov/ahps2/ hydrograph.php?wfo=cle&gage=LARO1 , which also forecasts flood hydrographs at this site.

Introduction of digital soil mapping techniques for the nationwide regionalization of soil condition in Hungary; the first results of the DOSoReMI.hu (Digital, Optimized, Soil Related Maps and Information in Hungary) project

NASA Astrophysics Data System (ADS)

Pásztor, László; Laborczi, Annamária; Szatmári, Gábor; Takács, Katalin; Bakacsi, Zsófia; Szabó, József; Dobos, Endre

2014-05-01

Due to the former soil surveys and mapping activities significant amount of soil information has accumulated in Hungary. Present soil data requirements are mainly fulfilled with these available datasets either by their direct usage or after certain specific and generally fortuitous, thematic and/or spatial inference. Due to the more and more frequently emerging discrepancies between the available and the expected data, there might be notable imperfection as for the accuracy and reliability of the delivered products. With a recently started project (DOSoReMI.hu; Digital, Optimized, Soil Related Maps and Information in Hungary) we would like to significantly extend the potential, how countrywide soil information requirements could be satisfied in Hungary. We started to compile digital soil related maps which fulfil optimally the national and international demands from points of view of thematic, spatial and temporal accuracy. The spatial resolution of the targeted countrywide, digital, thematic maps is at least 1:50.000 (approx. 50-100 meter raster resolution). DOSoReMI.hu results are also planned to contribute to the European part of GSM.net products. In addition to the auxiliary, spatial data themes related to soil forming factors and/or to indicative environmental elements we heavily lean on the various national soil databases. The set of the applied digital soil mapping techniques is gradually broadened incorporating and eventually integrating geostatistical, data mining and GIS tools. In our paper we will present the first results. - Regression kriging (RK) has been used for the spatial inference of certain quantitative data, like particle size distribution components, rootable depth and organic matter content. In the course of RK-based mapping spatially segmented categorical information provided by the SMUs of Digital Kreybig Soil Information System (DKSIS) has been also used in the form of indicator variables. - Classification and regression trees (CART) were used to improve the spatial resolution of category-type soil maps (thematic downscaling), like genetic soil type and soil productivity maps. The approach was justified by the fact that certain thematic soil maps are not available in the required scale. Decision trees were applied for the understanding of the soil-landscape models involved in existing soil maps, and for the post-formalization of survey/compilation rules. The relationships identified and expressed in decision rules made the creation of spatially refined maps possible with the aid of high resolution environmental auxiliary variables. Among these co-variables, a special role was played by larger scale spatial soil information with diverse attributes. As a next step, the testing of random forests for the same purposes has been started. - Due to the simultaneous richness of available Hungarian legacy soil data, spatial inference methods and auxiliary environmental information, there is a high versatility of possible approaches for the compilation of a given soil (related) map. This suggests the opportunity of optimization. For the creation of an object specific soil (related) map with predefined parameters (resolution, accuracy, reliability etc.) one might intend to identify the optimum set of soil data, method and auxiliary co-variables optimized for the resources (data costs, computation requirements etc.). The first findings on the inclusion and joint usage of spatial soil data as well as on the consistency of various evaluations of the result maps will be also presented. Acknowledgement: Our work has been supported by the Hungarian National Scientific Research Foundation (OTKA, Grant No. K105167).

76 FR 7226 - Commercial Wind Lease Issuance and Site Characterization Activities; Atlantic Outer Continental...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-09

... Interior's (DOI) ``Smart from the Start'' wind energy initiative, to identify areas for wind energy leasing... November 23, 2010, Secretary of the Interior Ken Salazar announced the ``Smart from the Start'' renewable... the ``Smart from the Start'' initiative can be found at http://www.boemre.gov/offshore/RenewableEnergy...

Environmental variables across Pan troglodytes study sites correspond with the carbon, but not the nitrogen, stable isotope ratios of chimpanzee hair.

PubMed

Schoeninger, Margaret J; Most, Corinna A; Moore, Jim J; Somerville, Andrew D

2016-10-01

Diet influences the stable isotope ratios of carbon and nitrogen (δ(13) C and δ(15) N values) in animal tissue; but here we explore the influences of particular aspects of the local environment on those values in chimpanzees (Pan troglodytes). In this article we present new δ(13) C and δ(15) N values in Gombe chimpanzees using hairs collected from night nests in 1989. Then, we explore the influence of environmental factors by comparing our Gombe data to those from eight additional Pan study sites with previously published stable isotope data. We compare chimpanzee δ(13) Chair and δ(15) Nhar values to specific characteristics of local site ecology (biome and ecoregion) and to local Mean Annual Precipitation (MAP) to test hypotheses based on known effects of these variables on the δ(13) C and δ(15) N values in plant tissues. The comparison shows that hair from chimpanzees living in savanna sites with lower MAP have higher δ(13) Chair values than do chimpanzees living in woodland and forested sites with higher MAP. These results demonstrate the potential of using δ(13) C values in primate tissue to indicate aspects of their local ecology in cases where the ecology is uncertain, such as samples collected early in the last century and in fossil hominins. In contrast to expectations, however, chimpanzee δ(15) Nhair values from some savanna sites with lower MAP are lower, not higher, than those living in more forested areas with higher MAP. It is likely that diet selectivity by chimpanzees affects δ(15) Nhair values to a greater extent than does the influence of precipitation on plants. Am. J. Primatol. 78:1055-1069, 2016. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

MOLA-Based Landing Site Characterization

NASA Technical Reports Server (NTRS)

Duxbury, T. C.; Ivanov, A. B.

2001-01-01

The Mars Global Surveyor (MGS) Mars Orbiter Laser Altimeter (MOLA) data provide the basis for site characterization and selection never before possible. The basic MOLA information includes absolute radii, elevation and 1 micrometer albedo with derived datasets including digital image models (DIM's illuminated elevation data), slopes maps and slope statistics and small scale surface roughness maps and statistics. These quantities are useful in downsizing potential sites from descent engineering constraints and landing/roving hazard and mobility assessments. Slope baselines at the few hundred meter level and surface roughness at the 10 meter level are possible. Additionally, the MOLA-derived Mars surface offers the possibility to precisely register and map project other instrument datasets (images, ultraviolet, infrared, radar, etc.) taken at different resolution, viewing and lighting geometry, building multiple layers of an information cube for site characterization and selection. Examples of direct MOLA data, data derived from MOLA and other instruments data registered to MOLA arc given for the Hematite area.

The use of unmanned aerial systems for the mapping of legacy uranium mines.

PubMed

Martin, P G; Payton, O D; Fardoulis, J S; Richards, D A; Scott, T B

2015-05-01

Historical mining of uranium mineral veins within Cornwall, England, has resulted in a significant amount of legacy radiological contamination spread across numerous long disused mining sites. Factors including the poorly documented and aged condition of these sites as well as the highly localised nature of radioactivity limit the success of traditional survey methods. A newly developed terrain-independent unmanned aerial system [UAS] carrying an integrated gamma radiation mapping unit was used for the radiological characterisation of a single legacy mining site. Using this instrument to produce high-spatial-resolution maps, it was possible to determine the radiologically contaminated land areas and to rapidly identify and quantify the degree of contamination and its isotopic nature. The instrument was demonstrated to be a viable tool for the characterisation of similar sites worldwide. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Utilization of LANDSAT imagery for mapping vegetation on the millionth scale

NASA Technical Reports Server (NTRS)

Williams, D. L.; Coiner, J. C.

1975-01-01

A series of test sites were examined to determine if the information content of the LANDSAT imagery that may be obtained of these sites is sufficient to permit their mapping according to the vegetation classification system recently published by Unesco. These sites include examples from the humid tropics, arid and semi-arid subtropics and temperature zones: Western Highlands of Papua New Guinea, Mindoro Island in the Philippines, Great Smoky Mountains of the southeastern United States, East Tennessee Valley, interior of Western Australia, northeastern Uganda, and south-central Kansas. The results of the experiment were presented in the form of vegetation maps and annotated images which serve to illustrate the detectability of various formations. It was concluded that, for the test sites examined, the formations of the Unesco vegetation classification can be satisfactorily distinguished on LANDSAT MSS images, especially when used as color composites and judiciously chosen as to season.

e23D: database and visualization of A-to-I RNA editing sites mapped to 3D protein structures.

PubMed

Solomon, Oz; Eyal, Eran; Amariglio, Ninette; Unger, Ron; Rechavi, Gidi

2016-07-15

e23D, a database of A-to-I RNA editing sites from human, mouse and fly mapped to evolutionary related protein 3D structures, is presented. Genomic coordinates of A-to-I RNA editing sites are converted to protein coordinates and mapped onto 3D structures from PDB or theoretical models from ModBase. e23D allows visualization of the protein structure, modeling of recoding events and orientation of the editing with respect to nearby genomic functional sites from databases of disease causing mutations and genomic polymorphism. http://www.sheba-cancer.org.il/e23D CONTACT: oz.solomon@live.biu.ac.il or Eran.Eyal@sheba.health.gov.il. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Mapping broom snakeweed through image analysis of color-infrared photography and digital imagery.

PubMed

Everitt, J H; Yang, C

2007-11-01

A study was conducted on a south Texas rangeland area to evaluate aerial color-infrared (CIR) photography and CIR digital imagery combined with unsupervised image analysis techniques to map broom snakeweed [Gutierrezia sarothrae (Pursh.) Britt. and Rusby]. Accuracy assessments performed on computer-classified maps of photographic images from two sites had mean producer's and user's accuracies for broom snakeweed of 98.3 and 88.3%, respectively; whereas, accuracy assessments performed on classified maps from digital images of the same two sites had mean producer's and user's accuracies for broom snakeweed of 98.3 and 92.8%, respectively. These results indicate that CIR photography and CIR digital imagery combined with image analysis techniques can be used successfully to map broom snakeweed infestations on south Texas rangelands.

37. Photo copy of map, (original in Forest Service Office, ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

37. Photo copy of map, (original in Forest Service Office, Elkins, WV, 'Blister Rust Survey Map), 1930. PARSONS NURSERY SITE PLAN - Parsons Nursery, South side of U.S. Route 219, Parsons, Tucker County, WV

Development and testing of a contamination potential mapping system for a portion of the General Separations Area, Savannah River Site, South Carolina

USGS Publications Warehouse

Rine, J.M.; Berg, R.C.; Shafer, J.M.; Covington, E.R.; Reed, J.K.; Bennett, C.B.; Trudnak, J.E.

1998-01-01

A methodology was developed to evaluate and map the contamination potential or aquifer sensitivity of the upper groundwater flow system of a portion of the General Separations Area (GSA) at the Department of Energy's Savannah River Site (SRS) in South Carolina. A Geographic Information System (GIS) was used to integrate diverse subsurface geologic data, soils data, and hydrology utilizing a stack-unit mapping approach to construct mapping layers. This is the first time that such an approach has been used to delineate the hydrogeology of a coastal plain environment. Unit surface elevation maps were constructed for the tops of six Tertiary units derived from over 200 boring logs. Thickness or isopach maps were created for five hydrogeologic units by differencing top and basal surface elevations. The geologic stack-unit map was created by stacking the five isopach maps and adding codes for each stack-unit polygon. Stacked-units were rated according to their hydrogeologic properties and ranked using a logarithmic approach (utility theory) to establish a contamination potential index. Colors were assigned to help display relative importance of stacked-units in preventing or promoting transport of contaminants. The sensitivity assessment included the effects of surface soils on contaminants which are particularly important for evaluating potential effects from surface spills. Hydrogeologic/hydrologic factors did not exhibit sufficient spatial variation to warrant incorporation into contamination potential assessment. Development of this contamination potential mapping system provides a useful tool for site planners, environmental scientists, and regulatory agencies.A methodology was developed to evaluate and map the contamination potential or aquifer sensitivity of the upper groundwater flow system of a portion of the General Separations Area (GSA) at the Department of Energy's Savannah River Site (SRS) in South Carolina. A Geographic Information System (GIS) was used to integrate diverse subsurface geologic data, soils data, and hydrology utilizing a stack-unit mapping approach to construct mapping layers. This is the first time that such an approach has been used to delineate the hydrogeology of a coastal plain environment. Unit surface elevation maps were constructed for the tops of six Tertiary units derived from over 200 boring logs. Thickness or isopach maps were created for five hydrogeologic units by differencing top and basal surface elevations. The geologic stack-unit map was created by stacking the five isopach maps and adding codes for each stack-unit polygon. Stacked-units were rated according to their hydrogeologic properties and ranked using a logarithmic approach (utility theory) to establish a contamination potential index. Colors were assigned to help display relative importance of stacked-units in preventing or promoting transport of contaminants. The sensitivity assessment included the effects of surface soils on contaminants which are particularly important for evaluating potential effects from surface spills. Hydrogeologic/hydrologic factors did not exhibit sufficient spatial variation to warrant incorporation into contamination potential assessment. Development of this contamination potential mapping system provides a useful tool for site planners, environmental scientists, and regulatory agencies.

Comparison of RS/GIS analysis with classic mapping approaches for siting low-yield boreholes for hand pumps in crystalline terrains. An application to rural communities of the Caimbambo province, Angola

NASA Astrophysics Data System (ADS)

Martín-Loeches, Miguel; Reyes-López, Jaime; Ramírez-Hernández, Jorge; Temiño-Vela, Javier; Martínez-Santos, Pedro

2018-02-01

In poverty-stricken regions of Sub-Saharan Africa, groundwater for supply is often obtained by means of hand pumps, which means that low-yield boreholes are acceptable. However, boreholes are often sited without sufficient hydrogeological information due to budget constraints, which leads to high failure rates. Cost-effective techniques for borehole siting need to be developed in order to maximize the success rate. In regions underlain by granite, weathered formations are usually targeted for drilling, as these are generally presented as a better cost-benefit ratio than the fractured basement. Within this context, this research focuses on a granite region of Angola. A comparison of two mapping techniques for borehole siting-groundwater prospect is presented. A classic hydrogeomorphological map was developed first based on aerial photographs, field mapping and a geophysical survey. This map represents a considerable time investment and was developed by qualified technicians. The second map (RS/GIS) is considerably simpler and more cost-effective. It was developed by the integration in a GIS platform of six maps of equal importance-slope, drainage density, vegetation vigor, presence of clay in the soil, lineaments and rock outcrops-prepared from Landsat 8 imagery and a Digital Elevation Model (DEM). Similar results were obtained in both cases. By means of a supervised classification of Landsat images, RS/GIS analysis allows for the identification of granitic outcrops, house clusters and sandy alluvial valleys. This in turn allows for the delineation of low-interest or contamination-prone areas, thus contributing additional qualitative information. The position of a well that is going to be powered by a handpump is chosen also upon social and local matters as the distance to the stakeholders, information that are not difficult to integrate in the GIS. Although the second map needs some field inputs (i.e. surveys to determine the thickness of the weathered pack), results show that RS/GIS analyses such as this one provide a valuable and cost-effective alternative for siting low-yield boreholes in remote regions.

Effectiveness of nest site restoration for the endangered northern map turtle : report 2 : use of artificial nesting sites and wildlife exclusion fence to enhance nesting success.

DOT National Transportation Integrated Search

2016-10-01

The Northern Map Turtle, Graptemys geographica, is a Maryland state endangered species, found only in the lower Susquehanna River in Maryland. The only area where nests of this species are not heavily impacted by predators occurs in the town of Port ...

OriDB, the DNA replication origin database updated and extended.

PubMed

Siow, Cheuk C; Nieduszynska, Sian R; Müller, Carolin A; Nieduszynski, Conrad A

2012-01-01

OriDB (http://www.oridb.org/) is a database containing collated genome-wide mapping studies of confirmed and predicted replication origin sites. The original database collated and curated Saccharomyces cerevisiae origin mapping studies. Here, we report that the OriDB database and web site have been revamped to improve user accessibility to curated data sets, to greatly increase the number of curated origin mapping studies, and to include the collation of replication origin sites in the fission yeast Schizosaccharomyces pombe. The revised database structure underlies these improvements and will facilitate further expansion in the future. The updated OriDB for S. cerevisiae is available at http://cerevisiae.oridb.org/ and for S. pombe at http://pombe.oridb.org/.

