WorldWideScience

Sample records for previously identified sites

  1. SitesIdentify: a protein functional site prediction tool

    Directory of Open Access Journals (Sweden)

    Doig Andrew J

    2009-11-01

    Full Text Available Abstract Background The rate of protein structures being deposited in the Protein Data Bank surpasses the capacity to experimentally characterise them and therefore computational methods to analyse these structures have become increasingly important. Identifying the region of the protein most likely to be involved in function is useful in order to gain information about its potential role. There are many available approaches to predict functional site, but many are not made available via a publicly-accessible application. Results Here we present a functional site prediction tool (SitesIdentify, based on combining sequence conservation information with geometry-based cleft identification, that is freely available via a web-server. We have shown that SitesIdentify compares favourably to other functional site prediction tools in a comparison of seven methods on a non-redundant set of 237 enzymes with annotated active sites. Conclusion SitesIdentify is able to produce comparable accuracy in predicting functional sites to its closest available counterpart, but in addition achieves improved accuracy for proteins with few characterised homologues. SitesIdentify is available via a webserver at http://www.manchester.ac.uk/bioinformatics/sitesidentify/

  2. Identifying suitable sites for Florida panther reintroduction

    Science.gov (United States)

    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.

  3. Previously unidentified changes in renal cell carcinoma gene expression identified by parametric analysis of microarray data

    International Nuclear Information System (INIS)

    Lenburg, Marc E; Liou, Louis S; Gerry, Norman P; Frampton, Garrett M; Cohen, Herbert T; Christman, Michael F

    2003-01-01

    Renal cell carcinoma is a common malignancy that often presents as a metastatic-disease for which there are no effective treatments. To gain insights into the mechanism of renal cell carcinogenesis, a number of genome-wide expression profiling studies have been performed. Surprisingly, there is very poor agreement among these studies as to which genes are differentially regulated. To better understand this lack of agreement we profiled renal cell tumor gene expression using genome-wide microarrays (45,000 probe sets) and compare our analysis to previous microarray studies. We hybridized total RNA isolated from renal cell tumors and adjacent normal tissue to Affymetrix U133A and U133B arrays. We removed samples with technical defects and removed probesets that failed to exhibit sequence-specific hybridization in any of the samples. We detected differential gene expression in the resulting dataset with parametric methods and identified keywords that are overrepresented in the differentially expressed genes with the Fisher-exact test. We identify 1,234 genes that are more than three-fold changed in renal tumors by t-test, 800 of which have not been previously reported to be altered in renal cell tumors. Of the only 37 genes that have been identified as being differentially expressed in three or more of five previous microarray studies of renal tumor gene expression, our analysis finds 33 of these genes (89%). A key to the sensitivity and power of our analysis is filtering out defective samples and genes that are not reliably detected. The widespread use of sample-wise voting schemes for detecting differential expression that do not control for false positives likely account for the poor overlap among previous studies. Among the many genes we identified using parametric methods that were not previously reported as being differentially expressed in renal cell tumors are several oncogenes and tumor suppressor genes that likely play important roles in renal cell

  4. Case-control study for colorectal cancer genetic susceptibility in EPICOLON: previously identified variants and mucins

    Directory of Open Access Journals (Sweden)

    Moreno Victor

    2011-08-01

    Full Text Available Abstract Background Colorectal cancer (CRC is the second leading cause of cancer death in developed countries. Familial aggregation in CRC is also important outside syndromic forms and, in this case, a polygenic model with several common low-penetrance alleles contributing to CRC genetic predisposition could be hypothesized. Mucins and GALNTs (N-acetylgalactosaminyltransferase are interesting candidates for CRC genetic susceptibility and have not been previously evaluated. We present results for ten genetic variants linked to CRC risk in previous studies (previously identified category and 18 selected variants from the mucin gene family in a case-control association study from the Spanish EPICOLON consortium. Methods CRC cases and matched controls were from EPICOLON, a prospective, multicenter, nationwide Spanish initiative, comprised of two independent stages. Stage 1 corresponded to 515 CRC cases and 515 controls, whereas stage 2 consisted of 901 CRC cases and 909 controls. Also, an independent cohort of 549 CRC cases and 599 controls outside EPICOLON was available for additional replication. Genotyping was performed for ten previously identified SNPs in ADH1C, APC, CCDN1, IL6, IL8, IRS1, MTHFR, PPARG, VDR and ARL11, and 18 selected variants in the mucin gene family. Results None of the 28 SNPs analyzed in our study was found to be associated with CRC risk. Although four SNPs were significant with a P-value ADH1C (OR = 1.63, 95% CI = 1.06-2.50, P-value = 0.02, recessive, rs1800795 in IL6 (OR = 1.62, 95% CI = 1.10-2.37, P-value = 0.01, recessive, rs3803185 in ARL11 (OR = 1.58, 95% CI = 1.17-2.15, P-value = 0.007, codominant, and rs2102302 in GALNTL2 (OR = 1.20, 95% CI = 1.00-1.44, P-value = 0.04, log-additive 0, 1, 2 alleles], only rs3803185 achieved statistical significance in EPICOLON stage 2 (OR = 1.34, 95% CI = 1.06-1.69, P-value = 0.01, recessive. In the joint analysis for both stages, results were only significant for rs3803185 (OR = 1

  5. Case-control study for colorectal cancer genetic susceptibility in EPICOLON: previously identified variants and mucins

    International Nuclear Information System (INIS)

    Abulí, Anna; Morillas, Juan D; Rigau, Joaquim; Latorre, Mercedes; Fernández-Bañares, Fernando; Peña, Elena; Riestra, Sabino; Payá, Artemio; Jover, Rodrigo; Xicola, Rosa M; Llor, Xavier; Fernández-Rozadilla, Ceres; Carvajal-Carmona, Luis; Villanueva, Cristina M; Moreno, Victor; Piqué, Josep M; Carracedo, Angel; Castells, Antoni; Andreu, Montserrat; Ruiz-Ponte, Clara; Castellví-Bel, Sergi; Alonso-Espinaco, Virginia; Muñoz, Jenifer; Gonzalo, Victoria; Bessa, Xavier; González, Dolors; Clofent, Joan; Cubiella, Joaquin

    2011-01-01

    Colorectal cancer (CRC) is the second leading cause of cancer death in developed countries. Familial aggregation in CRC is also important outside syndromic forms and, in this case, a polygenic model with several common low-penetrance alleles contributing to CRC genetic predisposition could be hypothesized. Mucins and GALNTs (N-acetylgalactosaminyltransferase) are interesting candidates for CRC genetic susceptibility and have not been previously evaluated. We present results for ten genetic variants linked to CRC risk in previous studies (previously identified category) and 18 selected variants from the mucin gene family in a case-control association study from the Spanish EPICOLON consortium. CRC cases and matched controls were from EPICOLON, a prospective, multicenter, nationwide Spanish initiative, comprised of two independent stages. Stage 1 corresponded to 515 CRC cases and 515 controls, whereas stage 2 consisted of 901 CRC cases and 909 controls. Also, an independent cohort of 549 CRC cases and 599 controls outside EPICOLON was available for additional replication. Genotyping was performed for ten previously identified SNPs in ADH1C, APC, CCDN1, IL6, IL8, IRS1, MTHFR, PPARG, VDR and ARL11, and 18 selected variants in the mucin gene family. None of the 28 SNPs analyzed in our study was found to be associated with CRC risk. Although four SNPs were significant with a P-value < 0.05 in EPICOLON stage 1 [rs698 in ADH1C (OR = 1.63, 95% CI = 1.06-2.50, P-value = 0.02, recessive), rs1800795 in IL6 (OR = 1.62, 95% CI = 1.10-2.37, P-value = 0.01, recessive), rs3803185 in ARL11 (OR = 1.58, 95% CI = 1.17-2.15, P-value = 0.007, codominant), and rs2102302 in GALNTL2 (OR = 1.20, 95% CI = 1.00-1.44, P-value = 0.04, log-additive 0, 1, 2 alleles], only rs3803185 achieved statistical significance in EPICOLON stage 2 (OR = 1.34, 95% CI = 1.06-1.69, P-value = 0.01, recessive). In the joint analysis for both stages, results were only significant for rs3803185 (OR = 1.12, 95% CI = 1

  6. Survival of dental implants placed in sites of previously failed implants.

    Science.gov (United States)

    Chrcanovic, Bruno R; Kisch, Jenö; Albrektsson, Tomas; Wennerberg, Ann

    2017-11-01

    To assess the survival of dental implants placed in sites of previously failed implants and to explore the possible factors that might affect the outcome of this reimplantation procedure. Patients that had failed dental implants, which were replaced with the same implant type at the same site, were included. Descriptive statistics were used to describe the patients and implants; survival analysis was also performed. The effect of systemic, environmental, and local factors on the survival of the reoperated implants was evaluated. 175 of 10,096 implants in 98 patients were replaced by another implant at the same location (159, 14, and 2 implants at second, third, and fourth surgeries, respectively). Newly replaced implants were generally of similar diameter but of shorter length compared to the previously placed fixtures. A statistically significant greater percentage of lost implants were placed in sites with low bone quantity. There was a statistically significant difference (P = 0.032) in the survival rates between implants that were inserted for the first time (94%) and implants that replaced the ones lost (73%). There was a statistically higher failure rate of the reoperated implants for patients taking antidepressants and antithrombotic agents. Dental implants replacing failed implants had lower survival rates than the rates reported for the previous attempts of implant placement. It is suggested that a site-specific negative effect may possibly be associated with this phenomenon, as well as the intake of antidepressants and antithrombotic agents. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  7. Using an epiphytic moss to identify previously unknown sources of atmospheric cadmium pollution

    Science.gov (United States)

    Geoffrey H. Donovan; Sarah E. Jovan; Demetrios Gatziolis; Igor Burstyn; Yvonne L. Michael; Michael C. Amacher; Vicente J. Monleon

    2016-01-01

    Urban networks of air-quality monitors are often too widely spaced to identify sources of air pollutants, especially if they do not disperse far from emission sources. The objectives of this study were to test the use of moss bio-indicators to develop a fine-scale map of atmospherically-derived cadmium and to identify the sources of cadmium in a complex urban setting....

  8. Detection of previously undiagnosed cases of COPD in a high-risk population identified in general practice

    DEFF Research Database (Denmark)

    Løkke, Anders; Ulrik, Charlotte Suppli; Dahl, Ronald

    2012-01-01

    Background and Aim: Under-diagnosis of COPD is a widespread problem. This study aimed to identify previously undiagnosed cases of COPD in a high-risk population identified through general practice. Methods: Participating GPs (n = 241) recruited subjects with no previous diagnosis of lung disease,...

  9. Cardiorespiratory interactions previously identified as mammalian are present in the primitive lungfish.

    Science.gov (United States)

    Monteiro, Diana A; Taylor, Edwin W; Sartori, Marina R; Cruz, André L; Rantin, Francisco T; Leite, Cleo A C

    2018-02-01

    The present study has revealed that the lungfish has both structural and functional features of its system for physiological control of heart rate, previously considered solely mammalian, that together generate variability (HRV). Ultrastructural and electrophysiological investigation revealed that the nerves connecting the brain to the heart are myelinated, conferring rapid conduction velocities, comparable to mammalian fibers that generate instantaneous changes in heart rate at the onset of each air breath. These respiration-related changes in beat-to-beat cardiac intervals were detected by complex analysis of HRV and shown to maximize oxygen uptake per breath, a causal relationship never conclusively demonstrated in mammals. Cardiac vagal preganglionic neurons, responsible for controlling heart rate via the parasympathetic vagus nerve, were shown to have multiple locations, chiefly within the dorsal vagal motor nucleus that may enable interactive control of the circulatory and respiratory systems, similar to that described for tetrapods. The present illustration of an apparently highly evolved control system for HRV in a fish with a proven ancient lineage, based on paleontological, morphological, and recent genetic evidence, questions much of the anthropocentric thinking implied by some mammalian physiologists and encouraged by many psychobiologists. It is possible that some characteristics of mammalian respiratory sinus arrhythmia, for which functional roles have been sought, are evolutionary relics that had their physiological role defined in ancient representatives of the vertebrates with undivided circulatory systems.

  10. Cardiorespiratory interactions previously identified as mammalian are present in the primitive lungfish

    Science.gov (United States)

    Monteiro, Diana A.; Taylor, Edwin W.; Sartori, Marina R.; Cruz, André L.; Rantin, Francisco T.; Leite, Cleo A. C.

    2018-01-01

    The present study has revealed that the lungfish has both structural and functional features of its system for physiological control of heart rate, previously considered solely mammalian, that together generate variability (HRV). Ultrastructural and electrophysiological investigation revealed that the nerves connecting the brain to the heart are myelinated, conferring rapid conduction velocities, comparable to mammalian fibers that generate instantaneous changes in heart rate at the onset of each air breath. These respiration-related changes in beat-to-beat cardiac intervals were detected by complex analysis of HRV and shown to maximize oxygen uptake per breath, a causal relationship never conclusively demonstrated in mammals. Cardiac vagal preganglionic neurons, responsible for controlling heart rate via the parasympathetic vagus nerve, were shown to have multiple locations, chiefly within the dorsal vagal motor nucleus that may enable interactive control of the circulatory and respiratory systems, similar to that described for tetrapods. The present illustration of an apparently highly evolved control system for HRV in a fish with a proven ancient lineage, based on paleontological, morphological, and recent genetic evidence, questions much of the anthropocentric thinking implied by some mammalian physiologists and encouraged by many psychobiologists. It is possible that some characteristics of mammalian respiratory sinus arrhythmia, for which functional roles have been sought, are evolutionary relics that had their physiological role defined in ancient representatives of the vertebrates with undivided circulatory systems. PMID:29507882

  11. A new commelinid monocot seed fossil from the early Eocene previously identified as Solanaceae.

    Science.gov (United States)

    Särkinen, Tiina; Kottner, Sören; Stuppy, Wolfgang; Ahmed, Farah; Knapp, Sandra

    2018-01-01

    Fossils provide minimum age estimates for extant lineages. Here we critically evaluate Cantisolanum daturoides Reid & Chandler and two other early putative seed fossils of Solanaceae, an economically important plant family in the Asteridae. Three earliest seed fossil taxa of Solanaceae from the London Clay Formation (Cantisolanum daturoides) and the Poole and Branksome Sand Formations (Solanum arnense Chandler and Solanispermum reniforme Chandler) were studied using x-ray microcomputed tomography (MCT) and scanning electron microscopy (SEM). The MCT scans of Cantisolanum daturoides revealed a high level of pyrite preservation at the cellular level. Cantisolanum daturoides can be clearly excluded from Solanaceae and has more affinities to the commelinid monocots based on a straight longitudinal axis, a prominent single layer of relatively thin-walled cells in the testa, and a clearly differentiated micropyle surrounded by radially elongated and inwardly curved testal cells. While the MCT scans show no internal preservation in Solanum arnense and Solanispermum reniforme, SEM images show the presence of several characteristics that allow the placement of these taxa at the stem node of Solanaceae. Cantisolanum daturoides is likely a member of commelinid monocots and not Solanaceae as previously suggested. The earliest fossil record of Solanaceae is revised to consist of fruit fossil with inflated calyces from the early Eocene of Patagonia (52 Ma) and fossilized seeds from the early to mid-Eocene of Europe (48-46 Ma). The new identity for Cantisolanum daturoides does not alter a late Cretaceous minimum age for commelinids. © 2018 Botanical Society of America.

  12. Using an epiphytic moss to identify previously unknown sources of atmospheric cadmium pollution

    Energy Technology Data Exchange (ETDEWEB)

    Donovan, Geoffrey H., E-mail: gdonovan@fs.fed.us [USDA Forest Service, PNW Research Station, 620 SW Main, Suite 400, Portland, OR 97205 (United States); Jovan, Sarah E., E-mail: sjovan@fs.fed.us [USDA Forest Service, PNW Research Station, 620 SW Main, Suite 400, Portland, OR 97205 (United States); Gatziolis, Demetrios, E-mail: dgatziolis@fs.fed.us [USDA Forest Service, PNW Research Station, 620 SW Main, Suite 400, Portland, OR 97205 (United States); Burstyn, Igor, E-mail: igor.burstyn@drexel.edu [Dornsife School of Public Health, Drexel University, Nesbitt Hall, 3215 Market St, Philadelphia, PA 19104 (United States); Michael, Yvonne L., E-mail: ylm23@drexel.edu [Dornsife School of Public Health, Drexel University, Nesbitt Hall, 3215 Market St, Philadelphia, PA 19104 (United States); Amacher, Michael C., E-mail: mcamacher1@outlook.com [USDA Forest Service, Logan Forest Sciences Laboratory, 860 North 1200 East, Logan, UT 84321 (United States); Monleon, Vicente J., E-mail: vjmonleon@fs.fed.us [USDA Forest Service, PNW Research Station, 3200 SW Jefferson Way, Corvallis, OR 97331 (United States)

    2016-07-15

    Urban networks of air-quality monitors are often too widely spaced to identify sources of air pollutants, especially if they do not disperse far from emission sources. The objectives of this study were to test the use of moss bio-indicators to develop a fine-scale map of atmospherically-derived cadmium and to identify the sources of cadmium in a complex urban setting. We collected 346 samples of the moss Orthotrichum lyellii from deciduous trees in December, 2013 using a modified randomized grid-based sampling strategy across Portland, Oregon. We estimated a spatial linear model of moss cadmium levels and predicted cadmium on a 50 m grid across the city. Cadmium levels in moss were positively correlated with proximity to two stained-glass manufacturers, proximity to the Oregon–Washington border, and percent industrial land in a 500 m buffer, and negatively correlated with percent residential land in a 500 m buffer. The maps showed very high concentrations of cadmium around the two stained-glass manufacturers, neither of which were known to environmental regulators as cadmium emitters. In addition, in response to our findings, the Oregon Department of Environmental Quality placed an instrumental monitor 120 m from the larger stained-glass manufacturer in October, 2015. The monthly average atmospheric cadmium concentration was 29.4 ng/m{sup 3}, which is 49 times higher than Oregon's benchmark of 0.6 ng/m{sup 3}, and high enough to pose a health risk from even short-term exposure. Both stained-glass manufacturers voluntarily stopped using cadmium after the monitoring results were made public, and the monthly average cadmium levels precipitously dropped to 1.1 ng/m{sup 3} for stained-glass manufacturer #1 and 0.67 ng/m{sup 3} for stained-glass manufacturer #2. - Highlights: • Bio-indicators are a valid method for measuring atmospheric pollutants • We used moss to map atmospheric cadmium in Portland, Oregon • Using a spatial linear model, we identified two

  13. Using an epiphytic moss to identify previously unknown sources of atmospheric cadmium pollution

    International Nuclear Information System (INIS)

    Donovan, Geoffrey H.; Jovan, Sarah E.; Gatziolis, Demetrios; Burstyn, Igor; Michael, Yvonne L.; Amacher, Michael C.; Monleon, Vicente J.

    2016-01-01

    Urban networks of air-quality monitors are often too widely spaced to identify sources of air pollutants, especially if they do not disperse far from emission sources. The objectives of this study were to test the use of moss bio-indicators to develop a fine-scale map of atmospherically-derived cadmium and to identify the sources of cadmium in a complex urban setting. We collected 346 samples of the moss Orthotrichum lyellii from deciduous trees in December, 2013 using a modified randomized grid-based sampling strategy across Portland, Oregon. We estimated a spatial linear model of moss cadmium levels and predicted cadmium on a 50 m grid across the city. Cadmium levels in moss were positively correlated with proximity to two stained-glass manufacturers, proximity to the Oregon–Washington border, and percent industrial land in a 500 m buffer, and negatively correlated with percent residential land in a 500 m buffer. The maps showed very high concentrations of cadmium around the two stained-glass manufacturers, neither of which were known to environmental regulators as cadmium emitters. In addition, in response to our findings, the Oregon Department of Environmental Quality placed an instrumental monitor 120 m from the larger stained-glass manufacturer in October, 2015. The monthly average atmospheric cadmium concentration was 29.4 ng/m"3, which is 49 times higher than Oregon's benchmark of 0.6 ng/m"3, and high enough to pose a health risk from even short-term exposure. Both stained-glass manufacturers voluntarily stopped using cadmium after the monitoring results were made public, and the monthly average cadmium levels precipitously dropped to 1.1 ng/m"3 for stained-glass manufacturer #1 and 0.67 ng/m"3 for stained-glass manufacturer #2. - Highlights: • Bio-indicators are a valid method for measuring atmospheric pollutants • We used moss to map atmospheric cadmium in Portland, Oregon • Using a spatial linear model, we identified two stained

  14. Using an epiphytic moss to identify previously unknown sources of atmospheric cadmium pollution.

    Science.gov (United States)

    Donovan, Geoffrey H; Jovan, Sarah E; Gatziolis, Demetrios; Burstyn, Igor; Michael, Yvonne L; Amacher, Michael C; Monleon, Vicente J

    2016-07-15

    Urban networks of air-quality monitors are often too widely spaced to identify sources of air pollutants, especially if they do not disperse far from emission sources. The objectives of this study were to test the use of moss bio-indicators to develop a fine-scale map of atmospherically-derived cadmium and to identify the sources of cadmium in a complex urban setting. We collected 346 samples of the moss Orthotrichum lyellii from deciduous trees in December, 2013 using a modified randomized grid-based sampling strategy across Portland, Oregon. We estimated a spatial linear model of moss cadmium levels and predicted cadmium on a 50m grid across the city. Cadmium levels in moss were positively correlated with proximity to two stained-glass manufacturers, proximity to the Oregon-Washington border, and percent industrial land in a 500m buffer, and negatively correlated with percent residential land in a 500m buffer. The maps showed very high concentrations of cadmium around the two stained-glass manufacturers, neither of which were known to environmental regulators as cadmium emitters. In addition, in response to our findings, the Oregon Department of Environmental Quality placed an instrumental monitor 120m from the larger stained-glass manufacturer in October, 2015. The monthly average atmospheric cadmium concentration was 29.4ng/m(3), which is 49 times higher than Oregon's benchmark of 0.6ng/m(3), and high enough to pose a health risk from even short-term exposure. Both stained-glass manufacturers voluntarily stopped using cadmium after the monitoring results were made public, and the monthly average cadmium levels precipitously dropped to 1.1ng/m(3) for stained-glass manufacturer #1 and 0.67ng/m(3) for stained-glass manufacturer #2. Published by Elsevier B.V.