Measuring Physical Activity Intensity

MedlinePlus Videos and Cool Tools

... Skip directly to site content Start of Search Controls Search Form Controls Cancel Submit Search the CDC CDC A-Z ... V W X Y Z # Start of Search Controls Search Form Controls Search The CDC Cancel Submit ...

Potential effects of existing and proposed groundwater withdrawals on water levels and natural groundwater discharge in Snake Valley and surrounding areas, Utah and Nevada

USGS Publications Warehouse

Masbruch, Melissa D.; Brooks, Lynette E.

2017-04-14

Several U.S. Department of Interior (DOI) agencies are concerned about the cumulative effects of groundwater development on groundwater resources managed by, and other groundwater resources of interest to, these agencies in Snake Valley and surrounding areas. The new water uses that potentially concern the DOI agencies include 12 water-right applications filed in 2005, totaling approximately 8,864 acre-feet per year. To date, only one of these applications has been approved and partially developed. In addition, the DOI agencies are interested in the potential effects of three new water-right applications (UT 18-756, UT 18-758, and UT 18-759) and one water-right change application (UT a40687), which were the subject of a water-right hearing on April 19, 2016.This report presents a hydrogeologic analysis of areas in and around Snake Valley to assess potential effects of existing and future groundwater development on groundwater resources, specifically groundwater discharge sites, of interest to the DOI agencies. A previously developed steady-state numerical groundwater-flow model was modified to transient conditions with respect to well withdrawals and used to quantify drawdown and capture (withdrawals that result in depletion) of natural discharge from existing and proposed groundwater withdrawals. The original steady-state model simulates and was calibrated to 2009 conditions. To investigate the potential effects of existing and proposed groundwater withdrawals on the groundwater resources of interest to the DOI agencies, 10 withdrawal scenarios were simulated. All scenarios were simulated for periods of 5, 10, 15, 30, 55, and 105 years from the start of 2010; additionally, all scenarios were simulated to a new steady state to determine the ultimate long-term effects of the withdrawals. Capture maps were also constructed as part of this analysis. The simulations used to develop the capture maps test the response of the system, specifically the reduction of natural discharge, to future stresses at a point in the area represented by the model. In this way, these maps can be used as a tool to determine the source of water to, and potential effects at specific areas from, future well withdrawals.Downward trends in water levels measured in wells indicate that existing groundwater withdrawals in Snake Valley are affecting water levels. The numerical model simulates similar downward trends in water levels; simulated drawdowns in the model, however, are generally less than observed water-level declines. At the groundwater discharge sites of interest to the DOI agencies, simulated drawdowns from existing well withdrawals (projected into the future) range from 0 to about 50 feet. Following the addition of the proposed withdrawals, simulated drawdowns at some sites increase by 25 feet. Simulated drawdown resulting from the proposed withdrawals began in as few as 5 years after 2014 at several of the sites. At the groundwater discharge sites of interest to the DOI agencies, simulated capture of natural discharge resulting from the existing withdrawals ranged from 0 to 87 percent. Following the addition of the proposed withdrawals, simulated capture at several of the sites reached 100 percent, indicating that groundwater discharge at that site would cease. Simulated capture following the addition of the proposed withdrawals increased in as few as 5 years after 2014 at several of the sites.

The uses of ERTS-1 imagery in the analysis of landscape change. [agriculture, strip mining forests, urban-suburban growth, and flooding in Tennessee, Kentucky, Mississippi, and Alabama

NASA Technical Reports Server (NTRS)

Rehder, J. B. (Principal Investigator)

1974-01-01

The author has identified the following significant results. The analysis of strip mining from ERTS-1 data has resulted in the mapping of landscape changes for the Cumberland Plateau Test Site. Several mapping experiments utilizing ERTS-1 data have been established for the mapping of state-wide land use regions. The first incorporates 12 frames of ERTS-1 imagery for the generalized thematic mapping of forest cover for the state of Tennessee. In another mapping effort, 14 ERTS-1 images have been analyzed for plowed ground signatures to produce a map of agricultural regions for Tennessee, Kentucky, and the northern portions of Mississippi and Alabama. Generalized urban land use categories and transportation networks have been determined from ERTS-1 imagery for the Knoxville Test Site. Finally, through the analysis of ERTS-1 imagery, short-lived phenomena such as the 1973 spring floods on the Mississippi River in western Tennessee, have been detected, monitored, and mapped.

Inland area contingency plan and maps for Pennsylvania (on CD-ROM). Data file

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1996-12-01

EPA Region III has assembled on this CD a multitude of environmental data, in both visual and textual formats. While targeted for Facility Response Planning under the Oil Pollution Act of 1990, this information will prove helpful to anyone in the environmental arena. Specifically, the CD will aid contingency planning and emergency response personnel. Combining innovative GIS technology with EPA`s state-specific data allows you to display maps, find and identify map features, look at tabular information about map features, and print out maps. The CD was designed to be easy to use and incorporates example maps as well as helpmore » sections describing the use of the environmental data on the CD, and introduces you to the IACP Viewer and its capabilities. These help features will make it easy for you to conduct analysis, produce maps, and browse the IACP Plan. The IACP data are included in two formats: shapefiles, which can be viewed with the IACP Viewer or ESRI`s ArcView software (Version 2.1 or higher), and ARC/INFO export files, which can be imported into ARC/INFO or converted to other GIS data formats. Point Data Sources: Sensitive Areas, Surface Drinking Water Intakes, Groundwater Intakes, Groundwater Supply Facilities, NPL (National Priority List) Sites, FRP (Facility Response Plan) Facilities, NPDES (National Pollutant Discharge Elimination System) Facilities, Hospitals, RCRA (Resource Conservation and Recovery Act) Sites, TRI (Toxic Release Inventory) Sites, CERCLA (Comprehensive Environmental Response, Compensation, and Liability Act) Sites Line Data Sources: TIGER Roads, TIGER Railroads, TIGER Hydrography, Pipelines Polygon Data Sources: State Boundaries, County Boundaries, Watershed Boundaries (8-digit HUC), TIGER Hydrography, Public Lands, Populated Places, IACP Boundaries, Coast Guard Boundaries, Forest Types, US Congressional Districts, One-half Mile Buffer of Surface Drinking Water Intakes.« less

Inland area contingency plan and maps for Virginia (on CD-ROM). Data file

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1996-12-01

EPA Region III has assembled on this CD a multitude of environmental data, in both visual and textual formats. While targeted for Facility Response Planning under the Oil Pollution Act of 1990, this information will prove helpful to anyone in the environmental arena. Specifically, the CD will aid contingency planning and emergency response personnel. Combining innovative GIS technology with EPA`s state-specific data allows you to display maps, find and identify map features, look at tabular information about map features, and print out maps. The CD was designed to be easy to use and incorporates example maps as well as helpmore » sections describing the use of the environmental data on the CD, and introduces you to the IACP Viewer and its capabilities. These help features will make it easy for you to conduct analysis, produce maps, and browse the IACP Plan. The IACP data are included in two formats: shapefiles, which can be viewed with the IACP Viewer or ESRI`s ArcView software (Version 2.1 or higher), and ARC/INFO export files, which can be imported into ARC/INFO or converted to other GIS data formats. Point Data Sources: Sensitive Areas, Surface Drinking Water Intakes, Groundwater Intakes, Groundwater Supply Facilities, NPL (National Priority List) Sites, FRP (Facility Response Plan) Facilities, NPDES (National Pollutant Discharge Elimination System) Facilities, Hospitals, RCRA (Resource Conservation and Recovery Act) Sites, TRI (Toxic Release Inventory) Sites, CERCLA (Comprehensive Environmental Response, Compensation, and Liability Act) Sites Line Data Sources: TIGER Roads, TIGER Railroads, TIGER Hydrography, Pipelines Polygon Data Sources: State Boundaries, County Boundaries, Watershed Boundaries (8-digit HUC), TIGER Hydrography, Public Lands, Populated Places, IACP Boundaries, Coast Guard Boundaries, Forest Types, US Congressional Districts, One-half Mile Buffer of Surface Drinking Water Intakes.« less

Seismic design parameters - A user guide

USGS Publications Warehouse

Leyendecker, E.V.; Frankel, A.D.; Rukstales, K.S.

2001-01-01

The 1997 NEHRP Recommended Provisions for Seismic Regulations for New Buildings (1997 NEHRP Provisions) introduced seismic design procedure that is based on the explicit use of spectral response acceleration rather than the traditional peak ground acceleration and/or peak ground velocity or zone factors. The spectral response accelerations are obtained from spectral response acceleration maps accompanying the report. Maps are available for the United States and a number of U.S. territories. Since 1997 additional codes and standards have also adopted seismic design approaches based on the same procedure used in the NEHRP Provisions and the accompanying maps. The design documents using the 1997 NEHRP Provisions procedure may be divided into three categories -(1) Design of New Construction, (2) Design and Evaluation of Existing Construction, and (3) Design of Residential Construction. A CD-ROM has been prepared for use in conjunction with the design documents in each of these three categories. The spectral accelerations obtained using the software on the CD are the same as those that would be obtained by using the maps accompanying the design documents. The software has been prepared to operate on a personal computer using a Windows (Microsoft Corporation) operating environment and a point and click type of interface. The user can obtain the spectral acceleration values that would be obtained by use of the maps accompanying the design documents, include site factors appropriate for the Site Class provided by the user, calculate a response spectrum that includes the site factor, and plot a response spectrum. Sites may be located by providing the latitude-longitude or zip code for all areas covered by the maps. All of the maps used in the various documents are also included on the CDROM

Challenges, successes and patterns of enrolment in the INSIGHT Strategic Timing of AntiRetroviral Treatment (START) trial.

PubMed

Grarup, J; Rappoport, C; Engen, N W; Carey, C; Hudson, F; Denning, E; Sharma, S; Florence, E; Vjecha, M J

2015-04-01

The aim of this report is to describe the challenges, successes and patterns of enrolment in the Strategic Timing of AntiRetroviral Treatment (START) study. START is a collaboration of many partners with central coordination provided by the protocol team, the statistical and data management centre (SDMC), the International Network for Strategic Initiatives in Global HIV Trials (INSIGHT) network leadership, international coordinating centres and site coordinating centres. The SDMC prepared reports on study accrual, baseline characteristics and site performance that allowed monitoring of enrolment and data quality and helped to ensure the successful enrolment of this large international trial. We describe the pattern of enrolment and challenges faced during the enrolment period of the trial. An initial pilot phase began in April 2009 and established feasibility of accrual at 101 sites. In August 2010, funding approval for an expanded definitive phase led to the successful accrual of 4688 participants from 215 sites in 35 countries by December 2013. Challenges to accrual included regulatory delays (e.g. national/local ethics approval and drug importation approval) and logistical obstacles (e.g. execution of contracts with pharmaceutical companies, setting up of a central drug repository and translation of participant materials). The personal engagement of investigators, strong central study coordination, and frequent and transparent communication with site investigators, community members and participants were key contributing factors to this success. Accrual into START was completed in a timely fashion despite multiple challenges. This success was attributable to the efforts of site investigators committed to maintaining study equipoise, transparent and responsive study coordination, and community involvement in problem-solving. © 2015 British HIV Association.

Challenges, successes and patterns of enrolment in the INSIGHT Strategic Timing of AntiRetroviral Treatment (START) trial

PubMed Central

Rappoport, C; Engen, NW; Carey, C; Hudson, F; Denning, E; Sharma, S; Florence, E; Vjecha, MJ

2015-01-01

Objectives The aim of this report is to describe the challenges, successes and patterns of enrolment in the Strategic Timing of AntiRetroviral Treatment (START) study. Methods START is a collaboration of many partners with central coordination provided by the protocol team, the statistical and data management centre (SDMC), the International Network for Strategic Initiatives in Global HIV Trials (INSIGHT) network leadership, international coordinating centres and site coordinating centres. The SDMC prepared reports on study accrual, baseline characteristics and site performance that allowed monitoring of enrolment and data quality and helped to ensure the successful enrolment of this large international trial. We describe the pattern of enrolment and challenges faced during the enrolment period of the trial. Results An initial pilot phase began in April 2009 and established feasibility of accrual at 101 sites. In August 2010, funding approval for an expanded definitive phase led to the successful accrual of 4688 participants from 215 sites in 35 countries by December 2013. Challenges to accrual included regulatory delays (e.g. national/local ethics approval and drug importation approval) and logistical obstacles (e.g. execution of contracts with pharmaceutical companies, setting up of a central drug repository and translation of participant materials). The personal engagement of investigators, strong central study coordination, and frequent and transparent communication with site investigators, community members and participants were key contributing factors to this success. Conclusions Accrual into START was completed in a timely fashion despite multiple challenges. This success was attributable to the efforts of site investigators committed to maintaining study equipoise, transparent and responsive study coordination, and community involvement in problem‐solving. PMID:25711319

Earthquake Hazard Class Mapping by Parcel in Las Vegas Valley

NASA Astrophysics Data System (ADS)

Pancha, A.; Pullammanappallil, S.; Louie, J. N.; Hellmer, W. K.

2011-12-01

Clark County, Nevada completed the very first effort in the United States to map earthquake hazard class systematically through an entire urban area. The map is used in development and disaster response planning, in addition to its direct use for building code implementation and enforcement. The County contracted with the Nevada System of Higher Education to classify about 500 square miles including urban Las Vegas Valley, and exurban areas considered for future development. The Parcel Map includes over 10,000 surface-wave array measurements accomplished over three years using Optim's SeisOpt° ReMi measurement and processing techniques adapted for large scale data. These array measurements classify individual parcels on the NEHRP hazard scale. Parallel "blind" tests were conducted at 93 randomly selected sites. The rms difference between the Vs30 values yielded by the blind data and analyses and the Parcel Map analyses is 4.92%. Only six of the blind-test sites showed a difference with a magnitude greater than 10%. We describe a "C+" Class for sites with Class B average velocities but soft surface soil. The measured Parcel Map shows a clearly definable C+ to C boundary on the west side of the Valley. The C to D boundary is much more complex. Using the parcel map in computing shaking in the Valley for scenario earthquakes is crucial for obtaining realistic predictions of ground motions.

Closing the mycetoma knowledge gap.

PubMed

van de Sande, Wendy; Fahal, Ahmed; Ahmed, Sarah Abdalla; Serrano, Julian Alberto; Bonifaz, Alexandro; Zijlstra, Ed

2018-04-01

On 28th May 2016, mycetoma was recognized as a neglected tropical disease by the World Health Organization. This was the result of a 4-year journey starting in February 2013 with a meeting of global mycetoma experts. Knowledge gaps were identified and included the incidence, prevalence, and mapping of mycetoma; the mode of transmission; the development of methods for early diagnosis; and better treatment. In this review, we review the road to recognition, the ISHAM working group meeting in Argentina, and we address the progress made in closing the knowledge gaps since 2013. Progress included adding another 9000 patients to the literature, which allowed us to update the prevalence map on mycetoma. Furthermore, based on molecular phylogeny, species names were corrected and four novel mycetoma causative agents were identified. By mapping mycetoma causative agents an association with Acacia trees was found. For early diagnosis, three different isothermal amplification techniques were developed, and novel antigens were discovered. To develop better treatment strategies for mycetoma patients, in vitro susceptibility tests for the coelomycete agents of black grain mycetoma were developed, and the first randomized clinical trial for eumycetoma started early 2017.

Identification of a starting point of breast skin tears during chicken plucking.

PubMed

Pitcovski, J; Ohana, N; Amzaleg, L; Krispel, S; Bercovich, D; Pinchasov, Y

1997-02-01

A site (STP) was identified on the skin of the chicken, during defeathering in the slaughter house, at which about 90% of breast skin tears started. This site is on the ventral side of the pectoral tract area. There was no difference in location of this site with respect to different commercial lines, sexes, flocks, or time of the day. In order to demonstrate the importance of a small skin tear to ultimate damage, defeathered chickens with a minor tear at a particular site and undamaged defeathered chickens were passed through the defeathering machine a second time. Thirty-six percent of the STP chickens were torn further, but only a small percentage (about 4%) of the undamaged chickens were harmed.

Mapping wetlands in Nova Scotia with multi-beam RADARSAT-2 Polarimetric SAR, optical satellite imagery, and Lidar data

NASA Astrophysics Data System (ADS)

Jahncke, Raymond; Leblon, Brigitte; Bush, Peter; LaRocque, Armand

2018-06-01

Wetland maps currently in use by the Province of Nova Scotia, namely the Department of Natural Resources (DNR) wetland inventory map and the swamp wetland classes of the DNR forest map, need to be updated. In this study, wetlands were mapped in an area southwest of Halifax, Nova Scotia by classifying a combination of multi-date and multi-beam RADARSAT-2 C-band polarimetric SAR (polSAR) images with spring Lidar, and fall QuickBird optical data using the Random Forests (RF) classifier. The resulting map has five wetland classes (open-water/marsh complex, open bog, open fen, shrub/treed fen/bog, swamp), plus lakes and various upland classes. Its accuracy was assessed using data from 156 GPS wetland sites collected in 2012 and compared to the one obtained with the current wetland map of Nova Scotia. The best overall classification was obtained using a combination of Lidar, RADARSAT-2 HH, HV, VH, VV intensity with polarimetric variables, and QuickBird multispectral (89.2%). The classified image was compared to GPS validation sites to assess the mapping accuracy of the wetlands. It was first done considering a group consisting of all wetland classes including lakes. This showed that only 69.9% of the wetland sites were correctly identified when only the QuickBird classified image was used in the classification. With the addition of variables derived from lidar, the number of correctly identified wetlands increased to 88.5%. The accuracy remained the same with the addition of RADARSAT-2 (88.5%). When we tested the accuracy for identifying wetland classes (e.g. marsh complex vs. open bog) instead of grouped wetlands, the resulting wetland map performed best with either QuickBird and Lidar, or QuickBird, Lidar, and RADARSAT-2 (66%). The Province of Nova Scotia's current wetland inventory and its associated wetland classes (aerial-photo interpreted) were also assessed against the GPS wetland sites. This provincial inventory correctly identified 62.2% of the grouped wetlands and only 18.6% of the wetland classes. The current inventory's poor performance demonstrates the value of incorporating a combination of new data sources into the provincial wetland mapping.

An integrated multi criteria approach for landfill siting in a conflicting environmental, economical and socio-cultural area.

PubMed

Eskandari, Mahnaz; Homaee, Mehdi; Mahmodi, Shahla

2012-08-01

Landfill site selection is a complicated multi criteria land use planning that should convince all related stakeholders with different insights. This paper addresses an integrating approach for landfill siting based on conflicting opinions among environmental, economical and socio-cultural expertise. In order to gain optimized siting decision, the issue was investigated in different viewpoints. At first step based on opinion sampling and questionnaire results of 35 experts familiar with local situations, the national environmental legislations and international practices, 13 constraints and 15 factors were built in hierarchical structure. Factors divided into three environmental, economical and socio-cultural groups. In the next step, the GIS-database was developed based on the designated criteria. In the third stage, the criteria standardization and criteria weighting were accomplished. The relative importance weights of criteria and subcriteria were estimated, respectively, using analytical hierarchy process and rank ordering methods based on different experts opinions. Thereafter, by using simple additive weighting method, the suitability maps for landfill siting in Marvdasht, Iran, was evaluated in environmental, economical and socio-cultural visions. The importance of each group of criteria in its own vision was assigned to be higher than two other groups. In the fourth stage, the final suitability map was obtained after crossing three resulted maps in different visions and reported in five suitability classes for landfill construction. This map indicated that almost 1224 ha of the study area can be considered as best suitable class for landfill siting considering all visions. In the last stage, a comprehensive field visit was performed to verify the selected site obtained from the proposed model. This field inspection has confirmed the proposed integrating approach for the landfill siting. Copyright © 2012 Elsevier Ltd. All rights reserved.

Construction, Startup and Operation of a New LLRW Disposal Facility in Andrews County, Texas - 12151

DOE Office of Scientific and Technical Information (OSTI.GOV)

Van Vliet, James A.

2012-07-01

During this last year, Waste Control Specialists LLC (WCS) completed construction and achieved start of operations of a new low level radioactive waste (LLRW) disposal facility in Andrews County Texas. Disposal operations are underway for commercial LLRW, and start up evolutions are in progress for disposal of Department of Energy (DOE) LLRW. The overall approach to construction and start up are presented as well as some of the more significant challenges and how they were addressed to achieve initial operations of the first new commercial low level radioactive waste disposal facility in more than 30 years. The WCS disposal facilitymore » consists of two LLRW disposal cells, one for Texas Compact waste, and a separate disposal cell for DOE waste. Both disposal cells have very robust and unique designs. The cells themselves are constructed entirely in very low permeability red bed clay. The cell liners include a 0.91 meter thick clay liner meeting unprecedented permeability limits, 0.3 meter thick reinforced concrete barriers, as well as the standard geo-synthetic liners. Actions taken to meet performance criteria and install these liners will be discussed. Consistent with this highly protective landfill design, WCS chose to install a zero discharge site water management system. The considerations behind the design and construction of this system will be presented. Other activities essential to successful start of LLRW disposal operations included process and procedure development and refinement, staffing and staff development, and training. Mock ups were built and used for important evolutions and functions. Consistent with the extensive regulation of LLRW operations, engagement with the Texas Commission on Environmental Quality (TCEQ) was continuous and highly interactive. This included daily activity conference calls, weekly coordination calls and numerous topical conference calls and meetings. TCEQ staff and consultants frequently observed specific construction evolutions, such as geological feature mapping of designated excavation faces, disposal cell clay liner installation, disposal cell concrete barrier construction, etc. (author)« less

Aerobiological monitoring and mapping of Ambrosia plants in the province of Parma (northern Italy, southern Po valley), a useful tool for targeted preventive measures.

PubMed

Albertini, R; Ugolotti, M; Ghillani, L; Adorni, M; Vitali, P; Signorelli, C; Pasquarella, C

2017-01-01

Ambrosia is an annual anemophilous weed producing allergenic pollen affecting public health in European countries. In Italy, the most infested region is Lombardy where, in some areas, it is the major cause of hay fever. In the Parma district, until 2007, Ambrosia seemed to be very rare, despite an observed increase of Seasonal Pollen Index (SPI), of pollen peak value and of asthma among ragweed sensitized patients. The aims of this study were to calculate ragweed pollen season and trends from 1996 to 2015, to assess the relationships between pollen season characteristics and selected meteorological data, to map plants in the territory and to evaluate the presence of beetle Ophraella communa (Ophraella), known as an eater of Ambrosia leaves. The following pollination parameters: start, end, duration, peak concentration date, peak values, SPI and the following climatic parameters: temperature, relative humidity, rainfall, were analyzed. The ragweed plants sites were mapped and the presence of Ophraella was assessed during naturalistic activities. Significant SPI and pollen peak value increase until 2011 were observed, but recently, 2012-2015 vs 2009-2011, a strong reduction (about 50%) of these parameters was observed. The spring average air temperature increased significantly. The results of the correlation analysis showed Ambrosia season characteristics significantly related. We identified the sites source of Ambrosia, even downtown at the confluence between Parma and Baganza rivers. Ophraella was observed for the first time in 2014. The results showed the spread of ragweed plants over the territory and the risk of allergy increase that ragweed could cause. It remains to evaluate the role of the Ophraella in the reduction of Ambrosia pollen concentration. It is important to consider the potential risk Ophraella may represent for sunflower and other taxonomically related crop plants and other native and exotic species. The lack of initiatives by the Health Authorities to prevent and to contrast the spread of Ambrosia in the Parma area could cause public health consequences and an increase in health expenditures.

Brain/MINDS: brain-mapping project in Japan

PubMed Central

Okano, Hideyuki; Miyawaki, Atsushi; Kasai, Kiyoto

2015-01-01

There is an emerging interest in brain-mapping projects in countries across the world, including the USA, Europe, Australia and China. In 2014, Japan started a brain-mapping project called Brain Mapping by Integrated Neurotechnologies for Disease Studies (Brain/MINDS). Brain/MINDS aims to map the structure and function of neuronal circuits to ultimately understand the vast complexity of the human brain, and takes advantage of a unique non-human primate animal model, the common marmoset (Callithrix jacchus). In Brain/MINDS, the RIKEN Brain Science Institute acts as a central institute. The objectives of Brain/MINDS can be categorized into the following three major subject areas: (i) structure and functional mapping of a non-human primate brain (the marmoset brain); (ii) development of innovative neurotechnologies for brain mapping; and (iii) human brain mapping; and clinical research. Brain/MINDS researchers are highly motivated to identify the neuronal circuits responsible for the phenotype of neurological and psychiatric disorders, and to understand the development of these devastating disorders through the integration of these three subject areas. PMID:25823872

Climate Prediction Center - Expert Assessments Index

Science.gov Websites

Weather Service NWS logo - Click to go to the NWS home page Climate Prediction Center Home Site Map News Web resources and services. HOME > Monitoring and Data > Global Climate Data & Maps > ; Global Regional Climate Maps Regional Climate Maps Banner The Monthly regional analyses products are

Documentation for the 2008 Update of the United States National Seismic Hazard Maps

USGS Publications Warehouse

Petersen, Mark D.; Frankel, Arthur D.; Harmsen, Stephen C.; Mueller, Charles S.; Haller, Kathleen M.; Wheeler, Russell L.; Wesson, Robert L.; Zeng, Yuehua; Boyd, Oliver S.; Perkins, David M.; Luco, Nicolas; Field, Edward H.; Wills, Chris J.; Rukstales, Kenneth S.

2008-01-01

The 2008 U.S. Geological Survey (USGS) National Seismic Hazard Maps display earthquake ground motions for various probability levels across the United States and are applied in seismic provisions of building codes, insurance rate structures, risk assessments, and other public policy. This update of the maps incorporates new findings on earthquake ground shaking, faults, seismicity, and geodesy. The resulting maps are derived from seismic hazard curves calculated on a grid of sites across the United States that describe the frequency of exceeding a set of ground motions. The USGS National Seismic Hazard Mapping Project developed these maps by incorporating information on potential earthquakes and associated ground shaking obtained from interaction in science and engineering workshops involving hundreds of participants, review by several science organizations and State surveys, and advice from two expert panels. The National Seismic Hazard Maps represent our assessment of the 'best available science' in earthquake hazards estimation for the United States (maps of Alaska and Hawaii as well as further information on hazard across the United States are available on our Web site at http://earthquake.usgs.gov/research/hazmaps/).

Implications of NGA for NEHRP site coefficients

USGS Publications Warehouse

Borcherdt, Roger D.

2012-01-01

Three proposals are provided to update tables 11.4-1 and 11.4-2 of Minimum Design Loads for Buildings and Other Structures (7-10), by the American Society of Civil Engineers (2010) (ASCE/SEI 7-10), with site coefficients implied directly by NGA (Next Generation Attenuation) ground motion prediction equations (GMPEs). Proposals include a recommendation to use straight-line interpolation to infer site coefficients at intermediate values of ̅vs (average shear velocity). Site coefficients are recommended to ensure consistency with ASCE/SEI 7-10 MCER (Maximum Considered Earthquake) seismic-design maps and simplified site-specific design spectra procedures requiring site classes with associated tabulated site coefficients and a reference site class with unity site coefficients. Recommended site coefficients are confirmed by independent observations of average site amplification coefficients inferred with respect to an average ground condition consistent with that used for the MCER maps. The NGA coefficients recommended for consideration are implied directly by the NGA GMPEs and do not require introduction of additional models.

Glossary of Common Site Terms

MedlinePlus

... Maps Downloading Content for Analysis About Site What's New ClinicalTrials.gov Background About the Results Database History, Policies, and Laws Media/Press Resources Linking to This Site Terms and ...

Home Start Evaluation Study. Interim Report II: Program Analysis. Revised Draft.

ERIC Educational Resources Information Center

Deloria, Dennis; And Others

This document is the second in a series of evaluative reports directed to evaluation needs of Home Start planners and administrators. It focuses on implementation data about programs gathered during local site visits conducted in the spring and fall of 1972. The two basic evaluative questions asked are: (1) What was Home Start intended by its…

Preliminary analysis of Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) for mineralogic mapping at sites in Nevada and Colorado

NASA Technical Reports Server (NTRS)

Kruse, Fred A.; Taranik, Dan L.; Kierein-Young, Kathryn S.

1988-01-01

Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) data for sites in Nevada and Colorado were evaluated to determine their utility for mineralogical mapping in support of geologic investigations. Equal energy normalization is commonly used with imaging spectrometer data to reduce albedo effects. Spectra, profiles, and stacked, color-coded spectra were extracted from the AVIRIS data using an interactive analysis program (QLook) and these derivative data were compared to Airborne Imaging Spectrometer (AIS) results, field and laboratory spectra, and geologic maps. A feature extraction algorithm was used to extract and characterize absorption features from AVIRIS and laboratory spectra, allowing direct comparison of the position and shape of absorption features. Both muscovite and carbonate spectra were identified in the Nevada AVIRIS data by comparison with laboratory and AIS spectra, and an image was made that showed the distribution of these minerals for the entire site. Additional, distinctive spectra were located for an unknown mineral. For the two Colorado sites, the signal-to-noise problem was significantly worse and attempts to extract meaningful spectra were unsuccessful. Problems with the Colorado AVIRIS data were accentuated by the IAR reflectance technique because of moderate vegetation cover. Improved signal-to-noise and alternative calibration procedures will be required to produce satisfactory reflectance spectra from these data. Although the AVIRIS data were useful for mapping strong mineral absorption features and producing mineral maps at the Nevada site, it is clear that significant improvements to the instrument performance are required before AVIRIS will be an operational instrument.

PNAS Plus: Mapping patterns of long-term settlement in Northern Mesopotamia at a large scale

NASA Astrophysics Data System (ADS)

Menze, Bjoern H.; Ur, Jason A.

2012-04-01

The landscapes of the Near East show both the first settlements and the longest trajectories of settlement systems. Mounding is a characteristic property of these settlement sites, resulting from millennia of continuing settlement activity at distinguished places. So far, however, this defining feature of ancient settlements has not received much attention, or even been the subject of systematic evaluation. We propose a remote sensing approach for comprehensively mapping the pattern of human settlement at large scale and establish the largest archaeological record for a landscape in Mesopotamia, mapping about 14,000 settlement sites-spanning eight millennia-at 15-m resolution in a 23,000-km2 area in northeastern Syria. To map both low- and high-mounded places-the latter of which are often referred to as "tells"-we develop a strategy for detecting anthrosols in time series of multispectral satellite images and measure the volume of settlement sites in a digital elevation model. Using this volume as a proxy to continued occupation, we find a dependency of the long-term attractiveness of a site on local water availability, but also a strong relation to the relevance within a basin-wide exchange network that we can infer from our record and third millennium B.C. intersite routes visible on the ground until recent times. We believe it is possible to establish a nearly comprehensive map of human settlements in the fluvial plains of northern Mesopotamia and beyond, and site volume may be a key quantity to uncover long-term trends in human settlement activity from such a record.

Spatial correlation of shear-wave velocity in the San Francisco Bay Area sediments

USGS Publications Warehouse

Thompson, E.M.; Baise, L.G.; Kayen, R.E.

2007-01-01

Ground motions recorded within sedimentary basins are variable over short distances. One important cause of the variability is that local soil properties are variable at all scales. Regional hazard maps developed for predicting site effects are generally derived from maps of surficial geology; however, recent studies have shown that mapped geologic units do not correlate well with the average shear-wave velocity of the upper 30 m, Vs(30). We model the horizontal variability of near-surface soil shear-wave velocity in the San Francisco Bay Area to estimate values in unsampled locations in order to account for site effects in a continuous manner. Previous geostatistical studies of soil properties have shown horizontal correlations at the scale of meters to tens of meters while the vertical correlations are on the order of centimeters. In this paper we analyze shear-wave velocity data over regional distances and find that surface shear-wave velocity is correlated at horizontal distances up to 4 km based on data from seismic cone penetration tests and the spectral analysis of surface waves. We propose a method to map site effects by using geostatistical methods based on the shear-wave velocity correlation structure within a sedimentary basin. If used in conjunction with densely spaced shear-wave velocity profiles in regions of high seismic risk, geostatistical methods can produce reliable continuous maps of site effects. ?? 2006 Elsevier Ltd. All rights reserved.

Microzonation Mapping Of The Yanbu Industrial City, Western Saudi Arabia: A Multicriteria Decision Analysis Approach

NASA Astrophysics Data System (ADS)

Moustafa, Sayed, Sr.; Alarifi, Nassir S.; Lashin, Aref A.