  15. Regulatory O-GlcNAcylation sites on FoxO1 are yet to be identified

    Energy Technology Data Exchange (ETDEWEB)

    Fardini, Yann [INSERM, U1016, Institut Cochin, Paris (France); CNRS, UMR8104, Paris (France); Université Paris Descartes, Sorbonne Paris Cité, Paris (France); Perez-Cervera, Yobana [Structural and Functional Glycobiology Unit, Lille 1 University, CNRS (UMR 8576), IFR 117, Villeneuve d' Ascq (France); Facultad de Odontología, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca (Mexico); Camoin, Luc [INSERM, U1068, CRCM, Marseille Protéomique IBiSA, Marseille, F-13009 (France); Institut Paoli-Calmettes Team, Cell Polarity, Cell Signaling and Cancer, Marseille, F-13009 (France); Aix-Marseille Université, F-13284, Marseille (France); CNRS, UMR7258, CRCM, Marseille, F-13009 (France); Pagesy, Patrick [INSERM, U1016, Institut Cochin, Paris (France); CNRS, UMR8104, Paris (France); Université Paris Descartes, Sorbonne Paris Cité, Paris (France); Lefebvre, Tony [Structural and Functional Glycobiology Unit, Lille 1 University, CNRS (UMR 8576), IFR 117, Villeneuve d' Ascq (France); Issad, Tarik, E-mail: tarik.issad@inserm.fr [INSERM, U1016, Institut Cochin, Paris (France); CNRS, UMR8104, Paris (France); Université Paris Descartes, Sorbonne Paris Cité, Paris (France)

    2015-06-26

    O-GlcNAcylation is a reversible post-translational modification that regulates cytosolic and nuclear proteins. We and others previously demonstrated that FoxO1 is O-GlcNAcylated in different cell types, resulting in an increase in its transcriptional activity. Four O-GlcNAcylation sites were identified in human FOXO1 but directed mutagenesis of each site individually had modest (T317) or no effect (S550, T648, S654) on its O-GlcNAcylation status and transcriptional activity. Moreover, the consequences of mutating all four sites had not been investigated. In the present work, we mutated these sites in the mouse Foxo1 and found that mutation of all four sites did not decrease Foxo1 O-GlcNAcylation status and transcriptional activity, and would even tend to increase them. In an attempt to identify other O-GlcNAcylation sites, we immunoprecipitated wild-type O-GlcNAcylated Foxo1 and analysed the tryptic digest peptides by mass spectrometry using High-energy Collisional Dissociation. We identified T646 as a new O-GlcNAcylation site on Foxo1. However, site directed mutagenesis of this site individually or together with all four previously identified residues did not impair Foxo1 O-GlcNAcylation and transcriptional activity. These results suggest that residues important for the control of Foxo1 activity by O-GlcNAcylation still remain to be identified. - Highlights: • We mutate four previously identified O-GlcNAcylation sites on Foxo1. • Unexpectedly, these mutations do not reduce Foxo1 O-GlcNAcylation. • These mutation do not reduce Foxo1 transcriptional activity. • We identify a new O-GlcNAcylation site on Foxo1 by mass spectrometry. • Mutation of this site increases Foxo1 transcriptional activity.

  16. Regulatory O-GlcNAcylation sites on FoxO1 are yet to be identified

    International Nuclear Information System (INIS)

    Fardini, Yann; Perez-Cervera, Yobana; Camoin, Luc; Pagesy, Patrick; Lefebvre, Tony; Issad, Tarik

    2015-01-01

    O-GlcNAcylation is a reversible post-translational modification that regulates cytosolic and nuclear proteins. We and others previously demonstrated that FoxO1 is O-GlcNAcylated in different cell types, resulting in an increase in its transcriptional activity. Four O-GlcNAcylation sites were identified in human FOXO1 but directed mutagenesis of each site individually had modest (T317) or no effect (S550, T648, S654) on its O-GlcNAcylation status and transcriptional activity. Moreover, the consequences of mutating all four sites had not been investigated. In the present work, we mutated these sites in the mouse Foxo1 and found that mutation of all four sites did not decrease Foxo1 O-GlcNAcylation status and transcriptional activity, and would even tend to increase them. In an attempt to identify other O-GlcNAcylation sites, we immunoprecipitated wild-type O-GlcNAcylated Foxo1 and analysed the tryptic digest peptides by mass spectrometry using High-energy Collisional Dissociation. We identified T646 as a new O-GlcNAcylation site on Foxo1. However, site directed mutagenesis of this site individually or together with all four previously identified residues did not impair Foxo1 O-GlcNAcylation and transcriptional activity. These results suggest that residues important for the control of Foxo1 activity by O-GlcNAcylation still remain to be identified. - Highlights: • We mutate four previously identified O-GlcNAcylation sites on Foxo1. • Unexpectedly, these mutations do not reduce Foxo1 O-GlcNAcylation. • These mutation do not reduce Foxo1 transcriptional activity. • We identify a new O-GlcNAcylation site on Foxo1 by mass spectrometry. • Mutation of this site increases Foxo1 transcriptional activity

  17. A tool for identifying potential Eucalyptus nitens seed orchard sites ...

    African Journals Online (AJOL)

    Shy seed production in orchards of Eucalyptus nitens is a major barrier to the deployment of genetic gain in South African plantations. A machine learning method was used to identify optimal sites for the establishment of E. nitens seed orchards within the plantation forestry landscape of the summer rainfall region of South ...

  18. Short communication: Calving site selection of multiparous, group-housed dairy cows is influenced by site of a previous calving

    DEFF Research Database (Denmark)

    Rørvang, Maria Vilain; Nielsen, B.L.; Herskin, Mette S.

    2017-01-01

    A calving cow and her newborn calf appear to have an attracting effect on periparturient cows, which may potentially influence the functionality of future motivation-based calving pen designs. In this pilot study we examined whether calving site selection of group-housed Holstein dairy cows...

  19. Benign colonic metaplasia at a previous stoma site in a patient without adenomatous polyposis.

    Science.gov (United States)

    Prouty, Megan; Patrawala, Samit; Vogt, Adam; Kelleher, Michael; Lee, Michael; Parker, Douglas C

    2016-03-01

    There are few reported cases of cutaneous intestinal metaplasia or primary adenocarcinoma arising at the ileostomy site following panproctocolectomy. These complications have been seen almost exclusively in patients with familial adenomatous polyposis and inflammatory bowel disease (IBD). However, benign intraepidermal colonic mucosa at a reversed ileostomy site in a patient without familial adenomatous polyposis or IBD has not been documented. We report a case of a 51-year-old female with a history of colonic adenocarcinoma who presented with pruritic, erythematous, scaly plaques on the right lower abdomen, present since reversal of her ileostomy in 2007. Skin biopsy revealed benign foci of colonic epithelium with no evidence of adenomatous change. Benign intraepidermal colonic mucosa was diagnosed based on histopathologic findings and immunohistochemistry. To our knowledge, this is the first case of intraepidermal benign colonic metaplasia forming in a patient following ostomy reversal. The case emphasizes the importance of patient education and physical examination of the stoma or stoma remnants for detection of unusual or changing lesions due to the risk for malignant transformation. It also demonstrates that benign colonic mucosa should be considered in the differential diagnosis when evaluating lesions near ileostomy sites, regardless of whether the patient has a history of familial adenomatous polyposis or IBD. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  20. Use of geolocators reveals previously unknown Chinese and Korean scaly-sided merganser wintering sites

    DEFF Research Database (Denmark)

    Soloveyva, Diana; Afanasiev, Vsevolod; Fox, James W.

    2012-01-01

    areas in successive years, suggesting winter fidelity to catchments if not specific sites. A single female from the adjacent Avvakumovka catchment wintered on saltwater in Korea, at least 1300 km east of Chinese wintering birds. Most sea duck species (Tribe Mergini) form pairs away from breeding areas......, suggesting that this high level of winter dispersal amongst close-nesting females is a potential mechanism to maintain gene flow in this threatened species that has specialist habitat requirements. Hence, female scaly-sided mergansers disperse widely from breeding areas, but show fidelity to nesting areas...

  1. Evaluation of potential regulatory elements identified as DNase I hypersensitive sites in the CFTR gene

    DEFF Research Database (Denmark)

    Phylactides, M.; Rowntree, R.; Nuthall, H.

    2002-01-01

    hypersensitive sites (DHS) within the locus. We previously identified at least 12 clusters of DHS across the CFTR gene and here further evaluate DHS in introns 2,3,10,16,17a, 18, 20 and 21 to assess their functional importance in regulation of CFTR gene expression. Transient transfections of enhancer/reporter...

  2. Development of a Simple Tool for Identifying Alcohol Use Disorder in Female Korean Drinkers from Previous Questionnaires.

    Science.gov (United States)

    Seo, Yu Ri; Kim, Jong Sung; Kim, Sung Soo; Yoon, Seok Joon; Suh, Won Yoon; Youn, Kwangmi

    2016-01-01

    This study aimed to develop a simple tool for identifying alcohol use disorders in female Korean drinkers from previous questionnaires. This research was conducted on 400 women who consumed at least one alcoholic drink during the past month and visited the health promotion center at Chungnam National University Hospital between June 2013 to May 2014. Drinking habits and alcohol use disorders were assessed by structured interviews using the Diagnostic and Statistical Manual of Mental Disorders, 5th Edition diagnostic criteria. The subjects were also asked to answer the Alcohol Use Disorders Identification Test (AUDIT), AUDIT-Consumption, CAGE (Cut down, Annoyed, Guilty, Eye-opener), TWEAK (Tolerance, Worried, Eye-opener, Amnesia, Kut down), TACE (Tolerance, Annoyed, Cut down, Eye-opener), and NET (Normal drinker, Eye-opener, Tolerance) questionnaires. The area under receiver operating characteristic (AUROC) of each question of the questionnaires on alcohol use disorders was assessed. After combining two questions with the largest AUROC, it was compared to other previous questionnaires. Among the 400 subjects, 58 (14.5%) were identified as having an alcohol use disorder. Two questions with the largest AUROC were question no. 7 in AUDIT, "How often during the last year have you had a feeling of guilt or remorse after drinking?" and question no. 5 in AUDIT, "How often during the past year have you failed to do what was normally expected from you because of drinking?" with an AUROC (95% confidence interval [CI]) of 0.886 (0.850-0.915) and 0.862 (0.824-0.894), respectively. The AUROC (95% CI) of the combination of the two questions was 0.958 (0.934-0.976) with no significant difference as compared to the existing AUDIT with the largest AUROC. The above results suggest that the simple tool consisting of questions no. 5 and no. 7 in AUDIT is useful in identifying alcohol use disorders in Korean female drinkers.

  3. Identifying potential kidney donors using social networking web sites.

    Science.gov (United States)

    Chang, Alexander; Anderson, Emily E; Turner, Hang T; Shoham, David; Hou, Susan H; Grams, Morgan

    2013-01-01

    Social networking sites like Facebook may be a powerful tool for increasing rates of live kidney donation. They allow for wide dissemination of information and discussion and could lessen anxiety associated with a face-to-face request for donation. However, sparse data exist on the use of social media for this purpose. We searched Facebook, the most popular social networking site, for publicly available English-language pages seeking kidney donors for a specific individual, abstracting information on the potential recipient, characteristics of the page itself, and whether potential donors were tested. In the 91 pages meeting inclusion criteria, the mean age of potential recipients was 37 (range: 2-69); 88% were US residents. Other posted information included the individual's photograph (76%), blood type (64%), cause of kidney disease (43%), and location (71%). Thirty-two percent of pages reported having potential donors tested, and 10% reported receiving a live-donor kidney transplant. Those reporting donor testing shared more potential recipient characteristics, provided more information about transplantation, and had higher page traffic. Facebook is already being used to identify potential kidney donors. Future studies should focus on how to safely, ethically, and effectively use social networking sites to inform potential donors and potentially expand live kidney donation. © 2013 John Wiley & Sons A/S.

  4. Catalytic site identification—a web server to identify catalytic site structural matches throughout PDB

    Science.gov (United States)

    Kirshner, Daniel A.; Nilmeier, Jerome P.; Lightstone, Felice C.

    2013-01-01

    The catalytic site identification web server provides the innovative capability to find structural matches to a user-specified catalytic site among all Protein Data Bank proteins rapidly (in less than a minute). The server also can examine a user-specified protein structure or model to identify structural matches to a library of catalytic sites. Finally, the server provides a database of pre-calculated matches between all Protein Data Bank proteins and the library of catalytic sites. The database has been used to derive a set of hypothesized novel enzymatic function annotations. In all cases, matches and putative binding sites (protein structure and surfaces) can be visualized interactively online. The website can be accessed at http://catsid.llnl.gov. PMID:23680785

  5. Identifying high dose activities in industrial site radiography

    International Nuclear Information System (INIS)

    Heaton, B.