2016-04-01

Urban areas along the western coast of Saudi Arabia are susceptible to natural disasters and environmental damages due to lack of planning. To produce a site-specific microzonation map of the rapidly growing Yanbu industrial city, spatial distribution of different hazard entities are assessed using the Analytical Hierarchal Process (AHP) together with Geographical Information System (GIS). For this purpose six hazard parameter layers are considered, namely; fundamental frequency, site amplification, soil strength in terms of effective shear-wave velocity, overburden sediment thickness, seismic vulnerability index and peak ground acceleration. The weight and rank values are determined during AHP and are assigned to each layer and its corresponding classes, respectively. An integrated seismic microzonation map was derived using GIS platform. Based on the derived map, the study area is classified into five hazard categories: very low, low, moderate high, and very high. The western and central parts of the study area, as indicated from the derived microzonation map, are categorized as a high hazard zone as compared to other surrounding places. The produced microzonation map of the current study is envisaged as a first-level assessment of the site specific hazards in the Yanbu city area, which can be used as a platform by different stakeholders in any future land-use planning and environmental hazard management.

Adopt-A-Highway, Statewide M & O, Transportation & Public Facilities, State

Science.gov Websites

& Operations Search DOT&PF State of Alaska DOT&PF > Maintenance & Operations > Maintenance Subcommittee off site link FHWA Operations off site link U.S. DOT off site link Site Map Policies

Digital Geologic Map of the Nevada Test Site and Vicinity, Nye, Lincoln, and Clark Counties, Nevada, and Inyo County, California

USGS Publications Warehouse

Slate, Janet L.; Berry, Margaret E.; Rowley, Peter D.; Fridrich, Christopher J.; Morgan, Karen S.; Workman, Jeremiah B.; Young, Owen D.; Dixon, Gary L.; Williams, Van S.; McKee, Edwin H.; Ponce, David A.; Hildenbrand, Thomas G.; Swadley, W.C.; Lundstrom, Scott C.; Ekren, E. Bartlett; Warren, Richard G.; Cole, James C.; Fleck, Robert J.; Lanphere, Marvin A.; Sawyer, David A.; Minor, Scott A.; Grunwald, Daniel J.; Laczniak, Randell J.; Menges, Christopher M.; Yount, James C.; Jayko, Angela S.

1999-01-01

This digital geologic map of the Nevada Test Site (NTS) and vicinity, as well as its accompanying digital geophysical maps, are compiled at 1:100,000 scale. The map compilation presents new polygon (geologic map unit contacts), line (fault, fold axis, metamorphic isograd, dike, and caldera wall) and point (structural attitude) vector data for the NTS and vicinity, Nye, Lincoln, and Clark Counties, Nevada, and Inyo County, California. The map area covers two 30 x 60-minute quadrangles-the Pahute Mesa quadrangle to the north and the Beatty quadrangle to the south-plus a strip of 7.5-minute quadrangles on the east side-72 quadrangles in all. In addition to the NTS, the map area includes the rest of the southwest Nevada volcanic field, part of the Walker Lane, most of the Amargosa Desert, part of the Funeral and Grapevine Mountains, some of Death Valley, and the northern Spring Mountains. This geologic map improves on previous geologic mapping of the same area (Wahl and others, 1997) by providing new and updated Quaternary and bedrock geology, new geophysical interpretations of faults beneath the basins, and improved GIS coverages. Concurrent publications to this one include a new isostatic gravity map (Ponce and others, 1999) and a new aeromagnetic map (Ponce, 1999).

Effectiveness of nest site restoration for the endangered northern map turtle. Report no. 1 : nest site selection and nest success from 2013-2014 and establishment of environmental center : [research summary].

DOT National Transportation Integrated Search

2015-05-01

The Northern Map Turtle, Graptemys geographica, is a Maryland state : Endangered Species, found only in the lower Susquehanna River in Maryland. : The only area where nests of this species are not heavily impacted by predators : occurs in the town of...

Effectiveness of nest site restoration for the endangered northern map turtle : report 2 : use of artificial nesting sites and wildlife exclusion fences to enhance nesting success : research summary.

DOT National Transportation Integrated Search

2016-10-01

The Northern Map Turtle, is a state Endangered Species, found only in the : lower Susquehanna River in Maryland. The only area where nests of this : species are not heavily impacted by predators is in the town of Port Deposit. : However, turtles nest...

Effectiveness of nest site restoration for the endangered northern map turtle. Report no. 1 : nest site selection and nest success from 2013-2014 and establishment of environmental center.

DOT National Transportation Integrated Search

2015-05-01

The Northern Map Turtle, Graptemys geographica, is a Maryland state Endangered Species, found only in the : lower Susquehanna River in Maryland. The only area where nests of this species are not heavily impacted by : predators occurs in the town of P...

Monitoring and mapping selected riparian habitat along the lower Snake River

DOE Office of Scientific and Technical Information (OSTI.GOV)

Downs, J. L; Tiller, B. L; Witter, M.

Studies in this document were initiated to establish baseline information on riparian and wetland habitat conditions at the areas studied under the current reservoir operations on the lower Snake River. Two approaches were used to assess habitat at 28 study sites selected on the four pools on the lower Snake River. These areas all contribute significant riparian habitat along the river, and several of these areas are designated habitat management units. At 14 of the 28 sites, we monitored riparian habitat on three dates during the growing season to quantify vegetation abundance and composition along three transects: soil nutrients, moisture,more » and pH and water level and pH. A second approach involved identifying any differences in the extent and amount of riparian/wetland habitat currently found at the study areas from that previously documented. We used both ground and boat surveys to map and classify the changes in vegetative cover along the shoreline at the 14 monitoring sites and at 14 additional sites along the lower Snake selected to represent various riparian/wetland habitat conditions. Results of these mapping efforts are compared with maps of cover types previously generated using aerial photography taken in 1987.« less

Mutation of a putative MAP kinase consensus site regulates NCAM endocytosis and NCAM-dependent neurite outgrowth.

PubMed

Goschzik, Tobias; Cremer, Harold; Gnanapragassam, Vinayaga S; Horstkorte, Rüdiger; Bork, Kaya; Diestel, Simone

2017-07-01

The cytoplasmic domain of the neural cell adhesion molecule NCAM contains several putative serine/threonine phosphorylation sites whose functions are largely unknown. Human NCAM140 (NCAM140) possesses a potential MAP kinase phosphorylation site at threonine (T) 803. The aim of this study was to analyze a possible phosphorylation of NCAM140 by MAP kinases and to identify the functional role of T803. We found that NCAM140 is phosphorylated by the MAP kinase ERK2 in vitro. Exchange of T803 to aspartic acid (D) which mimics constitutive phosphorylation at the respective position resulted in increased endocytosis compared to NCAM140 in neuroblastoma cells and primary neurons. Consistently, NCAM140 endocytosis was inhibited by the MEK inhibitor U0126 in contrast to NCAM140-T803D or NCAM140-T803A endocytosis supporting a role of a potential ERK2 mediated phosphorylation at this site in endocytosis. Furthermore, cells expressing NCAM140-T803D developed significantly shorter neurites than NCAM140 expressing cells indicating that a potential phosphorylation of NCAM by ERK2 also regulates NCAM-dependent neurite outgrowth. Copyright © 2017 Elsevier Ireland Ltd and Japan Neuroscience Society. All rights reserved.

Using Web Maps to Analyze the Construction of Global Scale Cognitive Maps

ERIC Educational Resources Information Center

Pingel, Thomas J.

2018-01-01

Game-based Web sites and applications are changing the ways in which students learn the world map. In this study, a Web map-based digital learning tool was used as a study aid for a university-level geography course in order to examine the way in which global scale cognitive maps are constructed. A network analysis revealed that clicks were…

Geologic Surface Effects of Underground Nuclear Testing, Buckboard Mesa, Climax Stock, Dome Mountain, Frenchman Flat, Rainier/Aqueduct Mesa, and Shoshone Mountain, Nevada Test Site, Nevada

USGS Publications Warehouse

Grasso, Dennis N.

2003-01-01

Surface effects maps were produced for 72 of 89 underground detonations conducted at the Frenchman Flat, Rainier Mesa and Aqueduct Mesa, Climax Stock, Shoshone Mountain, Buckboard Mesa, and Dome Mountain testing areas of the Nevada Test Site between August 10, 1957 (Saturn detonation, Area 12) and September 18, 1992 (Hunters Trophy detonation, Area 12). The ?Other Areas? Surface Effects Map Database, which was used to construct the maps shown in this report, contains digital reproductions of these original maps. The database is provided in both ArcGIS (v. 8.2) geodatabase format and ArcView (v. 3.2) shapefile format. This database contains sinks, cracks, faults, and other surface effects having a combined (cumulative) length of 136.38 km (84.74 mi). In GIS digital format, the user can view all surface effects maps simultaneously, select and view the surface effects of one or more sites of interest, or view specific surface effects by area or site. Three map layers comprise the database. They are: (1) the surface effects maps layer (oase_n27f), (2) the bar symbols layer (oase_bar_n27f), and (3) the ball symbols layer (oase_ball_n27f). Additionally, an annotation layer, named 'Ball_and_Bar_Labels,' and a polygon features layer, named 'Area12_features_poly_n27f,' are contained in the geodatabase version of the database. The annotation layer automatically labels all 295 ball-and-bar symbols shown on these maps. The polygon features layer displays areas of ground disturbances, such as rock spall and disturbed ground caused by the detonations. Shapefile versions of the polygon features layer in Nevada State Plane and Universal Transverse Mercator projections, named 'area12_features_poly_n27f.shp' and 'area12_features_poly_u83m.shp,' are also provided in the archive.

Tetrahymena thermophila acidic ribosomal protein L37 contains an archaebacterial type of C-terminus.

PubMed

Hansen, T S; Andreasen, P H; Dreisig, H; Højrup, P; Nielsen, H; Engberg, J; Kristiansen, K

1991-09-15

We have cloned and characterized a Tetrahymena thermophila macronuclear gene (L37) encoding the acidic ribosomal protein (A-protein) L37. The gene contains a single intron located in the 3'-part of the coding region. Two major and three minor transcription start points (tsp) were mapped 39 to 63 nucleotides upstream from the translational start codon. The uppermost tsp mapped to the first T in a putative T. thermophila RNA polymerase II initiator element, TATAA. The coding region of L37 predicts a protein of 109 amino acid (aa) residues. A substantial part of the deduced aa sequence was verified by protein sequencing. The T. thermophila L37 clearly belongs to the P1-type family of eukaryotic A-proteins, but the C-terminal region has the hallmarks of archaebacterial A-proteins.

Identification of wild areas in southern lower Michigan. [terrain analysis from aerial photography, and satellite imagery

NASA Technical Reports Server (NTRS)

Habowski, S.; Cialek, C.

1978-01-01

An inventory methodology was developed to identify potential wild area sites. A list of site criteria were formulated and tested in six selected counties. Potential sites were initially identified from LANDSAT satellite imagery. A detailed study of the soil, vegetation and relief characteristics of each site based on both high-altitude aerial photographs and existing map data was conducted to eliminate unsuitable sites. Ground reconnaissance of the remaining wild areas was made to verify suitability and acquire information on wildlife and general aesthetics. Physical characteristics of the wild areas in each county are presented in tables. Maps show the potential sites to be set aside for natural preservation and regulation by the state under the Wilderness and Natural Areas Act of 1972.

Soil mapping and process modeling for sustainable land use management: a brief historical review

NASA Astrophysics Data System (ADS)

Brevik, Eric C.; Pereira, Paulo; Muñoz-Rojas, Miriam; Miller, Bradley A.; Cerdà, Artemi; Parras-Alcántara, Luis; Lozano-García, Beatriz

2017-04-01

Basic soil management goes back to the earliest days of agricultural practices, approximately 9,000 BCE. Through time humans developed soil management techniques of ever increasing complexity, including plows, contour tillage, terracing, and irrigation. Spatial soil patterns were being recognized as early as 3,000 BCE, but the first soil maps didn't appear until the 1700s and the first soil models finally arrived in the 1880s (Brevik et al., in press). The beginning of the 20th century saw an increase in standardization in many soil science methods and wide-spread soil mapping in many parts of the world, particularly in developed countries. However, the classification systems used, mapping scale, and national coverage varied considerably from country to country. Major advances were made in pedologic modeling starting in the 1940s, and in erosion modeling starting in the 1950s. In the 1970s and 1980s advances in computing power, remote and proximal sensing, geographic information systems (GIS), global positioning systems (GPS), and statistics and spatial statistics among other numerical techniques significantly enhanced our ability to map and model soils (Brevik et al., 2016). These types of advances positioned soil science to make meaningful contributions to sustainable land use management as we moved into the 21st century. References Brevik, E., Pereira, P., Muñoz-Rojas, M., Miller, B., Cerda, A., Parras-Alcantara, L., Lozano-Garcia, B. Historical perspectives on soil mapping and process modelling for sustainable land use management. In: Pereira, P., Brevik, E., Muñoz-Rojas, M., Miller, B. (eds) Soil mapping and process modelling for sustainable land use management (In press). Brevik, E., Calzolari, C., Miller, B., Pereira, P., Kabala, C., Baumgarten, A., Jordán, A. 2016. Historical perspectives and future needs in soil mapping, classification and pedological modelling, Geoderma, 264, Part B, 256-274.

DNA sequence requirements for the accurate transcription of a protein-coding plastid gene in a plastid in vitro system from mustard (Sinapis alba L.)

PubMed Central

Link, Gerhard

1984-01-01

A nuclease-treated plastid extract from mustard (Sinapis alba L.) allows efficient transcription of cloned plastid DNA templates. In this in vitro system, the major runoff transcript of the truncated gene for the 32 000 mol. wt. photosystem II protein was accurately initiated from a site close to or identical with the in vivo start site. By using plasmids with deletions in the 5'-flanking region of this gene as templates, a DNA region required for efficient and selective initiation was detected ˜28-35 nucleotides upstream of the transcription start site. This region contains the sequence element TTGACA, which matches the consensus sequence for prokaryotic `−35' promoter elements. In the absence of this region, a region ˜13-27 nucleotides upstream of the start site still enables a basic level of specific transcription. This second region contains the sequence element TATATAA, which matches the consensus sequence for the `TATA' box of genes transcribed by RNA polymerase II (or B). The region between the `TATA'-like element and the transcription start site is not sufficient but may be required for specific transcription of the plastid gene. This latter region contains the sequence element TATACT, which resembles the prokaryotic `−10' (Pribnow) box. Based on the structural and transcriptional features of the 5' upstream region, a `promoter switch' mechanism is proposed, which may account for the developmentally regulated expression of this plastid gene. ImagesFig. 1.Fig. 2.Fig. 3.Fig. 4.Figure 5. PMID:16453540

Alteration, slope-classified alteration, and potential lahar inundation maps of volcanoes for the Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) Volcano Archive

USGS Publications Warehouse

Mars, John C.; Hubbard, Bernard E.; Pieri, David; Linick, Justin

2015-01-01

This study was undertaken during 2012–2013 in cooperation with the National Aeronautics and Space Administration (NASA). Since completion of this study, a new lahar modeling program (LAHAR_pz) has been released, which may produce slightly different modeling results from the LAHARZ model used in this study. The maps and data from this study should not be used in place of existing volcano hazard maps published by local authorities. For volcanoes without hazard maps and (or) published lahar-related hazard studies, this work will provide a starting point from which more accurate hazard maps can be produced. This is the first dataset to provide digital maps of altered volcanoes and adjacent watersheds that can be used for assessing volcanic hazards, hydrothermal alteration, and other volcanic processes in future studies.

A Mathematical Model for Storage and Recall of Images using Targeted Synchronization of Coupled Maps.

PubMed

Palaniyandi, P; Rangarajan, Govindan

2017-08-21

We propose a mathematical model for storage and recall of images using coupled maps. We start by theoretically investigating targeted synchronization in coupled map systems wherein only a desired (partial) subset of the maps is made to synchronize. A simple method is introduced to specify coupling coefficients such that targeted synchronization is ensured. The principle of this method is extended to storage/recall of images using coupled Rulkov maps. The process of adjusting coupling coefficients between Rulkov maps (often used to model neurons) for the purpose of storing a desired image mimics the process of adjusting synaptic strengths between neurons to store memories. Our method uses both synchronisation and synaptic weight modification, as the human brain is thought to do. The stored image can be recalled by providing an initial random pattern to the dynamical system. The storage and recall of the standard image of Lena is explicitly demonstrated.