    2000-01-01

    Although the radiation doses received by industrial radiographers in the UK have progressively fallen over the last few years, with most now receiving less than 1 mSv/y, a few still receive, relative to the rest, much higher doses. As a percentage of all radiographers the number stays surprisingly constant from year to year. This paper describes a survey to identify the work causing these doses and suggest possible solutions. The UK Central Index of Dose Information was interrogated to identify the industrial radiography companies having staff (not necessarily the same person) with doses of greater than 5mSv/y in the last three years for which information was available. This was 15 in total. The people on the staff receiving these doses were identified and a questionnaire sent to the companies concerned requesting information about their work. A general questionnaire about the operation of the company was also included. With the agreement of the company these questionnaires were followed up by a visit to the company to interviews a number of the management and the radiographers if available. Both groups were generally very open about their problems and every discussion had a positive outcome. Several areas of work/reasons for the doses have been identified. These are: pipeline radiography, ultra sound radiographers working on nuclear reactors, complex plant work often with several teams in the area, inability to retreat from the wind out equipment due to height or access problems, site pressure to not follow the best practices and a lack of appreciation when a dose was being received or, alternatively, carelessness. Some o these problem areas are very difficult to resolve. However ways in which the Health and Safety can help influence the doses have been identified together with practical suggestions radiographers could adopt. These will be reported. (author)

  6. Identifying Key Factors Relevant for Base Camp Siting

    Science.gov (United States)

    2017-12-01

    centers. 3.2.6.3 Religious and historical sites Respecting sacred sites helps build rapport with the host nation. 3.2.6.4 Local infrastructure...churches, mosques, national libraries, hospitals, cemeteries, historical ruins, religious sites, cultural areas, and other protected sites...controlled and protected wells. • Electricity: town engineer • Academic: government and religious leaders • Trash: private business (local

  7. Association between previously identified loci affecting telomere length and coronary heart disease (CHD in Han Chinese population

    Directory of Open Access Journals (Sweden)

    Ding H

    2014-05-01

    Full Text Available Hui Ding,1 Fen Yan,1 Lin-Lin Zhou,2 Xiu-Hai Ji,3 Xin-Nan Gu,1 Zhi-Wei Tang,1 Ru-Hua Chen11Department of Pulmonary Medicine, The Affiliated Yixing People's Hospital, Jiangsu University, Zhenjiang, Jiangsu Province, 2Department of Cardiology, Affiliated Cixi Hospital, Wenzhou Medical University, Wenzhou, Zhejiang Province, 3Department of Oncology, Affiliated Taicang Hospital of Traditional Chinese Medicine, Suzhou, Jiangsu Province, People's Republic of ChinaPurpose: To replicate previously confirmed telomere-length loci in a Chinese Han population with coronary heart disease (CHD, and investigate these loci and the possibility of and age at onset of CHD.Patients and methods: 1514 CHD patients and 2470 normal controls were recruited. Medical data including age, sex, body mass index, lipid profiles, history of hypertension, type 2 diabetes mellitus, and dyslipidemia were collected from all the participants. Seven previously identified single-nucleotide polymorphisms (SNPs related to leucocyte telomere length were genotyped, including rs10936599 in TERC, rs2736100 in TERT, rs7675998 in NAF1, rs9420907 in OBFC1, rs8105767 in ZNF208, rs755017 in RTEL1, and rs11125529 in ACYP2.Results: No significant difference in genotype frequencies from the Hardy–Weinberg equilibrium test was noted for all tested SNPs both in the CHD patients and the normal controls. No polymorphism was observed for rs9420907, and AA genotype was noted in both the CHD patients and the controls. Neither the genotype nor the allele frequencies of rs2736100, rs8105767, rs11125529, and rs2967374 were significantly different between the CHD patients and the normal controls. For rs10936599 and rs755017, statistical difference was found for the allele frequency but not genotype. Distributions of genotype and allele were significantly different between the two groups for rs7675998. The odds ratio for carriers of CHD was 2.127 (95% confidence interval: 1.909–2.370 for the A allele of rs

  8. Common integration sites of published datasets identified using a graph-based framework

    Directory of Open Access Journals (Sweden)

    Alessandro Vasciaveo

    2016-01-01

    Full Text Available With next-generation sequencing, the genomic data available for the characterization of integration sites (IS has dramatically increased. At present, in a single experiment, several thousand viral integration genome targets can be investigated to define genomic hot spots. In a previous article, we renovated a formal CIS analysis based on a rigid fixed window demarcation into a more stretchy definition grounded on graphs. Here, we present a selection of supporting data related to the graph-based framework (GBF from our previous article, in which a collection of common integration sites (CIS was identified on six published datasets. In this work, we will focus on two datasets, ISRTCGD and ISHIV, which have been previously discussed. Moreover, we show in more detail the workflow design that originates the datasets.

  9. Transcriptomic analysis in a Drosophila model identifies previously implicated and novel pathways in the therapeutic mechanism in neuropsychiatric disorders

    Directory of Open Access Journals (Sweden)

    Priyanka eSingh

    2011-03-01

    Full Text Available We have taken advantage of a newly described Drosophila model to gain insights into the potential mechanism of antiepileptic drugs (AEDs, a group of drugs that are widely used in the treatment of several neurological and psychiatric conditions besides epilepsy. In the recently described Drosophila model that is inspired by pentylenetetrazole (PTZ induced kindling epileptogenesis in rodents, chronic PTZ treatment for seven days causes a decreased climbing speed and an altered CNS transcriptome, with the latter mimicking gene expression alterations reported in epileptogenesis. In the model, an increased climbing speed is further observed seven days after withdrawal from chronic PTZ. We used this post-PTZ withdrawal regime to identify potential AED mechanism. In this regime, treatment with each of the five AEDs tested, namely, ethosuximide (ETH, gabapentin (GBP, vigabatrin (VGB, sodium valproate (NaVP and levetiracetam (LEV, resulted in rescuing of the altered climbing behavior. The AEDs also normalized PTZ withdrawal induced transcriptomic perturbation in fly heads; whereas AED untreated flies showed a large number of up- and down-regulated genes which were enriched in several processes including gene expression and cell communication, the AED treated flies showed differential expression of only a small number of genes that did not enrich gene expression and cell communication processes. Gene expression and cell communication related upregulated genes in AED untreated flies overrepresented several pathways - spliceosome, RNA degradation, and ribosome in the former category, and inositol phosphate metabolism, phosphatidylinositol signaling, endocytosis and hedgehog signaling in the latter. Transcriptome remodeling effect of AEDs was overall confirmed by microarray clustering that clearly separated the profiles of AED treated and untreated flies. Besides being consistent with previously implicated pathways, our results provide evidence for a role of

  10. Evolutionary Analysis Predicts Sensitive Positions of MMP20 and Validates Newly- and Previously-Identified MMP20 Mutations Causing Amelogenesis Imperfecta.

    Science.gov (United States)

    Gasse, Barbara; Prasad, Megana; Delgado, Sidney; Huckert, Mathilde; Kawczynski, Marzena; Garret-Bernardin, Annelyse; Lopez-Cazaux, Serena; Bailleul-Forestier, Isabelle; Manière, Marie-Cécile; Stoetzel, Corinne; Bloch-Zupan, Agnès; Sire, Jean-Yves

    2017-01-01

    Amelogenesis imperfecta (AI) designates a group of genetic diseases characterized by a large range of enamel disorders causing important social and health problems. These defects can result from mutations in enamel matrix proteins or protease encoding genes. A range of mutations in the enamel cleavage enzyme matrix metalloproteinase-20 gene ( MMP20 ) produce enamel defects of varying severity. To address how various alterations produce a range of AI phenotypes, we performed a targeted analysis to find MMP20 mutations in French patients diagnosed with non-syndromic AI. Genomic DNA was isolated from saliva and MMP20 exons and exon-intron boundaries sequenced. We identified several homozygous or heterozygous mutations, putatively involved in the AI phenotypes. To validate missense mutations and predict sensitive positions in the MMP20 sequence, we evolutionarily compared 75 sequences extracted from the public databases using the Datamonkey webserver. These sequences were representative of mammalian lineages, covering more than 150 million years of evolution. This analysis allowed us to find 324 sensitive positions (out of the 483 MMP20 residues), pinpoint functionally important domains, and build an evolutionary chart of important conserved MMP20 regions. This is an efficient tool to identify new- and previously-identified mutations. We thus identified six functional MMP20 mutations in unrelated families, finding two novel mutated sites. The genotypes and phenotypes of these six mutations are described and compared. To date, 13 MMP20 mutations causing AI have been reported, making these genotypes and associated hypomature enamel phenotypes the most frequent in AI.

  11. Previous Fractures at Multiple Sites Increase the Risk for Subsequent Fractures: The Global Longitudinal Study of Osteoporosis in Women

    Science.gov (United States)

    Gehlbach, Stephen; Saag, Kenneth G.; Adachi, Jonathan D.; Hooven, Fred H.; Flahive, Julie; Boonen, Steven; Chapurlat, Roland D.; Compston, Juliet E.; Cooper, Cyrus; Díez-Perez, Adolfo; Greenspan, Susan L.; LaCroix, Andrea Z.; Netelenbos, J. Coen; Pfeilschifter, Johannes; Rossini, Maurizio; Roux, Christian; Sambrook, Philip N.; Silverman, Stuart; Siris, Ethel S.; Watts, Nelson B.; Lindsay, Robert

    2016-01-01

    Previous fractures of the hip, spine, or wrist are well-recognized predictors of future fracture, but the role of other fracture sites is less clear. We sought to assess the relationship between prior fracture at 10 skeletal locations and incident fracture. The Global Longitudinal Study of Osteoporosis in Women (GLOW) is an observational cohort study being conducted in 17 physician practices in 10 countries. Women ≥ 55 years answered questionnaires at baseline and at 1 and/or 2 years (fractures in previous year). Of 60,393 women enrolled, follow-up data were available for 51,762. Of these, 17.6%, 4.0%, and 1.6% had suffered 1, 2, or ≥3 fractures since age 45. During the first 2 years of follow-up, 3149 women suffered 3683 incident fractures. Compared with women with no prior fractures, women with 1, 2, or ≥ 3 prior fractures were 1.8-, 3.0-, and 4.8-fold more likely to have any incident fracture; those with ≥3 prior fractures were 9.1-fold more likely to sustain a new vertebral fracture. Nine of 10 prior fracture locations were associated with an incident fracture. The strongest predictors of incident spine and hip fractures were prior spine fracture (hazard ratio 7.3) and hip (hazard ratio 3.5). Prior rib fractures were associated with a 2.3-fold risk of subsequent vertebral fracture, previous upper leg fracture predicted a 2.2-fold increased risk of hip fracture; women with a history of ankle fracture were at 1.8-fold risk of future fracture of a weight-bearing bone. Our findings suggest that a broad range of prior fracture sites are associated with an increased risk of incident fractures, with important implications for clinical assessments and risk model development. PMID:22113888

  12. Evolutionary Analysis Predicts Sensitive Positions of MMP20 and Validates Newly- and Previously-Identified MMP20 Mutations Causing Amelogenesis Imperfecta

    Directory of Open Access Journals (Sweden)

    Barbara Gasse

    2017-06-01

    Full Text Available Amelogenesis imperfecta (AI designates a group of genetic diseases characterized by a large range of enamel disorders causing important social and health problems. These defects can result from mutations in enamel matrix proteins or protease encoding genes. A range of mutations in the enamel cleavage enzyme matrix metalloproteinase-20 gene (MMP20 produce enamel defects of varying severity. To address how various alterations produce a range of AI phenotypes, we performed a targeted analysis to find MMP20 mutations in French patients diagnosed with non-syndromic AI. Genomic DNA was isolated from saliva and MMP20 exons and exon-intron boundaries sequenced. We identified several homozygous or heterozygous mutations, putatively involved in the AI phenotypes. To validate missense mutations and predict sensitive positions in the MMP20 sequence, we evolutionarily compared 75 sequences extracted from the public databases using the Datamonkey webserver. These sequences were representative of mammalian lineages, covering more than 150 million years of evolution. This analysis allowed us to find 324 sensitive positions (out of the 483 MMP20 residues, pinpoint functionally important domains, and build an evolutionary chart of important conserved MMP20 regions. This is an efficient tool to identify new- and previously-identified mutations. We thus identified six functional MMP20 mutations in unrelated families, finding two novel mutated sites. The genotypes and phenotypes of these six mutations are described and compared. To date, 13 MMP20 mutations causing AI have been reported, making these genotypes and associated hypomature enamel phenotypes the most frequent in AI.