Method for removing atomic-model bias in macromolecular crystallography

DOEpatents

Terwilliger, Thomas C [Santa Fe, NM

2006-08-01

Structure factor bias in an electron density map for an unknown crystallographic structure is minimized by using information in a first electron density map to elicit expected structure factor information. Observed structure factor amplitudes are combined with a starting set of crystallographic phases to form a first set of structure factors. A first electron density map is then derived and features of the first electron density map are identified to obtain expected distributions of electron density. Crystallographic phase probability distributions are established for possible crystallographic phases of reflection k, and the process is repeated as k is indexed through all of the plurality of reflections. An updated electron density map is derived from the crystallographic phase probability distributions for each one of the reflections. The entire process is then iterated to obtain a final set of crystallographic phases with minimum bias from known electron density maps.

Thermal inertia mapping of below ground objects and voids

NASA Astrophysics Data System (ADS)

Del Grande, Nancy K.; Ascough, Brian M.; Rumpf, Richard L.

2013-05-01

Thermal inertia (effusivity) contrast marks the borders of naturally heated below ground object and void sites. The Dual Infrared Effusivity Computed Tomography (DIRECT) method, patent pending, detects and locates the presence of enhanced heat flows from below ground object and void sites at a given area. DIRECT maps view contrasting surface temperature differences between sites with normal soil and sites with soil disturbed by subsurface, hollow or semi-empty object voids (or air gaps) at varying depths. DIRECT utilizes an empirical database created to optimize the scheduling of daily airborne thermal surveys to view and characterize unseen object and void types, depths and volumes in "blind" areas.

Mapping of the Rsd Contact Site on the Sigma 70 Subunit of Escherichia coli RNA Polymerase

PubMed Central

Jishage, Miki; Dasgupta, Dipak; Ishihama, Akira

2001-01-01

Rsd (regulator of sigma D) is an anti-sigma factor for the Escherichia coli RNA polymerase ς70 subunit. The contact site of Rsd on ς70 was analyzed after mapping of the contact-dependent cleavage sites by Rsd-tethered iron-p-bromoacetamidobenzyl EDTA and by analysis of the complex formation between Ala-substituted ς70 and Rsd. Results indicate that the Rsd contact site is located downstream of the promoter −35 recognition helix-turn-helix motif within region 4, overlapping with the regions involved in interaction with both core enzyme and ς70 contact transcription factors. PMID:11292818

Mapping of the Rsd contact site on the sigma 70 subunit of Escherichia coli RNA polymerase.

PubMed

Jishage, M; Dasgupta, D; Ishihama, A

2001-05-01

Rsd (regulator of sigma D) is an anti-sigma factor for the Escherichia coli RNA polymerase sigma(70) subunit. The contact site of Rsd on sigma(70) was analyzed after mapping of the contact-dependent cleavage sites by Rsd-tethered iron-p-bromoacetamidobenzyl EDTA and by analysis of the complex formation between Ala-substituted sigma(70) and Rsd. Results indicate that the Rsd contact site is located downstream of the promoter -35 recognition helix-turn-helix motif within region 4, overlapping with the regions involved in interaction with both core enzyme and sigma(70) contact transcription factors.

Factors reducing the expected deflection in initial orientation in clock-shifted homing pigeons.

PubMed

Gagliardo, Anna; Odetti, Francesca; Ioalè, Paolo

2005-02-01

To orient from familiar sites, homing pigeons can rely on both an olfactory map and visual familiar landmarks. The latter can in principle be used in two different ways: either within a topographical map exploited for piloting or in a so-called mosaic map associated with a compass bearing. One way to investigate the matter is to put the compass and the topographical information in conflict by releasing clock-shifted pigeons from familiar locations. Although the compass orientation is in general dominant over a piloting strategy, a stronger or weaker tendency to correct towards the home direction by clock-shifted pigeons released from very familiar sites has often been observed. To investigate which factors are involved in the reduction of the deviation due to clock-shift, we performed a series of releases with intact and anosmic pigeons from familiar sites in unshifted and clock-shifted conditions and a series of releases from the same sites with naive clock-shifted birds. Our data suggest that the following factors have a role in reducing deviation due to the clock-shift: familiarity with the release site, the lack of olfactory information and some unknown site-dependent features.

Feasibility study for locating archaeological village sites by satellite remote sensing techniques. [multispectral photography of Alaska

NASA Technical Reports Server (NTRS)

Cook, J. P. (Principal Investigator); Stringer, W. J.

1974-01-01

The author has identified the following significant results. The objective is to determine the feasibility of detecting large Alaskan archaeological sites by satellite remote sensing techniques and mapping such sites. The approach used is to develop digital multispectral signatures of dominant surface features including vegetation, exposed soils and rock, hydrological patterns and known archaeological sites. ERTS-1 scenes are then printed out digitally in a map-like array with a letter reflecting the most appropriate classification representing each pixel. Preliminary signatures were developed and tested. It was determined that there was a need to tighten up the archaeological site signature by developing accurate signatures for all naturally-occurring vegetation and surface conditions in the vicinity of the test area. These second generation signatures have been tested by means of computer printouts and classified tape displays on the University of Alaska CDU-200 and by comparison with aerial photography. It has been concluded that the archaeological signatures now in use are as good as can be developed. Plans are to print out signatures for the entire test area and locate on topographic maps the likely locations of archaeological sites within the test area.

Using 15N-Ammonium to Characterise and Map Potassium Binding Sites in Proteins by NMR Spectroscopy

PubMed Central

Werbeck, Nicolas D; Kirkpatrick, John; Reinstein, Jochen; Hansen, D Flemming

2014-01-01

A variety of enzymes are activated by the binding of potassium ions. The potassium binding sites of these enzymes are very specific, but ammonium ions can often replace potassium ions in vitro because of their similar ionic radii. In these cases, ammonium can be used as a proxy for potassium to characterise potassium binding sites in enzymes: the 1H,15N spin-pair of enzyme-bound 15NH4+ can be probed by 15N-edited heteronuclear NMR experiments. Here, we demonstrate the use of NMR spectroscopy to characterise binding of ammonium ions to two different enzymes: human histone deacetylase 8 (HDAC8), which is activated allosterically by potassium, and the bacterial Hsp70 homologue DnaK, for which potassium is an integral part of the active site. Ammonium activates both enzymes in a similar way to potassium, thus supporting this non-invasive approach. Furthermore, we present an approach to map the observed binding site onto the structure of HDAC8. Our method for mapping the binding site is general and does not require chemical shift assignment of the enzyme resonances. PMID:24520048

Cartilage T2 assessment: differentiation of normal hyaline cartilage and reparative tissue after arthroscopic cartilage repair in equine subjects.

PubMed

White, Lawrence M; Sussman, Marshall S; Hurtig, Mark; Probyn, Linda; Tomlinson, George; Kandel, Rita

2006-11-01

To prospectively assess T2 mapping characteristics of normal articular cartilage and of cartilage at sites of arthroscopic repair, including comparison with histologic results and collagen organization assessed at polarized light microscopy (PLM). Study protocol was compliant with the Canadian Council on Animal Care Guidelines and approved by the institutional animal care committee. Arthroscopic osteochondral autograft transplantation (OAT) and microfracture arthroplasty (MFx) were performed in knees of 10 equine subjects (seven female, three male; age range, 3-5 years). A site of arthroscopically normal cartilage was documented in each joint as a control site. Joints were harvested at 12 (n = 5) and 24 (n = 5) weeks postoperatively and were imaged at 1.5-T magnetic resonance (MR) with a 10-echo sagittal fast spin-echo acquisition. T2 maps of each site (21 OAT harvest, 10 MFx, 12 OAT plug, and 10 control sites) were calculated with linear least-squares curve fitting. Cartilage T2 maps were qualitatively graded as "organized" (normal transition of low-to-high T2 signal from deep to superficial cartilage zones) or "disorganized." Quantitative mean T2 values were calculated for deep, middle, and superficial cartilage at each location. Results were compared with histologic and PLM assessments by using kappa analysis. T2 maps were qualitatively graded as organized at 20 of 53 sites and as disorganized at 33 sites. Perfect agreement was seen between organized T2 and histologic findings of hyaline cartilage and between disorganized T2 and histologic findings of fibrous reparative tissue (kappa = 1.0). Strong agreement was seen between organized T2 and normal PLM findings and between disorganized T2 and abnormal PLM findings (kappa = .92). Quantitative assessment of the deep, middle, and superficial cartilage, respectively, showed mean T2 values of 53.3, 58.6, and 54.9 msec at reparative fibrous tissue sites and 40.7, 53.6, and 61.6 msec at hyaline cartilage sites. A significant trend of increasing T2 values (from deep to superficial) was found in hyaline cartilage (P < .01). Fibrous tissue sites had no significant change with depth (P > .59). Qualitative and quantitative T2 mapping helped differentiate hyaline cartilage from reparative fibrocartilage after cartilage repair at 1.5-T MR imaging.

Mapping of epitopes and structural analysis of antigenic sites in the nucleoprotein of rabies virus.

PubMed

Goto, H; Minamoto, N; Ito, H; Ito, N; Sugiyama, M; Kinjo, T; Kawai, A

2000-01-01

Linear epitopes on the rabies virus nucleoprotein (N) recognized by six MAbs raised against antigenic sites I (MAbs 6-4, 12-2 and 13-27) and IV (MAbs 6-9, 7-12 and 8-1) were investigated. Based on our previous studies on sites I and IV, 24 consecutively overlapping octapeptides and N- and C-terminal-deleted mutant N proteins were prepared. Results showed that all three site I epitopes studied and two site IV epitopes (for MAbs 8-1 and 6-9) mapped to aa 358-367, and that the other site IV epitope of MAb 7-12 mapped to aa 375-383. Tests using chimeric and truncated proteins showed that MAb 8-1 also requires the N-terminal sequence of the N protein to recognize its binding region more efficiently. Immunofluorescence studies demonstrated that all three site I-specific MAbs and one site IV-specific MAb (7-12) stained the N antigen that was diffusely distributed in the whole cytoplasm; the other two site IV-specific MAbs (6-9 and 8-1) detected only the N antigen in the cytoplasmic inclusion bodies (CIB). An antigenic site II-specific MAb (6-17) also detected CIB-associated N antigen alone. Furthermore, the level of diffuse N antigens decreased after treatment of infected cells with cycloheximide. These results suggest that epitopes at site I are expressed on the immature form of the N protein, but epitope structures of site IV MAbs 6-9 and 8-1 are created and/or exposed only after maturation of the N protein.

LiDAR-Derived Flood-Inundation Maps for Real-Time Flood-Mapping Applications, Tar River Basin, North Carolina

USGS Publications Warehouse

Bales, Jerad D.; Wagner, Chad R.; Tighe, Kirsten C.; Terziotti, Silvia

2007-01-01

Flood-inundation maps were created for selected streamgage sites in the North Carolina Tar River basin. Light detection and ranging (LiDAR) data with a vertical accuracy of about 20 centimeters, provided by the Floodplain Mapping Information System of the North Carolina Floodplain Mapping Program, were processed to produce topographic data for the inundation maps. Bare-earth mass point LiDAR data were reprocessed into a digital elevation model with regularly spaced 1.5-meter by 1.5-meter cells. A tool was developed as part of this project to connect flow paths, or streams, that were inappropriately disconnected in the digital elevation model by such features as a bridge or road crossing. The Hydraulic Engineering Center-River Analysis System (HEC-RAS) model, developed by the U.S. Army Corps of Engineers, was used for hydraulic modeling at each of the study sites. Eleven individual hydraulic models were developed for the Tar River basin sites. Seven models were developed for reaches with a single gage, and four models were developed for reaches of the Tar River main stem that receive flow from major gaged tributaries, or reaches in which multiple gages were near one another. Combined, the Tar River hydraulic models included 272 kilometers of streams in the basin, including about 162 kilometers on the Tar River main stem. The hydraulic models were calibrated to the most current stage-discharge relations at 11 long-term streamgages where rating curves were available. Medium- to high-flow discharge measurements were made at some of the sites without rating curves, and high-water marks from Hurricanes Fran and Floyd were available for high-stage calibration. Simulated rating curves matched measured curves over the full range of flows. Differences between measured and simulated water levels for a specified flow were no more than 0.44 meter and typically were less. The calibrated models were used to generate a set of water-surface profiles for each of the 11 modeled reaches at 0.305-meter increments for water levels ranging from bankfull to approximately the highest recorded water level at the downstream-most gage in each modeled reach. Inundated areas were identified by subtracting the water-surface elevation in each 1.5-meter by 1.5-meter grid cell from the land-surface elevation in the cell through an automated routine that was developed to identify all inundated cells hydraulically connected to the cell at the downstream-most gage in the model domain. Inundation maps showing transportation networks and orthoimagery were prepared for display on the Internet. These maps also are linked to the U.S. Geological Survey North Carolina Water Science Center real-time streamflow website. Hence, a user can determine the near real-time stage and water-surface elevation at a U.S. Geological Survey streamgage site in the Tar River basin and link directly to the flood-inundation maps for a depiction of the estimated inundated area at the current water level. Although the flood-inundation maps represent distinct boundaries of inundated areas, some uncertainties are associated with these maps. These are uncertainties in the topographic data for the hydraulic model computational grid and inundation maps, effective friction values (Manning's n), model-validation data, and forecast hydrographs, if used. The Tar River flood-inundation maps were developed by using a steady-flow hydraulic model. This assumption clearly has less of an effect on inundation maps produced for low flows than for high flows when it typically takes more time to inundate areas. A flood in which water levels peak and fall slowly most likely will result in more inundation than a similar flood in which water levels peak and fall quickly. Limitations associated with the steady-flow assumption for hydraulic modeling vary from site to site. The one-dimensional modeling approach used in this study resulted in good agreement between measurements and simulations. T

Rodent Control: Seal Up! Trap Up! Clean Up!

MedlinePlus

... Skip directly to site content Start of Search Controls Search Form Controls Cancel Submit Search The CDC CDC A-Z ... V W X Y Z # Start of Search Controls Search Form Controls Cancel Submit Search The CDC ...

Infection Control: The Use and Handling of Toothbrushes

MedlinePlus

... Skip directly to site content Start of Search Controls Search Form Controls Cancel Submit Search the CDC CDC A-Z ... V W X Y Z # Start of Search Controls Search Form Controls Search The CDC Cancel Submit ...

DOE Office of Scientific and Technical Information (OSTI.GOV)

Inam, A., E-mail: aqil.ceet@pu.edu.pk; Brydson, R., E-mail: mtlrmdb@leeds.ac.uk; Edmonds, D.V., E-mail: d.v.edmonds@leeds.ac.uk

The potential for using graphite particles as an internal lubricant during machining is considered. Graphite particles were found to form during graphitisation of experimental medium-carbon steel alloyed with Si and Al. The graphite nucleation sites were strongly influenced by the starting microstructure, whether ferrite–pearlite, bainite or martensite, as revealed by light and electron microscopy. Favourable nucleation sites in the ferrite–pearlite starting microstructure were, not unexpectedly, found to be located within pearlite colonies, no doubt due to the presence of abundant cementite as a source of carbon. In consequence, the final distribution of graphite nodules in ferrite–pearlite microstructures was less uniformmore » than for the bainite microstructure studied. In the case of martensite, this study found a predominance of nucleation at grain boundaries, again leading to less uniform graphite dispersions. - Highlights: • Metallography of formation of graphite particles in experimental carbon steel. • Potential for using graphite in steel as an internal lubricant during machining. • Microstructure features expected to influence improved machinability studied. • Influence of pre-anneal starting microstructure on graphite nucleation sites. • Influence of pre-anneal starting microstructure on graphite distribution. • Potential benefit is new free-cutting steel compositions without e.g. Pb alloying.« less

Ano Nuevo to Santa Cruz, California : a photographic tour of the coastline

USGS Publications Warehouse

Chezar, Henry; Wong, Florence L.

2000-01-01

This interactive CD ROM contains over 500 overlapping photographic images of the California coastline from A?o Nuevo to Santa Cruz. The images were taken from the R/V David Johnston to illustrate the coastal geology adjacent to part of the Monterey Bay National Marine Sanctuary. The introductory home page starts a series of links to a regional map, more detailed area maps, and finally the individual photographic images.

Malaysia’s Experience in War Against Communist Insurgency and Its Relevance to the Present Situation in Iraq

DTIC Science & Technology

2005-01-01

Shangri - La Hotel , Makati City 48 Ibid. 49 Stanley S. Bedlington. Malaysia and Singapore. The Building of New States. Cornell University Press Ltd...Page Preface i Contents ii Executive Summary iii Map on Malaya iv INTRODUCTION 1 THE INSURGENCY AGAINST THE MCP 3 The First Emergency...will be a good start. MAP OF MALAYA (Peninsular Malaysia) iv 1 INTRODUCTION In mid June 1948 the

ASW Reach-Back Cell Oceanography Analysis System (ARCOAS) Version 3 User’s Guide

DTIC Science & Technology

2012-02-24

65 Table of Figures Figure 2.1: Warning dialog box indicating ActiveX ...Click OK in response to the message box indicating that ActiveX controls are being used by the application (Figure 2.1). Figure 2.1: Warning...dialog box indicating ActiveX controls could be unsafe. 3. Open an existing map or create a new empty map. 4. Start ARCOAS by clicking the ARCOAS

Large-scale Activities Associated with the 2005 Sep. 7th Event

NASA Astrophysics Data System (ADS)

Zong, Weiguo

We present a multi-wavelength study on large-scale activities associated with a significant solar event. On 2005 September 7, a flare classified as bigger than X17 was observed. Combining with Hα 6562.8 ˚, He I 10830 ˚and soft X-ray observations, three large-scale activities were A A found to propagate over a long distance on the solar surface. 1) The first large-scale activity emanated from the flare site, which propagated westward around the solar equator and appeared as sequential brightenings. With MDI longitudinal magnetic field map, the activity was found to propagate along the magnetic network. 2) The second large-scale activity could be well identified both in He I 10830 ˚images and soft X-ray images and appeared as diffuse emission A enhancement propagating away. The activity started later than the first one and was not centric on the flare site. Moreover, a rotation was found along with the bright front propagating away. 3) The third activity was ahead of the second one, which was identified as a "winking" filament. The three activities have different origins, which were seldom observed in one event. Therefore this study is useful to understand the mechanism of large-scale activities on solar surface.

GENCODE: the reference human genome annotation for The ENCODE Project.

PubMed

Harrow, Jennifer; Frankish, Adam; Gonzalez, Jose M; Tapanari, Electra; Diekhans, Mark; Kokocinski, Felix; Aken, Bronwen L; Barrell, Daniel; Zadissa, Amonida; Searle, Stephen; Barnes, If; Bignell, Alexandra; Boychenko, Veronika; Hunt, Toby; Kay, Mike; Mukherjee, Gaurab; Rajan, Jeena; Despacio-Reyes, Gloria; Saunders, Gary; Steward, Charles; Harte, Rachel; Lin, Michael; Howald, Cédric; Tanzer, Andrea; Derrien, Thomas; Chrast, Jacqueline; Walters, Nathalie; Balasubramanian, Suganthi; Pei, Baikang; Tress, Michael; Rodriguez, Jose Manuel; Ezkurdia, Iakes; van Baren, Jeltje; Brent, Michael; Haussler, David; Kellis, Manolis; Valencia, Alfonso; Reymond, Alexandre; Gerstein, Mark; Guigó, Roderic; Hubbard, Tim J

2012-09-01

The GENCODE Consortium aims to identify all gene features in the human genome using a combination of computational analysis, manual annotation, and experimental validation. Since the first public release of this annotation data set, few new protein-coding loci have been added, yet the number of alternative splicing transcripts annotated has steadily increased. The GENCODE 7 release contains 20,687 protein-coding and 9640 long noncoding RNA loci and has 33,977 coding transcripts not represented in UCSC genes and RefSeq. It also has the most comprehensive annotation of long noncoding RNA (lncRNA) loci publicly available with the predominant transcript form consisting of two exons. We have examined the completeness of the transcript annotation and found that 35% of transcriptional start sites are supported by CAGE clusters and 62% of protein-coding genes have annotated polyA sites. Over one-third of GENCODE protein-coding genes are supported by peptide hits derived from mass spectrometry spectra submitted to Peptide Atlas. New models derived from the Illumina Body Map 2.0 RNA-seq data identify 3689 new loci not currently in GENCODE, of which 3127 consist of two exon models indicating that they are possibly unannotated long noncoding loci. GENCODE 7 is publicly available from gencodegenes.org and via the Ensembl and UCSC Genome Browsers.

Physical and Functional Interaction between the Eukaryotic Orthologs of Prokaryotic Translation Initiation Factors IF1 and IF2

PubMed Central

Choi, Sang Ki; Olsen, DeAnne S.; Roll-Mecak, Antonina; Martung, Agnes; Remo, Keith L.; Burley, Stephen K.; Hinnebusch, Alan G.; Dever, Thomas E.

2000-01-01

To initiate protein synthesis, a ribosome with bound initiator methionyl-tRNA must be assembled at the start codon of an mRNA. This process requires the coordinated activities of three translation initiation factors (IF) in prokaryotes and at least 12 translation initiation factors in eukaryotes (eIF). The factors eIF1A and eIF5B from eukaryotes show extensive amino acid sequence similarity to the factors IF1 and IF2 from prokaryotes. By a combination of two-hybrid, coimmunoprecipitation, and in vitro binding assays eIF1A and eIF5B were found to interact directly, and the eIF1A binding site was mapped to the C-terminal region of eIF5B. This portion of eIF5B was found to be critical for growth in vivo and for translation in vitro. Overexpression of eIF1A exacerbated the slow-growth phenotype of yeast strains expressing C-terminally truncated eIF5B. These findings indicate that the physical interaction between the evolutionarily conserved factors eIF1A and eIF5B plays an important role in translation initiation, perhaps to direct or stabilize the binding of methionyl-tRNA to the ribosomal P site. PMID:10982835

Exon-Specific QTLs Skew the Inferred Distribution of Expression QTLs Detected Using Gene Expression Array Data

PubMed Central

Veyrieras, Jean-Baptiste; Gaffney, Daniel J.; Pickrell, Joseph K.; Gilad, Yoav; Stephens, Matthew; Pritchard, Jonathan K.

2012-01-01

Mapping of expression quantitative trait loci (eQTLs) is an important technique for studying how genetic variation affects gene regulation in natural populations. In a previous study using Illumina expression data from human lymphoblastoid cell lines, we reported that cis-eQTLs are especially enriched around transcription start sites (TSSs) and immediately upstream of transcription end sites (TESs). In this paper, we revisit the distribution of eQTLs using additional data from Affymetrix exon arrays and from RNA sequencing. We confirm that most eQTLs lie close to the target genes; that transcribed regions are generally enriched for eQTLs; that eQTLs are more abundant in exons than introns; and that the peak density of eQTLs occurs at the TSS. However, we find that the intriguing TES peak is greatly reduced or absent in the Affymetrix and RNA-seq data. Instead our data suggest that the TES peak observed in the Illumina data is mainly due to exon-specific QTLs that affect 3′ untranslated regions, where most of the Illumina probes are positioned. Nonetheless, we do observe an overall enrichment of eQTLs in exons versus introns in all three data sets, consistent with an important role for exonic sequences in gene regulation. PMID:22359548

Geoelectric Hazard Maps for the Mid-Atlantic United States: 100 Year Extreme Values and the 1989 Magnetic Storm

NASA Astrophysics Data System (ADS)

Love, Jeffrey J.; Lucas, Greg M.; Kelbert, Anna; Bedrosian, Paul A.

2018-01-01

Maps of extreme value geoelectric field amplitude are constructed for the Mid-Atlantic United States, a region with high population density and critically important power grid infrastructure. Geoelectric field time series for the years 1983-2014 are estimated by convolving Earth surface impedances obtained from 61 magnetotelluric survey sites across the Mid-Atlantic with historical 1 min (2 min Nyquist) measurements of geomagnetic variation obtained from a nearby observatory. Statistical models are fitted to the maximum geoelectric amplitudes occurring during magnetic storms, and extrapolations made to estimate threshold amplitudes only exceeded, on average, once per century. For the Mid-Atlantic region, 100 year geoelectric exceedance amplitudes have a range of almost 3 orders of magnitude (from 0.04 V/km at a site in southern Pennsylvania to 24.29 V/km at a site in central Virginia), and they have significant geographic granularity, all of which is due to site-to-site differences in magnetotelluric impedance. Maps of these 100 year exceedance amplitudes resemble those of the estimated geoelectric amplitudes attained during the March 1989 magnetic storm, and, in that sense, the March 1989 storm resembles what might be loosely called a "100 year" event. The geoelectric hazard maps reported here stand in stark contrast with the 100 year geoelectric benchmarks developed for the North American Electric Reliability Corporation.

Field trip to Nevada test site

USGS Publications Warehouse

,

1976-01-01

Two road logs guide the reader through the geologic scene from Las Vegas to Mercury and from Mercury through eight stops on the Nevada Test Site. Maps and cross sections depict the geology and hydrology of the area. Included among the tables is one showing the stratigraphic units in the southwestern Nevada volcanic field and another that lists the geologic maps covering the Nevada Test Site and vicinity. The relation of the geologic environment to nuclear-explosion effects is alluded to in brief discussions of collapse, surface subsidence, and cratering resulting from underground nuclear explosions.

Optical mapping reveals a large genetic inversion between two methicillin-resistant Staphylococcus aureus strains.

PubMed

Shukla, Sanjay K; Kislow, Jennifer; Briska, Adam; Henkhaus, John; Dykes, Colin

2009-09-01

Staphylococcus aureus is a highly versatile and evolving bacterium of great clinical importance. S. aureus can evolve by acquiring single nucleotide polymorphisms and mobile genetic elements and by recombination events. Identification and location of novel genomic elements in a bacterial genome are not straightforward, unless the whole genome is sequenced. Optical mapping is a new tool that creates a high-resolution, in situ ordered restriction map of a bacterial genome. These maps can be used to determine genomic organization and perform comparative genomics to identify genomic rearrangements, such as insertions, deletions, duplications, and inversions, compared to an in silico (virtual) restriction map of a known genome sequence. Using this technology, we report here the identification, approximate location, and characterization of a genetic inversion of approximately 500 kb of a DNA element between the NRS387 (USA800) and FPR3757 (USA300) strains. The presence of the inversion and location of its junction sites were confirmed by site-specific PCR and sequencing. At both the left and right junction sites in NRS387, an IS1181 element and a 73-bp sequence were identified as inverted repeats, which could explain the possible mechanism of the inversion event.

Determine the Impact of Novel BRCA1 Translation Start Sites on Therapy Resistance in Ovarian Cancer

DTIC Science & Technology

2017-09-01

Award Number: W81XWH-15-1-0197 TITLE: PRINCIPAL INVESTIGATOR: Neil Johnson, Ph.D. CONTRACTING ORGANIZATION: Institute for Cancer Research...Therapy Resistance in Ovarian Cancer The views, opinions and/or findings contained in this report are those of the author(s) and should not be...Start Sites on Therapy 5b. GRANT NUMBER Resistance in Ovarian Cancer W81XWH-15-1-0197 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER Neil

Smart Start and Preschool Child Care Quality in North Carolina: Change Over Time and Relation to Children's Readiness.

ERIC Educational Resources Information Center

Bryant, Donna; Maxwell, Kelly; Taylor, Karen; Poe, Michele; Peisner-Feinberg, Ellen; Bernier, Kathleen

The primary goal of Smart Start is to ensure that all children enter school healthy and prepared to succeed. Smart Start has funded a variety of technical assistance (TA) activities to improve child care, including on-site technical assistance, quality improvement and facility grant, teacher education scholarships, license upgrades, teacher salary…

Evaluating Systemic Change in the National Head Start-Public School Transition Project: Perspectives from Five States.

ERIC Educational Resources Information Center

Greene, Andrea; And Others

In 1991 the Department of Health and Human Services funded 32 sites throughout the United States to develop and implement Head Start-Public School Early Childhood Transition Demonstration Projects. The purpose of 31 projects, which are in their fourth year of operation, is to stimulate partnerships among Head Start agencies, public schools, and…

Costs in Serving Handicapped Children in Head Start: An Analysis of Methods and Cost Estimates. Final Report.

ERIC Educational Resources Information Center

Syracuse Univ., NY. Div. of Special Education and Rehabilitation.

An evaluation of the costs of serving handicapped children in Head Start was based on information collected in conjunction with on-site visits to regular Head Start programs, experimental programs, and specially selected model preschool programs, and from questionnaires completed by 1,353 grantees and delegate agencies of regular Head Start…

Astronaut Kevin Chilton displays map of Scandinavia on flight deck

NASA Image and Video Library

1994-04-14

STS059-16-032 (9-20 April 1994) --- Astronaut Kevin P. Chilton, pilot, displays a map of Scandinavia on the Space Shuttle Endeavour's flight deck. Large scale maps such as this were used by the crew to locate specific sites of interest to the Space Radar Laboratory scientists. The crew then photographed the sites at the same time as the radar in the payload bay imaged them. Chilton was joined in space by five other NASA astronauts for a week and a half of support to the Space Radar Laboratory (SRL-1) mission and other tasks.

Land and Hold Short Operations : A Primer

DOT National Transportation Integrated Search

1996-04-20

Michigan Department of Transportation (M-DOT) started its Systems Re-engineering process with a clear road map the PROSE initiative. PROSE, standing for PROject Support Environment, is an ambitious venture to develop strategic information systems aut...

Find a Hand Surgeon

MedlinePlus

... you agree to the user agreement and disclaimer . Search By Location Search By Doctor Search Results Map Enter a location ... by American Society for Surgery of the Hand × Search Tips Tip 1: Start with the basics like " ...

Integration of myocardial scar identified by preoperative delayed contrast-enhanced MRI into a high-resolution mapping system for planning and guidance of VT ablation procedures

NASA Astrophysics Data System (ADS)

Rettmann, M. E.; Suzuki, A.; Wang, S.; Pottinger, N.; Arter, J.; Netzer, A.; Parker, K.; Viker, K.; Packer, D. L.

2017-03-01

Myocardial scarring creates a substrate for reentrant circuits which can lead to ventricular tachycardia. In ventricular catheter ablation therapy, regions of myocardial scarring are targeted to interrupt arrhythmic electrical pathways. Low voltage regions are a surrogate for myocardial scar and are identified by generating an electro anatomic map at the start of the procedure. Recent efforts have focussed on integration of preoperative scar information generated from delayed contrast-enhanced MR imaging to augment intraprocedural information. In this work, we describe an initial feasibility study of integration of a preoperative MRI derived scar maps into a high-resolution mapping system to improve planning and guidance of VT ablation procedures.

Preliminary map of peak horizontal ground acceleration for the Hanshin-Awaji earthquake of January 17, 1995, Japan - Description of Mapped Data Sets

USGS Publications Warehouse

Borcherdt, R.D.; Mark, R.K.

1995-01-01

The Hanshin-Awaji earthquake (also known as the Hyogo-ken Nanbu and the Great Hanshin earthquake) provided an unprecedented set of measurements of strong ground shaking. The measurements constitute the most comprehensive set of strong- motion recordings yet obtained for sites underlain by soft soil deposits of Holocene age within a few kilometers of the crustal rupture zone. The recordings, obtained on or near many important structures, provide an important new empirical data set for evaluating input ground motion levels and site amplification factors for codes and site-specific design procedures world wide. This report describes the data used to prepare a preliminary map summarizing the strong motion data in relation to seismicity and underlying geology (Wentworth, Borcherdt, and Mark., 1995; Figure 1, hereafter referred to as Figure 1/I). The map shows station locations, peak acceleration values, and generalized acceleration contours superimposed on pertinent seismicity and the geologic map of Japan. The map (Figure 1/I) indicates a zone of high acceleration with ground motions throughout the zone greater than 400 gal and locally greater than 800 gal. This zone encompasses the area of most intense damage mapped as JMA intensity level 7, which extends through Kobe City. The zone of most intense damage is parallel, but displaced slightly from the surface projection of the crustal rupture zone implied by aftershock locations. The zone is underlain by soft-soil deposits of Holocene age.