  13. Methods and systems for identifying ligand-protein binding sites

    KAUST Repository

    Gao, Xin

    2016-05-06

    The invention provides a novel integrated structure and system-based approach for drug target prediction that enables the large-scale discovery of new targets for existing drugs Novel computer-readable storage media and computer systems are also provided. Methods and systems of the invention use novel sequence order-independent structure alignment, hierarchical clustering, and probabilistic sequence similarity techniques to construct a probabilistic pocket ensemble (PPE) that captures even promiscuous structural features of different binding sites for a drug on known targets. The drug\\'s PPE is combined with an approximation of the drug delivery profile to facilitate large-scale prediction of novel drug- protein interactions with several applications to biological research and drug development.

  14. Identifying suitable piercement salt domes for nuclear waste storage sites

    International Nuclear Information System (INIS)

    Kehle, R.; e.

    1980-08-01

    Piercement salt domes of the northern interior salt basins of the Gulf of Mexico are being considered as permanent storage sites for both nuclear and chemically toxic wastes. The suitable domes are stable and inactive, having reached their final evolutionary configuration at least 30 million years ago. They are buried to depths far below the level to which erosion will penetrate during the prescribed storage period and are not subject to possible future reactivation. The salt cores of these domes are themselves impermeable, permitting neither the entry nor exit of ground water or other unwanted materials. In part, a stable dome may be recognized by its present geometric configuration, but conclusive proof depends on establishing its evolutionary state. The evolutionary state of a dome is obtained by reconstructing the growth history of the dome as revealed by the configuration of sedimentary strata in a large area (commonly 3,000 square miles or more) surrounding the dome. A high quality, multifold CDP reflection seismic profile across a candidate dome will provide much of the necessary information when integrated with available subsurface control. Additional seismic profiles may be required to confirm an apparent configuration of the surrounding strata and an interpreted evolutionary history. High frequency seismic data collected in the near vicinity of a dome are also needed as a supplement to the CDP data to permit accurate depiction of the configuration of shallow strata. Such data must be tied to shallow drill hole control to confirm the geologic age at which dome growth ceased. If it is determined that a dome reached a terminal configuration many millions of years ago, such a dome is incapable of reactivation and thus constitutes a stable storage site for nuclear wastes

  15. Identifying protein phosphorylation sites with kinase substrate specificity on human viruses.

    Directory of Open Access Journals (Sweden)

    Neil Arvin Bretaña

    Full Text Available Viruses infect humans and progress inside the body leading to various diseases and complications. The phosphorylation of viral proteins catalyzed by host kinases plays crucial regulatory roles in enhancing replication and inhibition of normal host-cell functions. Due to its biological importance, there is a desire to identify the protein phosphorylation sites on human viruses. However, the use of mass spectrometry-based experiments is proven to be expensive and labor-intensive. Furthermore, previous studies which have identified phosphorylation sites in human viruses do not include the investigation of the responsible kinases. Thus, we are motivated to propose a new method to identify protein phosphorylation sites with its kinase substrate specificity on human viruses. The experimentally verified phosphorylation data were extracted from virPTM--a database containing 301 experimentally verified phosphorylation data on 104 human kinase-phosphorylated virus proteins. In an attempt to investigate kinase substrate specificities in viral protein phosphorylation sites, maximal dependence decomposition (MDD is employed to cluster a large set of phosphorylation data into subgroups containing significantly conserved motifs. The experimental human phosphorylation sites are collected from Phospho.ELM, grouped according to its kinase annotation, and compared with the virus MDD clusters. This investigation identifies human kinases such as CK2, PKB, CDK, and MAPK as potential kinases for catalyzing virus protein substrates as confirmed by published literature. Profile hidden Markov model is then applied to learn a predictive model for each subgroup. A five-fold cross validation evaluation on the MDD-clustered HMMs yields an average accuracy of 84.93% for Serine, and 78.05% for Threonine. Furthermore, an independent testing data collected from UniProtKB and Phospho.ELM is used to make a comparison of predictive performance on three popular kinase

  16. Identifying protein phosphorylation sites with kinase substrate specificity on human viruses.

    Science.gov (United States)

    Bretaña, Neil Arvin; Lu, Cheng-Tsung; Chiang, Chiu-Yun; Su, Min-Gang; Huang, Kai-Yao; Lee, Tzong-Yi; Weng, Shun-Long

    2012-01-01

    Viruses infect humans and progress inside the body leading to various diseases and complications. The phosphorylation of viral proteins catalyzed by host kinases plays crucial regulatory roles in enhancing replication and inhibition of normal host-cell functions. Due to its biological importance, there is a desire to identify the protein phosphorylation sites on human viruses. However, the use of mass spectrometry-based experiments is proven to be expensive and labor-intensive. Furthermore, previous studies which have identified phosphorylation sites in human viruses do not include the investigation of the responsible kinases. Thus, we are motivated to propose a new method to identify protein phosphorylation sites with its kinase substrate specificity on human viruses. The experimentally verified phosphorylation data were extracted from virPTM--a database containing 301 experimentally verified phosphorylation data on 104 human kinase-phosphorylated virus proteins. In an attempt to investigate kinase substrate specificities in viral protein phosphorylation sites, maximal dependence decomposition (MDD) is employed to cluster a large set of phosphorylation data into subgroups containing significantly conserved motifs. The experimental human phosphorylation sites are collected from Phospho.ELM, grouped according to its kinase annotation, and compared with the virus MDD clusters. This investigation identifies human kinases such as CK2, PKB, CDK, and MAPK as potential kinases for catalyzing virus protein substrates as confirmed by published literature. Profile hidden Markov model is then applied to learn a predictive model for each subgroup. A five-fold cross validation evaluation on the MDD-clustered HMMs yields an average accuracy of 84.93% for Serine, and 78.05% for Threonine. Furthermore, an independent testing data collected from UniProtKB and Phospho.ELM is used to make a comparison of predictive performance on three popular kinase-specific phosphorylation site

  17. Mass spectrometry identifies multiple organophosphorylated sites on tubulin

    International Nuclear Information System (INIS)

    Grigoryan, Hasmik; Schopfer, Lawrence M.; Peeples, Eric S.; Duysen, Ellen G.; Grigoryan, Marine; Thompson, Charles M.; Lockridge, Oksana

    2009-01-01

    Acute toxicity of organophosphorus poisons (OP) is explained by inhibition of acetylcholinesterase in nerve synapses. Low-dose effects are hypothesized to result from modification of other proteins, whose identity is not yet established. The goal of the present work was to obtain information that would make it possible to identify tubulin as a target of OP exposure. Tubulin was selected for study because live mice injected with a nontoxic dose of a biotinylated organophosphorus agent appeared to have OP-labeled tubulin in brain as determined by binding to avidin beads and mass spectrometry. The experiments with live mice were not conclusive because binding to avidin beads could be nonspecific. To be convincing, it is necessary to find and characterize the OP-labeled tubulin peptide. The search for OP-labeled tubulin peptides was begun by identifying residues capable of making a covalent bond with OP. Pure bovine tubulin (0.012 mM) was treated with 0.01-0.5 mM chlorpyrifos oxon for 24 h at 37 o C in pH 8.3 buffer. The identity of labeled amino acids and percent labeling was determined by mass spectrometry. Chlorpyrifos oxon bound covalently to tyrosines 83, 103, 108, 161, 224, 262, 272, 357, and 399 in bovine alpha tubulin, and to tyrosines 50, 51, 59, 106, 159, 281, 310, and 340 in bovine beta tubulin. The most reactive were tyrosine 83 in alpha and tyrosine 281 in beta tubulin. In the presence of 1 mM GTP, percent labeling increased 2-fold. Based on the crystal structure of the tubulin heterodimer (PDB 1jff) tyrosines 83 and 281 are well exposed to solvent. In conclusion seventeen tyrosines in tubulin have the potential to covalently bind chlorpyrifos oxon. These results will be useful when searching for OP-labeled tubulin in live animals.

  18. Target and identify: triazene linker helps identify azidation sites of labelled proteins via click and cleave strategy.

    Science.gov (United States)

    Lohse, Jonas; Schindl, Alexandra; Danda, Natasha; Williams, Chris P; Kramer, Karl; Kuster, Bernhard; Witte, Martin D; Médard, Guillaume

    2017-10-31

    A method for identifying probe modification of proteins via tandem mass spectrometry was developed. Azide bearing molecules are immobilized on functionalised sepharose beads via copper catalysed Huisgen-type click chemistry and selectively released under acidic conditions by chemical cleavage of the triazene linkage. We applied this method to identify the modification site of targeted-diazotransfer on BirA.

  19. Central site monitoring: results from a test of accuracy in identifying trials and sites failing Food and Drug Administration inspection.

    Science.gov (United States)

    Lindblad, Anne S; Manukyan, Zorayr; Purohit-Sheth, Tejashri; Gensler, Gary; Okwesili, Paul; Meeker-O'Connell, Ann; Ball, Leslie; Marler, John R

    2014-04-01

    Site monitoring and source document verification account for 15%-30% of clinical trial costs. An alternative is to streamline site monitoring to focus on correcting trial-specific risks identified by central data monitoring. This risk-based approach could preserve or even improve the quality of clinical trial data and human subject protection compared to site monitoring focused primarily on source document verification. To determine whether a central review by statisticians using data submitted to the Food and Drug Administration (FDA) by clinical trial sponsors can identify problem sites and trials that failed FDA site inspections. An independent Analysis Center (AC) analyzed data from four anonymous new drug applications (NDAs) where FDA had performed site inspections overseen by FDA's Office of Scientific Investigations (OSI). FDA team members in the OSI chose the four NDAs from among all NDAs with data in Study Data Tabulation Model (SDTM) format. Two of the NDAs had data that OSI had deemed unreliable in support of the application after FDA site inspections identified serious data integrity problems. The other two NDAs had clinical data that OSI deemed reliable after site inspections. At the outset, the AC knew only that the experimental design specified two NDAs with significant problems. FDA gave the AC no information about which NDAs had problems, how many sites were inspected, or how many were found to have problems until after the AC analysis was complete. The AC evaluated randomization balance, enrollment patterns, study visit scheduling, variability of reported data, and last digit reference. The AC classified sites as 'High Concern', 'Moderate Concern', 'Mild Concern', or 'No Concern'. The AC correctly identified the two NDAs with data deemed unreliable by OSI. In addition, central data analysis correctly identified 5 of 6 (83%) sites for which FDA recommended rejection of data and 13 of 15 sites (87%) for which any regulatory deviations were

  20. SNOSite: exploiting maximal dependence decomposition to identify cysteine S-nitrosylation with substrate site specificity.

    Directory of Open Access Journals (Sweden)

    Tzong-Yi Lee

    Full Text Available S-nitrosylation, the covalent attachment of a nitric oxide to (NO the sulfur atom of cysteine, is a selective and reversible protein post-translational modification (PTM that regulates protein activity, localization, and stability. Despite its implication in the regulation of protein functions and cell signaling, the substrate specificity of cysteine S-nitrosylation remains unknown. Based on a total of 586 experimentally identified S-nitrosylation sites from SNAP/L-cysteine-stimulated mouse endothelial cells, this work presents an informatics investigation on S-nitrosylation sites including structural factors such as the flanking amino acids composition, the accessible surface area (ASA and physicochemical properties, i.e. positive charge and side chain interaction parameter. Due to the difficulty to obtain the conserved motifs by conventional motif analysis, maximal dependence decomposition (MDD has been applied to obtain statistically significant conserved motifs. Support vector machine (SVM is applied to generate predictive model for each MDD-clustered motif. According to five-fold cross-validation, the MDD-clustered SVMs could achieve an accuracy of 0.902, and provides a promising performance in an independent test set. The effectiveness of the model was demonstrated on the correct identification of previously reported S-nitrosylation sites of Bos taurus dimethylarginine dimethylaminohydrolase 1 (DDAH1 and human hemoglobin subunit beta (HBB. Finally, the MDD-clustered model was adopted to construct an effective web-based tool, named SNOSite (http://csb.cse.yzu.edu.tw/SNOSite/, for identifying S-nitrosylation sites on the uncharacterized protein sequences.