Using fuzzy logic analysis for siting decisions of infiltration trenches for highway runoff control.

PubMed

Ki, Seo Jin; Ray, Chittaranjan

2014-09-15

Determining optimal locations for best management practices (BMPs), including their field considerations and limitations, plays an important role for effective stormwater management. However, these issues have been often overlooked in modeling studies that focused on downstream water quality benefits. This study illustrates the methodology of locating infiltration trenches at suitable locations from spatial overlay analyses which combine multiple layers that address different aspects of field application into a composite map. Using seven thematic layers for each analysis, fuzzy logic was employed to develop a site suitability map for infiltration trenches, whereas the DRASTIC method was used to produce a groundwater vulnerability map on the island of Oahu, Hawaii, USA. In addition, the analytic hierarchy process (AHP), one of the most popular overlay analyses, was used for comparison to fuzzy logic. The results showed that the AHP and fuzzy logic methods developed significantly different index maps in terms of best locations and suitability scores. Specifically, the AHP method provided a maximum level of site suitability due to its inherent aggregation approach of all input layers in a linear equation. The most eligible areas in locating infiltration trenches were determined from the superposition of the site suitability and groundwater vulnerability maps using the fuzzy AND operator. The resulting map successfully balanced qualification criteria for a low risk of groundwater contamination and the best BMP site selection. The results of the sensitivity analysis showed that the suitability scores were strongly affected by the algorithms embedded in fuzzy logic; therefore, caution is recommended with their use in overlay analysis. Accordingly, this study demonstrates that the fuzzy logic analysis can not only be used to improve spatial decision quality along with other overlay approaches, but also is combined with general water quality models for initial and refined searches for the best locations of BMPs at the sub-basin level. Copyright © 2014. Published by Elsevier B.V.

Genomic localization of the Z/EG transgene in the mouse genome.

PubMed

Colombo, Sophie; Kumasaka, Mayuko; Lobe, Corrinne; Larue, Lionel

2010-02-01

The Z/EG transgenic mouse line, produced by Novak et al., displays tissue-specific EGFP expression after Cre-mediated recombination. The autofluorescence of EGFP allows the visualization of cells of interest displaying Cre recombination. The initial construct was designed such that cells without Cre recombination express the beta-galactosidase marker, facilitating counterselection. We used inverse PCR to identify the site of integration of the Z/EG transgene, to improve the efficiency of homozygous Z/EG mouse production. Recombined cells produced large amounts of EGFP protein, resulting in higher levels of fluorescence and therefore greater contrast with nonrecombined cells. We mapped the transgene to the G1 region of chromosome 5. This random insertion was found to have occurred 230-bp upstream from the start codon of the Rasa4 gene. The insertion of the Z/EG transgene in the C57BL/6 genetic background had no effect on Rasa4 expression. Homozygous Z/EG mice therefore had no obvious phenotype. (c) 2009 Wiley-Liss, Inc.

DNA replication origins—where do we begin?

PubMed Central

Prioleau, Marie-Noëlle; MacAlpine, David M.

2016-01-01

For more than three decades, investigators have sought to identify the precise locations where DNA replication initiates in mammalian genomes. The development of molecular and biochemical approaches to identify start sites of DNA replication (origins) based on the presence of defining and characteristic replication intermediates at specific loci led to the identification of only a handful of mammalian replication origins. The limited number of identified origins prevented a comprehensive and exhaustive search for conserved genomic features that were capable of specifying origins of DNA replication. More recently, the adaptation of origin-mapping assays to genome-wide approaches has led to the identification of tens of thousands of replication origins throughout mammalian genomes, providing an unprecedented opportunity to identify both genetic and epigenetic features that define and regulate their distribution and utilization. Here we summarize recent advances in our understanding of how primary sequence, chromatin environment, and nuclear architecture contribute to the dynamic selection and activation of replication origins across diverse cell types and developmental stages. PMID:27542827

(S)-3-hydroxy-3-methylglutaryl coenzyme A reductase, a product of the mva operon of Pseudomonas mevalonii, is regulated at the transcriptional level.

PubMed Central

Wang, Y L; Beach, M J; Rodwell, V W

1989-01-01

We have cloned and sequenced a 505-base-pair (bp) segment of DNA situated upstream of mvaA, the structural gene for (S)-3-hydroxy-3-methylglutaryl coenzyme A reductase (EC 1.1.1.88) of Pseudomonas mevalonii. The DNA segment that we characterized includes the promoter region for the mva operon. Nuclease S1 mapping and primer extension analysis showed that mvaA is the promoter-proximal gene of the mva operon. Transcription initiates at -56 bp relative to the first A (+1) of the translation start site. Transcription in vivo was induced by mevalonate. Structural features of the mva promoter region include an 80-bp A + T-rich region, and -12, -24 consensus sequences that resemble sequences of sigma 54 promoters in enteric organisms. The relative amplitudes of catalytic activity, enzyme protein, and mvaA mRNA are consistent with a model of regulation of this operon at the transcriptional level. Images PMID:2477360

Growing Bacteriophage M13 in Liquid Culture.

PubMed

Green, Michael R; Sambrook, Joseph

2017-11-01

Stocks of bacteriophage M13 are usually grown in liquid culture. The infected bacteria do not lyse but, instead, grow at a slower than normal rate to form a dilute suspension. The inoculum of bacteriophage is almost always a freshly picked plaque or a suspension of bacteriophage particles obtained from a single plaque, as described here. Infected cells contain up to 200 copies of double-stranded, replicative-form DNA and extrude several hundred bacteriophage particles per generation. Thus, a 1-mL culture of infected cells can produce enough double-stranded viral DNA (1-2 mg) for restriction mapping and recovery of cloned DNA inserts and sufficient single-stranded DNA (∼5-10 mg) for site-directed mutagenesis, DNA sequencing, or synthesis of radiolabeled probes. The titer of bacteriophages in the supernatant from infected cells is so high (∼10 12 pfu/mL) that a small aliquot serves as a permanent stock of the starting plaque. © 2017 Cold Spring Harbor Laboratory Press.

Establishment of a promoter-based chromatin architecture on recently replicated DNA can accommodate variable inter-nucleosome spacing.

PubMed

Fennessy, Ross T; Owen-Hughes, Tom

2016-09-06

Nucleosomes, the fundamental subunits of eukaryotic chromatin, are organized with respect to transcriptional start sites. A major challenge to the persistence of this organization is the disassembly of nucleosomes during DNA replication. Here, we use complimentary approaches to map the locations of nucleosomes on recently replicated DNA. We find that nucleosomes are substantially realigned with promoters during the minutes following DNA replication. As a result, the nucleosomal landscape is largely re-established before newly replicated chromosomes are partitioned into daughter cells and can serve as a platform for the re-establishment of gene expression programmes. When the supply of histones is disrupted through mutation of the chaperone Caf1, a promoter-based architecture is generated, but with increased inter-nucleosomal spacing. This indicates that the chromatin remodelling enzymes responsible for spacing nucleosomes are capable of organizing nucleosomes with a range of different linker DNA lengths. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

TERRA Promotes Telomere Shortening through Exonuclease 1–Mediated Resection of Chromosome Ends

PubMed Central

Pfeiffer, Verena; Lingner, Joachim

2012-01-01

The long noncoding telomeric repeat containing RNA (TERRA) is expressed at chromosome ends. TERRA upregulation upon experimental manipulation or in ICF (immunodeficiency, centromeric instability, facial anomalies) patients correlates with short telomeres. To study the mechanism of telomere length control by TERRA in Saccharomyces cerevisiae, we mapped the transcriptional start site of TERRA at telomere 1L and inserted a doxycycline regulatable promoter upstream. Induction of TERRA transcription led to telomere shortening of 1L but not of other chromosome ends. TERRA interacts with the Exo1-inhibiting Ku70/80 complex, and deletion of EXO1 but not MRE11 fully suppressed the TERRA–mediated short telomere phenotype in presence and absence of telomerase. Thus TERRA transcription facilitates the 5′-3′ nuclease activity of Exo1 at chromosome ends, providing a means to regulate the telomere shortening rate. Thereby, telomere transcription can regulate cellular lifespan through modulation of chromosome end processing activities. PMID:22719262

The chloroplast tRNALys(UUU) gene from mustard (Sinapis alba) contains a class II intron potentially coding for a maturase-related polypeptide.

PubMed

Neuhaus, H; Link, G

1987-01-01

The trnK gene endocing the tRNALys(UUU) has been located on mustard (Sinapis alba) chloroplast DNA, 263 bp upstream of the psbA gene on the same strand. The nucleotide sequence of the trnK gene and its flanking regions as well as the putative transcription start and termination sites are shown. The 5' end of the transcript lies 121 bp upstream of the 5' tRNA coding region and is preceded by procaryotic-type "-10" and "-35" sequence elements, while the 3' end maps 2.77 kb downstream to a DNA region with possible stemloop secondary structure. The anticodon loop of the tRNALys is interrupted by a 2,574 bp intron containing a long open reading frame, which codes for 524 amino acids. Based on conserved stem and loop structures, this intron has characteristic features of a class II intron. A region near the carboxyl terminus of the derived polypeptide appears structurally related to maturases.

Appliation of rad-sequencing to linkage mapping in citrus

USDA-ARS?s Scientific Manuscript database

High density linkage maps can be developed for modest cost using high-throughput DNA sequencing to genotype a defined fraction (representation) of the genome. We developed linkage maps in two citrus populations using the RAD (Restriction site Associated DNA) genotyping method which involves restrict...

An integrated map of the genome of the tubercle bacillus, Mycobacterium tuberculosis H37Rv, and comparison with Mycobacterium leprae.

PubMed Central

Philipp, W J; Poulet, S; Eiglmeier, K; Pascopella, L; Balasubramanian, V; Heym, B; Bergh, S; Bloom, B R; Jacobs, W R; Cole, S T

1996-01-01

An integrated map of the genome of the tubercle bacillus, Mycobacterium tuberculosis, was constructed by using a twin-pronged approach. Pulsed-field gel electrophoretic analysis enabled cleavage sites for Asn I and Dra I to be positioned on the 4.4-Mb circular chromosome, while, in parallel, clones from two cosmid libraries were ordered into contigs by means of fingerprinting and hybridization mapping. The resultant contig map was readily correlated with the physical map of the genome via the landmarked restriction sites. Over 165 genes and markers were localized on the integrated map, thus enabling comparisons with the leprosy bacillus, Mycobacterium leprae, to be undertaken. Mycobacterial genomes appear to have evolved as mosaic structures since extended segments with conserved gene order and organization are interspersed with different flanking regions. Repetitive sequences and insertion elements are highly abundant in M. tuberculosis, but the distribution of IS6110 is apparently nonrandom. Images Fig. 1 Fig. 2 PMID:8610181

Tampa Bay environmental atlas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kunneke, J.T.; Palik, T.F.

1984-12-01

Biological and water resource data for Tampa Bay were compiled and mapped at a scale of 1:24,000. This atlas consists of (1) composited information overlain on 18 biological and 20 water resource base maps and (2) an accompanying map narrative. Subjects mapped on the water resource maps are contours of the mean middepth specific conductivity which can be converted to salinity; bathymetry, sediments, tidal currents, the freshwater/saltwater interface, dredge spoil disposal sites; locations of industrial and municipal point source discharges, tide stations, and water quality sampling stations. The point source discharge locations show permitted capacity and the water quality samplingmore » stations show 5-year averages for chlorophyll, conductivity, turbidity, temperature, and total nitrogen. The subjects shown on the biological resource maps are clam and oyster beds, shellfish harvest areas, colonial bird nesting sites, manatee habitat, seagrass beds and artificial reefs. Spawning seasons, nursery habitats, and adult habitats are identified for major fish species. The atlas will provide useful information for coastal planning and management in Tampa Bay.« less

Interval data clustering using self-organizing maps based on adaptive Mahalanobis distances.

PubMed

Hajjar, Chantal; Hamdan, Hani

2013-10-01

The self-organizing map is a kind of artificial neural network used to map high dimensional data into a low dimensional space. This paper presents a self-organizing map for interval-valued data based on adaptive Mahalanobis distances in order to do clustering of interval data with topology preservation. Two methods based on the batch training algorithm for the self-organizing maps are proposed. The first method uses a common Mahalanobis distance for all clusters. In the second method, the algorithm starts with a common Mahalanobis distance per cluster and then switches to use a different distance per cluster. This process allows a more adapted clustering for the given data set. The performances of the proposed methods are compared and discussed using artificial and real interval data sets. Copyright © 2013 Elsevier Ltd. All rights reserved.

Fiber-dependent deautonomization of integrable 2D mappings and discrete Painlevé equations

NASA Astrophysics Data System (ADS)

Carstea, Adrian Stefan; Dzhamay, Anton; Takenawa, Tomoyuki

2017-10-01

It is well known that two-dimensional mappings preserving a rational elliptic fibration, like the Quispel-Roberts-Thompson mappings, can be deautonomized to discrete Painlevé equations. However, the dependence of this procedure on the choice of a particular elliptic fiber has not been sufficiently investigated. In this paper we establish a way of performing the deautonomization for a pair of an autonomous mapping and a fiber. Starting from a single autonomous mapping but varying the type of a chosen fiber, we obtain different types of discrete Painlevé equations using this deautonomization procedure. We also introduce a technique for reconstructing a mapping from the knowledge of its induced action on the Picard group and some additional geometric data. This technique allows us to obtain factorized expressions of discrete Painlevé equations, including the elliptic case. Further, by imposing certain restrictions on such non-autonomous mappings we obtain new and simple elliptic difference Painlevé equations, including examples whose symmetry groups do not appear explicitly in Sakai’s classification.

VEGETATION COVER ANALYSIS OF HAZARDOUS WASTE SITES IN UTAH AND ARIZONA USING HYPERSPECTRAL REMOTE SENSING

DOE Office of Scientific and Technical Information (OSTI.GOV)

Serrato, M.; Jungho, I.; Jensen, J.

2012-01-17

Remote sensing technology can provide a cost-effective tool for monitoring hazardous waste sites. This study investigated the usability of HyMap airborne hyperspectral remote sensing data (126 bands at 2.3 x 2.3 m spatial resolution) to characterize the vegetation at U.S. Department of Energy uranium processing sites near Monticello, Utah and Monument Valley, Arizona. Grass and shrub species were mixed on an engineered disposal cell cover at the Monticello site while shrub species were dominant in the phytoremediation plantings at the Monument Valley site. The specific objectives of this study were to: (1) estimate leaf-area-index (LAI) of the vegetation using threemore » different methods (i.e., vegetation indices, red-edge positioning (REP), and machine learning regression trees), and (2) map the vegetation cover using machine learning decision trees based on either the scaled reflectance data or mixture tuned matched filtering (MTMF)-derived metrics and vegetation indices. Regression trees resulted in the best calibration performance of LAI estimation (R{sup 2} > 0.80). The use of REPs failed to accurately predict LAI (R{sup 2} < 0.2). The use of the MTMF-derived metrics (matched filter scores and infeasibility) and a range of vegetation indices in decision trees improved the vegetation mapping when compared to the decision tree classification using just the scaled reflectance. Results suggest that hyperspectral imagery are useful for characterizing biophysical characteristics (LAI) and vegetation cover on capped hazardous waste sites. However, it is believed that the vegetation mapping would benefit from the use of 1 higher spatial resolution hyperspectral data due to the small size of many of the vegetation patches (< 1m) found on the sites.« less

Small Molecule Interactome Mapping by Photoaffinity Labeling Reveals Binding Site Hotspots for the NSAIDs.