  1. GSHSite: exploiting an iteratively statistical method to identify s-glutathionylation sites with substrate specificity.

    Directory of Open Access Journals (Sweden)

    Yi-Ju Chen

    Full Text Available S-glutathionylation, the covalent attachment of a glutathione (GSH to the sulfur atom of cysteine, is a selective and reversible protein post-translational modification (PTM that regulates protein activity, localization, and stability. Despite its implication in the regulation of protein functions and cell signaling, the substrate specificity of cysteine S-glutathionylation remains unknown. Based on a total of 1783 experimentally identified S-glutathionylation sites from mouse macrophages, this work presents an informatics investigation on S-glutathionylation sites including structural factors such as the flanking amino acids composition and the accessible surface area (ASA. TwoSampleLogo presents that positively charged amino acids flanking the S-glutathionylated cysteine may influence the formation of S-glutathionylation in closed three-dimensional environment. A statistical method is further applied to iteratively detect the conserved substrate motifs with statistical significance. Support vector machine (SVM is then applied to generate predictive model considering the substrate motifs. According to five-fold cross-validation, the SVMs trained with substrate motifs could achieve an enhanced sensitivity, specificity, and accuracy, and provides a promising performance in an independent test set. The effectiveness of the proposed method is demonstrated by the correct identification of previously reported S-glutathionylation sites of mouse thioredoxin (TXN and human protein tyrosine phosphatase 1b (PTP1B. Finally, the constructed models are adopted to implement an effective web-based tool, named GSHSite (http://csb.cse.yzu.edu.tw/GSHSite/, for identifying uncharacterized GSH substrate sites on the protein sequences.

  2. Continuation of the summarizing interim report on previous results of the Gorleben site survey as of May 1983

    International Nuclear Information System (INIS)

    1990-04-01

    In addition to results from the 1983 interim report, this report contains, in order to supplement the surface explorations, seismic reflection measurements, hydrogeologic and seismologic investigations, sorption experiments, and studies of glacial development in the site region and of long-term safety of final waste repositories in salt domes. The site's high grade of suitability for becoming a final radioactive waste repository, the legal basis as well as quality assurance are evaluated. (orig.) [de

  3. Benchmark data for identifying N6-methyladenosine sites in the Saccharomyces cerevisiae genome

    Directory of Open Access Journals (Sweden)

    Wei Chen

    2015-12-01

    Full Text Available This data article contains the benchmark dataset for training and testing iRNA-Methyl, a web-server predictor for identifying N6-methyladenosine sites in RNA (Chen et al., 2015 [15]. It can also be used to develop other predictors for identifying N6-methyladenosine sites in the Saccharomyces cerevisiae genome.

  4. Evidentiary requirements to identify potentially acceptable sites (PAS) in crystalline rock

    International Nuclear Information System (INIS)

    Comella, P.A.; Smith, B.H.

    1985-01-01

    This report contains information on the evidentiary requirements to identify potentially acceptable sites in crystalline rock for waste disposal. Topics addressed include: chronology, key regulatory assumptions, statutory framework for identifying potentially acceptable sites, application of 10 disqualifiers, consideration of favorable and potentially adverse conditions, a composite favorability analysis, and a proposed outline for PAS identification decision document

  5. Under What Assumptions Do Site-by-Treatment Instruments Identify Average Causal Effects?

    Science.gov (United States)

    Reardon, Sean F.; Raudenbush, Stephen W.

    2013-01-01

    The increasing availability of data from multi-site randomized trials provides a potential opportunity to use instrumental variables methods to study the effects of multiple hypothesized mediators of the effect of a treatment. We derive nine assumptions needed to identify the effects of multiple mediators when using site-by-treatment interactions…

  6. Deep mutational scanning identifies sites in influenza nucleoprotein that affect viral inhibition by MxA.

    Directory of Open Access Journals (Sweden)

    Orr Ashenberg

    2017-03-01

    Full Text Available The innate-immune restriction factor MxA inhibits influenza replication by targeting the viral nucleoprotein (NP. Human influenza virus is more resistant than avian influenza virus to inhibition by human MxA, and prior work has compared human and avian viral strains to identify amino-acid differences in NP that affect sensitivity to MxA. However, this strategy is limited to identifying sites in NP where mutations that affect MxA sensitivity have fixed during the small number of documented zoonotic transmissions of influenza to humans. Here we use an unbiased deep mutational scanning approach to quantify how all single amino-acid mutations to NP affect MxA sensitivity in the context of replication-competent virus. We both identify new sites in NP where mutations affect MxA resistance and re-identify mutations known to have increased MxA resistance during historical adaptations of influenza to humans. Most of the sites where mutations have the greatest effect are almost completely conserved across all influenza A viruses, and the amino acids at these sites confer relatively high resistance to MxA. These sites cluster in regions of NP that appear to be important for its recognition by MxA. Overall, our work systematically identifies the sites in influenza nucleoprotein where mutations affect sensitivity to MxA. We also demonstrate a powerful new strategy for identifying regions of viral proteins that affect inhibition by host factors.

  7. GASS-WEB: a web server for identifying enzyme active sites based on genetic algorithms.

    Science.gov (United States)

    Moraes, João P A; Pappa, Gisele L; Pires, Douglas E V; Izidoro, Sandro C

    2017-07-03

    Enzyme active sites are important and conserved functional regions of proteins whose identification can be an invaluable step toward protein function prediction. Most of the existing methods for this task are based on active site similarity and present limitations including performing only exact matches on template residues, template size restraints, despite not being capable of finding inter-domain active sites. To fill this gap, we proposed GASS-WEB, a user-friendly web server that uses GASS (Genetic Active Site Search), a method based on an evolutionary algorithm to search for similar active sites in proteins. GASS-WEB can be used under two different scenarios: (i) given a protein of interest, to match a set of specific active site templates; or (ii) given an active site template, looking for it in a database of protein structures. The method has shown to be very effective on a range of experiments and was able to correctly identify >90% of the catalogued active sites from the Catalytic Site Atlas. It also managed to achieve a Matthew correlation coefficient of 0.63 using the Critical Assessment of protein Structure Prediction (CASP 10) dataset. In our analysis, GASS was ranking fourth among 18 methods. GASS-WEB is freely available at http://gass.unifei.edu.br/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  8. Ligand-bound Structures and Site-directed Mutagenesis Identify the Acceptor and Secondary Binding Sites of Streptomyces coelicolor Maltosyltransferase GlgE*

    Science.gov (United States)

    Syson, Karl; Stevenson, Clare E. M.; Miah, Farzana; Barclay, J. Elaine; Tang, Minhong; Gorelik, Andrii; Rashid, Abdul M.; Lawson, David M.; Bornemann, Stephen

    2016-01-01

    GlgE is a maltosyltransferase involved in α-glucan biosynthesis in bacteria that has been genetically validated as a target for tuberculosis therapies. Crystals of the Mycobacterium tuberculosis enzyme diffract at low resolution so most structural studies have been with the very similar Streptomyces coelicolor GlgE isoform 1. Although the donor binding site for α-maltose 1-phosphate had been previously structurally defined, the acceptor site had not. Using mutagenesis, kinetics, and protein crystallography of the S. coelicolor enzyme, we have now identified the +1 to +6 subsites of the acceptor/product, which overlap with the known cyclodextrin binding site. The sugar residues in the acceptor subsites +1 to +5 are oriented such that they disfavor the binding of malto-oligosaccharides that bear branches at their 6-positions, consistent with the known acceptor chain specificity of GlgE. A secondary binding site remote from the catalytic center was identified that is distinct from one reported for the M. tuberculosis enzyme. This new site is capable of binding a branched α-glucan and is most likely involved in guiding acceptors toward the donor site because its disruption kinetically compromises the ability of GlgE to extend polymeric substrates. However, disruption of this site, which is conserved in the Streptomyces venezuelae GlgE enzyme, did not affect the growth of S. venezuelae or the structure of the polymeric product. The acceptor subsites +1 to +4 in the S. coelicolor enzyme are well conserved in the M. tuberculosis enzyme so their identification could help inform the design of inhibitors with therapeutic potential. PMID:27531751

  9. Efficient Culture Adaptation of Hepatitis C Virus Recombinants with Genotype-Specific Core-NS2 by Using Previously Identified Mutations

    DEFF Research Database (Denmark)

    Scheel, Troels Kasper Høyer; Gottwein, Judith M; Carlsen, Thomas H R

    2011-01-01

    Hepatitis C virus (HCV) is an important cause of chronic liver disease, and interferon-based therapy cures only 40 to 80% of patients, depending on HCV genotype. Research was accelerated by genotype 2a (strain JFH1) infectious cell culture systems. We previously developed viable JFH1-based...... (HC-TN and DH6), 1b (DH1 and DH5), and 3a (DBN) isolates, using previously identified adaptive mutations. Introduction of mutations from isolates of the same subtype either led to immediate efficient virus production or accelerated culture adaptation. The DH6 and DH5 recombinants without introduced...... mutations did not adapt to culture. Universal adaptive effects of mutations in NS3 (Q1247L, I1312V, K1398Q, R1408W, and Q1496L) and NS5A (V2418L) were investigated for JFH1-based genotype 1 to 5 core-NS2 recombinants; several mutations conferred adaptation to H77C (1a), J4 (1b), S52 (3a), and SA13 (5a...

  10. Toward identifying the next generation of superfund and hazardous waste site contaminants.

    Science.gov (United States)

    Ela, Wendell P; Sedlak, David L; Barlaz, Morton A; Henry, Heather F; Muir, Derek C G; Swackhamer, Deborah L; Weber, Eric J; Arnold, Robert G; Ferguson, P Lee; Field, Jennifer A; Furlong, Edward T; Giesy, John P; Halden, Rolf U; Henry, Tala; Hites, Ronald A; Hornbuckle, Keri C; Howard, Philip H; Luthy, Richard G; Meyer, Anita K; Sáez, A Eduardo; Vom Saal, Frederick S; Vulpe, Chris D; Wiesner, Mark R

    2011-01-01

    This commentary evolved from a workshop sponsored by the National Institute of Environmental Health Sciences titled "Superfund Contaminants: The Next Generation" held in Tucson, Arizona, in August 2009. All the authors were workshop participants. Our aim was to initiate a dynamic, adaptable process for identifying contaminants of emerging concern (CECs) that are likely to be found in future hazardous waste sites, and to identify the gaps in primary research that cause uncertainty in determining future hazardous waste site contaminants. Superfund-relevant CECs can be characterized by specific attributes: They are persistent, bioaccumulative, toxic, occur in large quantities, and have localized accumulation with a likelihood of exposure. Although still under development and incompletely applied, methods to quantify these attributes can assist in winnowing down the list of candidates from the universe of potential CECs. Unfortunately, significant research gaps exist in detection and quantification, environmental fate and transport, health and risk assessment, and site exploration and remediation for CECs. Addressing these gaps is prerequisite to a preventive approach to generating and managing hazardous waste sites. A need exists for a carefully considered and orchestrated expansion of programmatic and research efforts to identify, evaluate, and manage CECs of hazardous waste site relevance, including developing an evolving list of priority CECs, intensifying the identification and monitoring of likely sites of present or future accumulation of CECs, and implementing efforts that focus on a holistic approach to prevention.