PubMed

Gao, Jinxu; Mfuh, Adelphe; Amako, Yuka; Woo, Christina M

2018-03-28

Many therapeutics elicit cell-type specific polypharmacology that is executed by a network of molecular recognition events between a small molecule and the whole proteome. However, measurement of the structures that underpin the molecular associations between the proteome and even common therapeutics, such as the nonsteroidal anti-inflammatory drugs (NSAIDs), is limited by the inability to map the small molecule interactome. To address this gap, we developed a platform termed small molecule interactome mapping by photoaffinity labeling (SIM-PAL) and applied it to the in cellulo direct characterization of specific NSAID binding sites. SIM-PAL uses (1) photochemical conjugation of NSAID derivatives in the whole proteome and (2) enrichment and isotope-recoding of the conjugated peptides for (3) targeted mass spectrometry-based assignment. Using SIM-PAL, we identified the NSAID interactome consisting of over 1000 significantly enriched proteins and directly characterized nearly 200 conjugated peptides representing direct binding sites of the photo-NSAIDs with proteins from Jurkat and K562 cells. The enriched proteins were often identified as parts of complexes, including known targets of NSAID activity (e.g., NF-κB) and novel interactions (e.g., AP-2, proteasome). The conjugated peptides revealed direct NSAID binding sites from the cell surface to the nucleus and a specific binding site hotspot for the three photo-NSAIDs on histones H2A and H2B. NSAID binding stabilized COX-2 and histone H2A by cellular thermal shift assay. Since small molecule stabilization of protein complexes is a gain of function regulatory mechanism, it is conceivable that NSAIDs affect biological processes through these broader proteomic interactions. SIM-PAL enabled characterization of NSAID binding site hotspots and is amenable to map global binding sites for virtually any molecule of interest.

Accounting for geophysical information in geostatistical characterization of unexploded ordnance (UXO) sites.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saito, Hirotaka; Goovaerts, Pierre; McKenna, Sean Andrew

2003-06-01

Efficient and reliable unexploded ordnance (UXO) site characterization is needed for decisions regarding future land use. There are several types of data available at UXO sites and geophysical signal maps are one of the most valuable sources of information. Incorporation of such information into site characterization requires a flexible and reliable methodology. Geostatistics allows one to account for exhaustive secondary information (i.e.,, known at every location within the field) in many different ways. Kriging and logistic regression were combined to map the probability of occurrence of at least one geophysical anomaly of interest, such as UXO, from a limited numbermore » of indicator data. Logistic regression is used to derive the trend from a geophysical signal map, and kriged residuals are added to the trend to estimate the probabilities of the presence of UXO at unsampled locations (simple kriging with varying local means or SKlm). Each location is identified for further remedial action if the estimated probability is greater than a given threshold. The technique is illustrated using a hypothetical UXO site generated by a UXO simulator, and a corresponding geophysical signal map. Indicator data are collected along two transects located within the site. Classification performances are then assessed by computing proportions of correct classification, false positive, false negative, and Kappa statistics. Two common approaches, one of which does not take any secondary information into account (ordinary indicator kriging) and a variant of common cokriging (collocated cokriging), were used for comparison purposes. Results indicate that accounting for exhaustive secondary information improves the overall characterization of UXO sites if an appropriate methodology, SKlm in this case, is used.« less

Improved detection and mapping of deepwater hydrocarbon seeps: optimizing multibeam echosounder seafloor backscatter acquisition and processing techniques

NASA Astrophysics Data System (ADS)

Mitchell, Garrett A.; Orange, Daniel L.; Gharib, Jamshid J.; Kennedy, Paul

2018-06-01

Marine seep hunting surveys are a current focus of hydrocarbon exploration surveys due to recent advances in offshore geophysical surveying, geochemical sampling, and analytical technologies. Hydrocarbon seeps are ephemeral, small, discrete, and therefore difficult to sample on the deep seafloor. Multibeam echosounders are an efficient seafloor exploration tool to remotely locate and map seep features. Geophysical signatures from hydrocarbon seeps are acoustically-evident in bathymetric, seafloor backscatter, midwater backscatter datasets. Interpretation of these signatures in backscatter datasets is a fundamental component of commercial seep hunting campaigns. Degradation of backscatter datasets resulting from environmental, geometric, and system noise can interfere with the detection and delineation of seeps. We present a relative backscatter intensity normalization method and an oversampling acquisition technique that can improve the geological resolvability of hydrocarbon seeps. We use Green Canyon (GC) Block 600 in the Northern Gulf of Mexico as a seep calibration site for a Kongsberg EM302 30 kHz MBES prior to the start of the Gigante seep hunting program to analyze these techniques. At GC600, we evaluate the results of a backscatter intensity normalization, assess the effectiveness of 2X seafloor coverage in resolving seep-related features in backscatter data, and determine the off-nadir detection limits of bubble plumes using the EM302. Incorporating these techniques into seep hunting surveys can improve the detectability and sampling of seafloor seeps.

Non-AUG translation: a new start for protein synthesis in eukaryotes

PubMed Central

Kearse, Michael G.; Wilusz, Jeremy E.

2017-01-01

Although it was long thought that eukaryotic translation almost always initiates at an AUG start codon, recent advancements in ribosome footprint mapping have revealed that non-AUG start codons are used at an astonishing frequency. These non-AUG initiation events are not simply errors but instead are used to generate or regulate proteins with key cellular functions; for example, during development or stress. Misregulation of non-AUG initiation events contributes to multiple human diseases, including cancer and neurodegeneration, and modulation of non-AUG usage may represent a novel therapeutic strategy. It is thus becoming increasingly clear that start codon selection is regulated by many trans-acting initiation factors as well as sequence/structural elements within messenger RNAs and that non-AUG translation has a profound impact on cellular states. PMID:28982758

Transcription termination and RNA processing in the 3'-end spacer of mouse ribosomal RNA genes.

PubMed Central

Miwa, T; Kominami, R; Yoshikura, H; Sudo, K; Muramatsu, M

1987-01-01

The 3' termini of ribosomal RNA precursors from mouse FM3A cultured cells are mapped to eight sites within 625 bp downstream from the 3' terminus of 28 S rRNA. Three additional sites are mapped in liver RNA from C3H/He strain mice. Two of them, the sites at 570 bp and 625 bp are assumed to be termination sites in vivo, because they correspond to in vitro termination sites of RNA polymerase I, and 45 S RNAs having these 3' termini decay with kinetics distinct from others. The amount of 45 S RNA having the 3' terminus at other sites is variable among several mouse strains, despite their having the same DNA sequence in these regions. The ability to produce 3' termini in these sites seems to follow Mendel's law of inheritance. Therefore, we postulate that these nine sites are RNA processing sites which are controlled genetically. Images PMID:3031586

MaGa, a web-based collaborative database for gas emissions: a tool to improve the knowledge on Earth degassing

NASA Astrophysics Data System (ADS)

Frigeri, A.; Cardellini, C.; Chiodini, G.; Frondini, F.; Bagnato, E.; Aiuppa, A.; Fischer, T. P.; Lehnert, K. A.

2014-12-01

The study of the main pathways of carbon flux from the deep Earth requires the analysis of a large quantity and variety of data on volcanic and non-volcanic gas emissions. Hence, there is need for common frameworks to aggregate available data and insert new observations. Since 2010 we have been developing the Mapping Gas emissions (MaGa) web-based database to collect data on carbon degassing form volcanic and non-volcanic environments. MaGa uses an Object-relational model, translating the experience of field surveyors into the database schema. The current web interface of MaGa allows users to browse the data in tabular format or by browsing an interactive web-map. Enabled users can insert information as measurement methods, instrument details as well as the actual values collected in the field. Measurements found in the literature can be inserted as well as direct field observations made by human-operated instruments. Currently the database includes fluxes and gas compositions from active craters degassing, diffuse soil degassing and fumaroles both from dormant volcanoes and open-vent volcanoes from literature survey and data about non-volcanic emission of the Italian territory. Currently, MaGa holds more than 1000 volcanic plume degassing fluxes, data from 30 sites of diffuse soil degassing from italian volcanoes, and about 60 measurements from fumarolic and non volcanic emission sites. For each gas emission site, the MaGa holds data, pictures, descriptions on gas sampling, analysis and measurement methods, together with bibliographic references and contacts to researchers having experience on each site. From 2012, MaGa developments started to be focused towards the framework of the Deep Earth Carbon Degassing research initiative of the Deep Carbon Observatory. Whithin the DECADE initiative, there are others data systems, as EarthChem and the Smithsonian Institution's Global Volcanism Program. An interoperable interaction between the DECADE data systems is being planned. MaGa is showing good potentials to improve the knowledge on Earth degassing firstly by making data more accessible and encouraging participation among researchers, and secondly by allowing to observe and explore, for the first time, a gas emission dataset with spatial and temporal extents never analyzed before.

Geomorphological and Spectrophotometric Study of Philae Landing Site A

NASA Astrophysics Data System (ADS)

Pajola, M.; La Forgia, F.; Giacomini, L.; Oklay, N.; Massironi, M.; Bertini, I.; Simioni, E.; Marzari, F.; Barbieri, C.; Naletto, G.; Groussin, O.; Lazzarin, M.; Scholten, F.; Preusker, F.; Fornasier, S.; Vincent, J. B.; Sierks, H.

2015-10-01

On August 6, 2014, the European Space Agency's Rosetta spacecraft started orbiting the Jupiter family comet 67P/Churyumov-Gerasimenko (hereafter 67P). Afterwards, the OSIRIS instrument (Optical, Spectroscopic and Infrared Remote Imaging System [1]), got the highest-resolution-ever images of a cometary nucleus, reaching the unprecedented scale of 50 cm/px. A brief description of OSIRIS early analysis on the nucleus structure and activity of 67P is available in [2]. Despite its small dimensions, #4 km diameter, 67P shows a morphological diversity that is still puzzling the cometary community: boulders [3], highreflectivity particle clusters [4], local fracturing [5], pits [6], as well as dust covered terrains [7], are only few examples that can be found on 67P. Since the Rosetta arrival, an extremely detailed analysis of 67P surface has been performed to select five different landing sites candidates for the lander Philae. By using the OSIRIS images the comet shape model [8] has been produced to study the slope constraints, as well as the identification and measurements of boulders and production of hazard maps of the landing spots [3]. A final landing site, called Agilkia and located on the smaller lobe of the comet, was announced on October 15, 2014. Here, Philae, on November 12, 2014, made its historic comet touchdown [9]. Despite its unique scientific potential, one of the five finalists, called "site A", was avoided due to higher risks with respect to Agilkia, during both the landing phase and the surface operations. This area is located on the bigger lobe of the comet, on the Seth region [10] facing the Hathor cliff. Site A (Fig. 1) is close to the 'neck' region, i.e. the connecting bridge between the two lobes, where the main dust jet activity has been observed since the Rosetta arrival. This area is the biggest terrace of Seth region, delimited in the upper part by a steep wall showing multiple niches, strata heads and smaller terraces. Moreover, between the 5 finalists, this site has the unique value to provide detailed analysis of the multiple fractures present on its cliff and on the neighboring Hathor. Figure 1: Site A as imaged by the OSIRIS NAC camera on 6 August 2014 at 02:20:12 UT. The distance from the comet center is 117.24 km, the scale is 2.17 m/px. EPSC Abstracts Vol. 10, EPSC2015-526, 2015 European Planetary Science Congress 2015 c Author(s) 2015 EPSC European Planetary Science Congress We here present the geomorphological map coupled with the size-frequency distributions of boulders # 2 m located on the different types of terrains here identified, such as outcropping layered terrains, gravitational accumulation deposits, taluses and fine particle deposits. Gravitational slopes, derived through the 67P shape model by assuming uniform density, have been used to characterize and better interpret the various terrains. Moreover, we show the spectrophotometric properties of the area, studied through images taken by OSIRIS NAC with a scale of 50 cm/px. Albedo maps, as well as surface reflectance spectra have been obtained by taking advantage of the shape model and DTM in order to correct for the illumination and observing conditions of the terrain. This multidisciplinary analysis highlights that different types of deposits show different photometric properties.

STK Integrated Message Production List Editor (SIMPLE) for CEO Operations

NASA Technical Reports Server (NTRS)

Trenchard, Mike; Heydorn, James

2014-01-01

Late in fiscal year 2011, the Crew Earth Observations (CEO) team was tasked to upgrade and replace its mission planning and mission operations software systems, which were developed in the Space Shuttle era of the 1980s and 1990s. The impetuses for this change were the planned transition of all workstations to the Windows 7 64-bit operating system and the desire for more efficient and effective use of Satellite Tool Kit (STK) software required for reliable International Space Station (ISS) Earth location tracking. An additional requirement of this new system was the use of the same SQL database of CEO science sites from the SMMS, which was also being developed. STK Integrated Message Production List Editor (SIMPLE) is the essential, all-in-one tool now used by CEO staff to perform daily ISS mission planning to meet its requirement to acquire astronaut photography of specific sites on Earth. The sites are part of a managed, long-term database that has been defined and developed for scientific, educational, and public interest. SIMPLE's end product is a set of basic time and location data computed for an operator-selected set of targets that the ISS crew will be asked to photograph (photography is typically planned 12 to 36 hours out). The CEO operator uses SIMPLE to (a) specify a payload operations planning period; (b) acquire and validate the best available ephemeris data (vectors) for the ISS during the planning period; (c) ingest and display mission-specific site information from the CEO database; (d) identify and display potential current dynamic event targets as map features; (e) compute and display time and location information for each target; (f) screen and select targets based on known crew availability constraints, obliquity constraints, and real-time evaluated constraints to target visibility due to illumination (sun elevation) and atmospheric conditions (weather); and finally (g) incorporate basic, computed time and location information for each selected target into the daily CEO Target List product (message) for submission to ISS payload planning and integration teams for their review and approval prior to uplink. SIMPLE requires and uses the following resources: an ISS mission planning period Greenwich Mean Time start date/time and end date/time), the best available ISS mission ephemeris data (vectors) for that planning period, the STK software package configured for the ISS, and an ISS mission-specific subset of the CEO sites database. The primary advantages realized by the development and implementation of SIMPLE into the CEO payload operations support activity are a smooth transition to the Windows 7 operating system upon scheduled workstation refresh; streamlining of the input and verification of the current ISS ephemeris (vector data); seamless incorporation of selected contents of the SQL database of science sites; the ability to tag and display potential dynamic event opportunities on orbit track maps; simplification of the display and selection of encountered sites based on crew availability, illumination, obliquity, and weather constraints; the incorporation of high-quality mapping of the Earth with various satellite-based datasets for use in describing targets; and the ability to encapsulate and export the essential selected target elements in XML format for use by onboard Earth-location systems, such as Worldmap. SIMPLE is a carefully designed and crafted in-house software package that includes detailed help files for the user and meticulous internal documentation for future modifications. It was delivered in February 2012 for test and evaluation. Following acceptance, it was implemented for CEO mission operations support in May 2012.

Spectral signature selection for mapping unvegetated soils

NASA Technical Reports Server (NTRS)

May, G. A.; Petersen, G. W.

1975-01-01

Airborne multispectral scanner data covering the wavelength interval from 0.40-2.60 microns were collected at an altitude of 1000 m above the terrain in southeastern Pennsylvania. Uniform training areas were selected within three sites from this flightline. Soil samples were collected from each site and a procedure developed to allow assignment of scan line and element number from the multispectral scanner data to each sampling location. These soil samples were analyzed on a spectrophotometer and laboratory spectral signatures were derived. After correcting for solar radiation and atmospheric attenuation, the laboratory signatures were compared to the spectral signatures derived from these same soils using multispectral scanner data. Both signatures were used in supervised and unsupervised classification routines. Computer-generated maps using the laboratory and multispectral scanner derived signatures resulted in maps that were similar to maps resulting from field surveys. Approximately 90% agreement was obtained between classification maps produced using multispectral scanner derived signatures and laboratory derived signatures.

Testing Maternal Depression and Attachment Style as Moderators of Early Head Start's Effects on Parenting

PubMed Central

Berlin, Lisa J.; Whiteside-Mansell, Leanne; Roggman, Lori A.; Green, Beth L.; Robinson, JoAnn; Spieker, Susan

2010-01-01

This study examined maternal depression, attachment avoidance, and attachment anxiety as moderators of Early Head Start's effects on four parenting outcomes assessed at age 3. Participants (N = 947) were drawn from six sites of the Early Head Start National Research and Evaluation Project, a multi-site randomized trial. Findings suggest more positive program effects for mothers with less initial attachment avoidance or attachment anxiety. First, baseline attachment avoidance moderated EHS program effects on observed maternal supportiveness, such that program mothers with lower baseline attachment avoidance were rated as more supportive of their 3-year-olds than program mothers with higher baseline attachment avoidance. Second, program effects on spanking varied depending on mothers’ baseline attachment anxiety. PMID:21240694