  11. Identifying diabetes knowledge network nodes as sites for a diabetes prevention program.

    Science.gov (United States)

    Gesler, Wilbert M; Arcury, Thomas A; Skelly, Anne H; Nash, Sally; Soward, April; Dougherty, Molly

    2006-12-01

    This paper reports on the methods used and results of a study that identified specific places within a community that have the potential to be sites for a diabetes prevention program. These sites, termed diabetes knowledge network nodes (DKNNs), are based on the concept of socio-spatial knowledge networks (SSKNs), the web of social relationships within which people obtain knowledge about type 2 diabetes. The target population for the study was working poor African Americans, Latinos, and European Americans of both sexes in a small rural southern town who had not been diagnosed with diabetes. Information was collected from a sample of 121 respondents on the places they visited in carrying out their daily activities. Data on number of visits to specific sites, degree of familiarity with these sites, and ratings of sites as places to receive diabetes information were used to develop three categories of DKNNs for six subgroups based on ethnicity and sex. Primary potential sites of importance to one or more subgroups included churches, grocery stores, drugstores, the local library, a beauty salon, laundromats, a community service agency, and a branch of the County Health Department. Secondary potential sites included gas stations, restaurants, banks, and post offices. Latent potential sites included three medical facilities. Most of the DKNNs were located either in the downtown area or in one of two shopping areas along the most used highway that passed through the town. The procedures used in this study can be generalized to other communities and prevention programs for other chronic diseases.

  12. SABER: a computational method for identifying active sites for new reactions.

    Science.gov (United States)

    Nosrati, Geoffrey R; Houk, K N

    2012-05-01

    A software suite, SABER (Selection of Active/Binding sites for Enzyme Redesign), has been developed for the analysis of atomic geometries in protein structures, using a geometric hashing algorithm (Barker and Thornton, Bioinformatics 2003;19:1644-1649). SABER is used to explore the Protein Data Bank (PDB) to locate proteins with a specific 3D arrangement of catalytic groups to identify active sites that might be redesigned to catalyze new reactions. As a proof-of-principle test, SABER was used to identify enzymes that have the same catalytic group arrangement present in o-succinyl benzoate synthase (OSBS). Among the highest-scoring scaffolds identified by the SABER search for enzymes with the same catalytic group arrangement as OSBS were L-Ala D/L-Glu epimerase (AEE) and muconate lactonizing enzyme II (MLE), both of which have been redesigned to become effective OSBS catalysts, demonstrated by experiments. Next, we used SABER to search for naturally existing active sites in the PDB with catalytic groups similar to those present in the designed Kemp elimination enzyme KE07. From over 2000 geometric matches to the KE07 active site, SABER identified 23 matches that corresponded to residues from known active sites. The best of these matches, with a 0.28 Å catalytic atom RMSD to KE07, was then redesigned to be compatible with the Kemp elimination using RosettaDesign. We also used SABER to search for potential Kemp eliminases using a theozyme predicted to provide a greater rate acceleration than the active site of KE07, and used Rosetta to create a design based on the proteins identified. Copyright © 2012 The Protein Society.

  13. Treatment response in psychotic patients classified according to social and clinical needs, drug side effects, and previous treatment; a method to identify functional remission.

    Science.gov (United States)

    Alenius, Malin; Hammarlund-Udenaes, Margareta; Hartvig, Per; Sundquist, Staffan; Lindström, Leif

    2009-01-01

    Various approaches have been made over the years to classify psychotic patients according to inadequate treatment response, using terms such as treatment resistant or treatment refractory. Existing classifications have been criticized for overestimating positive symptoms; underestimating residual symptoms, negative symptoms, and side effects; or being to open for individual interpretation. The aim of this study was to present and evaluate a new method of classification according to treatment response and, thus, to identify patients in functional remission. A naturalistic, cross-sectional study was performed using patient interviews and information from patient files. The new classification method CANSEPT, which combines the Camberwell Assessment of Need rating scale, the Udvalg for Kliniske Undersøgelser side effect rating scale (SE), and the patient's previous treatment history (PT), was used to group the patients according to treatment response. CANSEPT was evaluated by comparison of expected and observed results. In the patient population (n = 123), the patients in functional remission, as defined by CANSEPT, had higher quality of life, fewer hospitalizations, fewer psychotic symptoms, and higher rate of workers than those with the worst treatment outcome. In the evaluation, CANSEPT showed validity in discriminating the patients of interest and was well tolerated by the patients. CANSEPT could secure inclusion of correct patients in the clinic or in research.

  14. Refinement of a Method for Identifying Probable Archaeological Sites from Remotely Sensed Data

    Science.gov (United States)

    Tilton, James C.; Comer, Douglas C.; Priebe, Carey E.; Sussman, Daniel; Chen, Li

    2012-01-01

    To facilitate locating archaeological sites before they are compromised or destroyed, we are developing approaches for generating maps of probable archaeological sites, through detecting subtle anomalies in vegetative cover, soil chemistry, and soil moisture by analyzing remotely sensed data from multiple sources. We previously reported some success in this effort with a statistical analysis of slope, radar, and Ikonos data (including tasseled cap and NDVI transforms) with Student's t-test. We report here on new developments in our work, performing an analysis of 8-band multispectral Worldview-2 data. The Worldview-2 analysis begins by computing medians and median absolute deviations for the pixels in various annuli around each site of interest on the 28 band difference ratios. We then use principle components analysis followed by linear discriminant analysis to train a classifier which assigns a posterior probability that a location is an archaeological site. We tested the procedure using leave-one-out cross validation with a second leave-one-out step to choose parameters on a 9,859x23,000 subset of the WorldView-2 data over the western portion of Ft. Irwin, CA, USA. We used 100 known non-sites and trained one classifier for lithic sites (n=33) and one classifier for habitation sites (n=16). We then analyzed convex combinations of scores from the Archaeological Predictive Model (APM) and our scores. We found that that the combined scores had a higher area under the ROC curve than either individual method, indicating that including WorldView-2 data in analysis improved the predictive power of the provided APM.

  15. Identifying potential surface water sampling sites for emerging chemical pollutants in Gauteng Province, South Africa

    OpenAIRE

    Petersen, F; Dabrowski, JM; Forbes, PBC

    2017-01-01

    Emerging chemical pollutants (ECPs) are defined as new chemicals which do not have a regulatory status, but which may have an adverse effect on human health and the environment. The occurrence and concentrations of ECPs in South African water bodies are largely unknown, so monitoring is required in order to determine the potential threat that these ECPs may pose. Relevant surface water sampling sites in the Gauteng Province of South Africa were identified utilising a geographic information sy...

  16. A model-based approach to identify binding sites in CLIP-Seq data.

    Directory of Open Access Journals (Sweden)

    Tao Wang

    Full Text Available Cross-linking immunoprecipitation coupled with high-throughput sequencing (CLIP-Seq has made it possible to identify the targeting sites of RNA-binding proteins in various cell culture systems and tissue types on a genome-wide scale. Here we present a novel model-based approach (MiClip to identify high-confidence protein-RNA binding sites from CLIP-seq datasets. This approach assigns a probability score for each potential binding site to help prioritize subsequent validation experiments. The MiClip algorithm has been tested in both HITS-CLIP and PAR-CLIP datasets. In the HITS-CLIP dataset, the signal/noise ratios of miRNA seed motif enrichment produced by the MiClip approach are between 17% and 301% higher than those by the ad hoc method for the top 10 most enriched miRNAs. In the PAR-CLIP dataset, the MiClip approach can identify ∼50% more validated binding targets than the original ad hoc method and two recently published methods. To facilitate the application of the algorithm, we have released an R package, MiClip (http://cran.r-project.org/web/packages/MiClip/index.html, and a public web-based graphical user interface software (http://galaxy.qbrc.org/tool_runner?tool_id=mi_clip for customized analysis.

  17. Hon-yaku: a biology-driven Bayesian methodology for identifying translation initiation sites in prokaryotes

    Directory of Open Access Journals (Sweden)

    de Hoon Michiel JL

    2007-02-01

    Full Text Available Abstract Background Computational prediction methods are currently used to identify genes in prokaryote genomes. However, identification of the correct translation initiation sites remains a difficult task. Accurate translation initiation sites (TISs are important not only for the annotation of unknown proteins but also for the prediction of operons, promoters, and small non-coding RNA genes, as this typically makes use of the intergenic distance. A further problem is that most existing methods are optimized for Escherichia coli data sets; applying these methods to newly sequenced bacterial genomes may not result in an equivalent level of accuracy. Results Based on a biological representation of the translation process, we applied Bayesian statistics to create a score function for predicting translation initiation sites. In contrast to existing programs, our combination of methods uses supervised learning to optimally use the set of known translation initiation sites. We combined the Ribosome Binding Site (RBS sequence, the distance between the translation initiation site and the RBS sequence, the base composition of the start codon, the nucleotide composition (A-rich sequences following start codons, and the expected distribution of the protein length in a Bayesian scoring function. To further increase the prediction accuracy, we also took into account the operon orientation. The outcome of the procedure achieved a prediction accuracy of 93.2% in 858 E. coli genes from the EcoGene data set and 92.7% accuracy in a data set of 1243 Bacillus subtilis 'non-y' genes. We confirmed the performance in the GC-rich Gamma-Proteobacteria Herminiimonas arsenicoxydans, Pseudomonas aeruginosa, and Burkholderia pseudomallei K96243. Conclusion Hon-yaku, being based on a careful choice of elements important in translation, improved the prediction accuracy in B. subtilis data sets and other bacteria except for E. coli. We believe that most remaining

  18. A method of identifying social structures in siting regions for deep geological repositories in Switzerland

    International Nuclear Information System (INIS)

    Brander, Simone

    2010-09-01

    Acceptance is a key element in the site selection process for deep geological repositories for high-level and low and intermediate-level radioactive waste in Switzerland. Participation requirements such as comprehensive negotiation issues and adequate resources have thus been defined by the Swiss Federal Office of Energy (SFOE). In 2008, on the basis of technical criteria Nagra (National Cooperative for the Disposal of Radioactive Waste) proposed several potential areas for deep geological repositories. The number of potential areas will be narrowed down within the next few years. All municipalities within the planning perimeter (the area in which surface facilities can be realised) are affected and form the siting region. In order to ensure that the local population have their say in the forthcoming discussions, regional participation bodies including all municipalities within a siting region are being set up by the SFOE. Regional participation ensures that local interests, needs and values are taken into account in the site selection process. Assembling the regional participation bodies is therefore of great importance. Before such bodies can be formed, however, the various interests, needs and values have to be identified, and special attention has to be paid to long-term interests of future generations, as well as to non-organised and under-represented interests. According to the concept of proportional representation, the interests, needs and values that are identified and weighted by the local population are to be represented in the regional participation procedure. The aim of this study is to share a method of mapping existing social structures in a defined geographical area. This involves a combination of an analysis of socio-economic statistical data and qualitative and quantitative social research methods

  19. Computerized analysis of the 12-lead electrocardiogram to identify epicardial ventricular tachycardia exit sites.

    Science.gov (United States)

    Yokokawa, Miki; Jung, Dae Yon; Joseph, Kim K; Hero, Alfred O; Morady, Fred; Bogun, Frank

    2014-11-01

    Twelve-lead electrocardiogram (ECG) criteria for epicardial ventricular tachycardia (VT) origins have been described. In patients with structural heart disease, the ability to predict an epicardial origin based on QRS morphology is limited and has been investigated only for limited regions in the heart. The purpose of this study was to determine whether a computerized algorithm is able to accurately differentiate epicardial vs endocardial origins of ventricular arrhythmias. Endocardial and epicardial pace-mapping were performed in 43 patients at 3277 sites. The 12-lead ECGs were digitized and analyzed using a mixture of gaussian model (MoG) to assess whether the algorithm was able to identify an epicardial vs endocardial origin of the paced rhythm. The MoG computerized algorithm was compared to algorithms published in prior reports. The computerized algorithm correctly differentiated epicardial vs endocardial pacing sites for 80% of the sites compared to an accuracy of 42% to 66% of other described criteria. The accuracy was higher in patients without structural heart disease than in those with structural heart disease (94% vs 80%, P = .0004) and for right bundle branch block (82%) compared to left bundle branch block morphologies (79%, P = .001). Validation studies showed the accuracy for VT exit sites to be 84%. A computerized algorithm was able to accurately differentiate the majority of epicardial vs endocardial pace-mapping sites. The algorithm is not region specific and performed best in patients without structural heart disease and with VTs having a right bundle branch block morphology. Copyright © 2014 Heart Rhythm Society. Published by Elsevier Inc. All rights reserved.

  20. Challenges in identifying sites climatically matched to the native ranges of animal invaders

    Science.gov (United States)

    Rodda, G.H.; Jarnevich, C.S.; Reed, R.N.

    2011-01-01

    Background: Species distribution models are often used to characterize a species' native range climate, so as to identify sites elsewhere in the world that may be climatically similar and therefore at risk of invasion by the species. This endeavor provoked intense public controversy over recent attempts to model areas at risk of invasion by the Indian Python (Python molurus). We evaluated a number of MaxEnt models on this species to assess MaxEnt's utility for vertebrate climate matching. Methodology/Principal Findings: Overall, we found MaxEnt models to be very sensitive to modeling choices and selection of input localities and background regions. As used, MaxEnt invoked minimal protections against data dredging, multi-collinearity of explanatory axes, and overfitting. As used, MaxEnt endeavored to identify a single ideal climate, whereas different climatic considerations may determine range boundaries in different parts of the native range. MaxEnt was extremely sensitive to both the choice of background locations for the python, and to selection of presence points: inclusion of just four erroneous localities was responsible for Pyron et al.'s conclusion that no additional portions of the U.S. mainland were at risk of python invasion. When used with default settings, MaxEnt overfit the realized climate space, identifying models with about 60 parameters, about five times the number of parameters justifiable when optimized on the basis of Akaike's Information Criterion. Conclusions/Significance: When used with default settings, MaxEnt may not be an appropriate vehicle for identifying all sites at risk of colonization. Model instability and dearth of protections against overfitting, multi-collinearity, and data dredging may combine with a failure to distinguish fundamental from realized climate envelopes to produce models of limited utility. A priori identification of biologically realistic model structure, combined with computational protections against these

  1. Challenges in identifying sites climatically matched to the native ranges of animal invaders.

    Directory of Open Access Journals (Sweden)

    Gordon H Rodda

    Full Text Available BACKGROUND: Species distribution models are often used to characterize a species' native range climate, so as to identify sites elsewhere in the world that may be climatically similar and therefore at risk of invasion by the species. This endeavor provoked intense public controversy over recent attempts to model areas at risk of invasion by the Indian Python (Python molurus. We evaluated a number of MaxEnt models on this species to assess MaxEnt's utility for vertebrate climate matching. METHODOLOGY/PRINCIPAL FINDINGS: Overall, we found MaxEnt models to be very sensitive to modeling choices and selection of input localities and background regions. As used, MaxEnt invoked minimal protections against data dredging, multi-collinearity of explanatory axes, and overfitting. As used, MaxEnt endeavored to identify a single ideal climate, whereas different climatic considerations may determine range boundaries in different parts of the native range. MaxEnt was extremely sensitive to both the choice of background locations for the python, and to selection of presence points: inclusion of just four erroneous localities was responsible for Pyron et al.'s conclusion that no additional portions of the U.S. mainland were at risk of python invasion. When used with default settings, MaxEnt overfit the realized climate space, identifying models with about 60 parameters, about five times the number of parameters justifiable when optimized on the basis of Akaike's Information Criterion. CONCLUSIONS/SIGNIFICANCE: When used with default settings, MaxEnt may not be an appropriate vehicle for identifying all sites at risk of colonization. Model instability and dearth of protections against overfitting, multi-collinearity, and data dredging may combine with a failure to distinguish fundamental from realized climate envelopes to produce models of limited utility. A priori identification of biologically realistic model structure, combined with computational protections

  2. Challenges in identifying sites climatically matched to the native ranges of animal invaders.

    Science.gov (United States)

    Rodda, Gordon H; Jarnevich, Catherine S; Reed, Robert N

    2011-02-09

    Species distribution models are often used to characterize a species' native range climate, so as to identify sites elsewhere in the world that may be climatically similar and therefore at risk of invasion by the species. This endeavor provoked intense public controversy over recent attempts to model areas at risk of invasion by the Indian Python (Python molurus). We evaluated a number of MaxEnt models on this species to assess MaxEnt's utility for vertebrate climate matching. Overall, we found MaxEnt models to be very sensitive to modeling choices and selection of input localities and background regions. As used, MaxEnt invoked minimal protections against data dredging, multi-collinearity of explanatory axes, and overfitting. As used, MaxEnt endeavored to identify a single ideal climate, whereas different climatic considerations may determine range boundaries in different parts of the native range. MaxEnt was extremely sensitive to both the choice of background locations for the python, and to selection of presence points: inclusion of just four erroneous localities was responsible for Pyron et al.'s conclusion that no additional portions of the U.S. mainland were at risk of python invasion. When used with default settings, MaxEnt overfit the realized climate space, identifying models with about 60 parameters, about five times the number of parameters justifiable when optimized on the basis of Akaike's Information Criterion. When used with default settings, MaxEnt may not be an appropriate vehicle for identifying all sites at risk of colonization. Model instability and dearth of protections against overfitting, multi-collinearity, and data dredging may combine with a failure to distinguish fundamental from realized climate envelopes to produce models of limited utility. A priori identification of biologically realistic model structure, combined with computational protections against these statistical problems, may produce more robust models of invasion risk.

  3. Presence in the pre-surgical fine-needle aspiration of potential thyroid biomarkers previously identified in the post-surgical one.

    Directory of Open Access Journals (Sweden)

    Federica Ciregia

    Full Text Available Fine-needle aspiration biopsy (FNA is usually applied to distinguish benign from malignant thyroid nodules. However, cytological analysis cannot always allow a proper diagnosis. We believe that the improvement of the diagnostic capability of pre-surgical FNA could avoid unnecessary thyroidectomy. In a previous study, we performed a proteome analysis to examine FNA collected after thyroidectomy. With the present study, we examined the applicability of these results on pre-surgical FNA. We collected pre-surgical FNA from 411 consecutive patients, and to obtain a correct comparison with our previous results, we processed only benign (n=114, papillary classical variant (cPTC (n=34 and papillary tall cell variant (TcPTC (n=14 FNA. We evaluated levels of five proteins previously found up-regulated in thyroid cancer with respect to benign nodules. ELISA and western blot (WB analysis were used to assay levels of L-lactate dehydrogenase B chain (LDHB, Ferritin heavy chain, Ferritin light chain, Annexin A1 (ANXA1, and Moesin in FNA. ELISA assays and WB analysis confirmed the increase of LDHB, Moesin, and ANXA1 in pre-surgical FNA of thyroid papillary cancer. Sensitivity and specificity of ANXA1 were respectively 87 and 94% for cPTC, 85 and 100% for TcPTC. In conclusion, a proteomic analysis of FNA from patients with thyroid nodules may help to distinguish benign versus malignant thyroid nodules. Moreover, ANXA1 appears to be an ideal candidate given the high sensitivity and specificity obtained from ROC curve analysis.

  4. Treatment response in psychotic patients classified according to social and clinical needs, drug side effects, and previous treatment; a method to identify functional remission

    DEFF Research Database (Denmark)

    Alenius, Malin; Hammarlund-Udenaes, Margareta; Honoré, Per Gustaf Hartvig

    2009-01-01

    , fewer psychotic symptoms, and higher rate of workers than those with the worst treatment outcome. CONCLUSION: In the evaluation, CANSEPT showed validity in discriminating the patients of interest and was well tolerated by the patients. CANSEPT could secure inclusion of correct patients in the clinic......BACKGROUND: Various approaches have been made over the years to classify psychotic patients according to inadequate treatment response, using terms such as treatment resistant or treatment refractory. Existing classifications have been criticized for overestimating positive symptoms......; underestimating residual symptoms, negative symptoms, and side effects; or being to open for individual interpretation. The aim of this study was to present and evaluate a new method of classification according to treatment response and, thus, to identify patients in functional remission. METHOD: A naturalistic...

  5. Using questions sent to an Ask-A-Scientist site to identify children's interests in science

    Science.gov (United States)

    Baram-Tsabari, Ayelet; Sethi, Ricky J.; Bry, Lynn; Yarden, Anat

    2006-11-01

    Interest is a powerful motivator; nonetheless, science educators often lack the necessary information to make use of the power of student-specific interests in the reform process of science curricula. This study suggests a novel methodology, which might be helpful in identifying such interests - using children's self-generated questions as an indication of their scientific interests. In this research, children's interests were measured by analyzing 1555 science-related questions submitted to an international Ask-A-Scientist Internet site. The analysis indicated that the popularity of certain topics varies with age and gender. Significant differences were found between children's spontaneous (intrinsically motivated) and school-related (extrinsically motivated) interests. Surprisingly, girls contributed most of the questions to the sample; however, the number of American girls dropped upon entering senior high school. We also found significant differences between girls' and boys' interests, with girls generally preferring biological topics. The two genders kept to their stereotypic fields of interest, in both their school-related and spontaneous questions. Children's science interests, as inferred from questions to Web sites, could ultimately inform classroom science teaching. This methodology extends the context in which children's interests can be investigated.

  6. Using transcranial magnetic stimulation of the undamaged brain to identify lesion sites that predict language outcome after stroke.

    Science.gov (United States)

    Lorca-Puls, Diego L; Gajardo-Vidal, Andrea; Seghier, Mohamed L; Leff, Alexander P; Sethi, Varun; Prejawa, Susan; Hope, Thomas M H; Devlin, Joseph T; Price, Cathy J

    2017-06-01

    Transcranial magnetic stimulation focused on either the left anterior supramarginal gyrus or opercular part of the left inferior frontal gyrus has been reported to transiently impair the ability to perform phonological more than semantic tasks. Here we tested whether phonological processing abilities were also impaired following lesions to these regions in right-handed, English speaking adults, who were investigated at least 1 year after a left-hemisphere stroke. When our regions of interest were limited to 0.5 cm3 of grey matter centred around sites that had been identified with transcranial magnetic stimulation-based functional localization, phonological impairments were observed in 74% (40/54) of patients with damage to the regions and 21% (21/100) of patients sparing these regions. This classification accuracy was better than that observed when using regions of interest centred on activation sites in previous functional magnetic resonance imaging studies of phonological processing, or transcranial magnetic stimulation sites that did not use functional localization. New regions of interest were generated by redefining the borders of each of the transcranial magnetic stimulation sites to include areas that were consistently damaged in the patients with phonological impairments. This increased the incidence of phonological impairments in the presence of damage to 85% (46/54) and also reduced the incidence of phonological impairments in the absence of damage to 15% (15/100). The difference in phonological processing abilities between those with and without damage to these 'transcranial magnetic stimulation-guided' regions remained highly significant even after controlling for the effect of lesion size. The classification accuracy of the transcranial magnetic stimulation-guided regions was validated in a second sample of 108 patients and found to be better than that for (i) functional magnetic resonance imaging-guided regions; (ii) a region identified from an

  7. Identifying malaria hotspots in Keur Soce health and demographic surveillance site in context of low transmission.

    Science.gov (United States)

    Ndiath, Mansour; Faye, Babacar; Cisse, Badara; Ndiaye, Jean Louis; Gomis, Jules François; Dia, Anta Tal; Gaye, Oumar

    2014-11-24

    Malaria is major public health problem in Senegal. In some parts of the country, it occurs almost permanently with a seasonal increase during the rainy season. There is evidence to suggest that the prevalence of malaria in Senegal has decreased considerably during the past few years. Recent data from the Senegalese National Malaria Control Programme (NMCP) indicates that the number of malaria cases decrease from 1,500,000 in 2006 to 174,339 in 2010. With the decline of malaria morbidity in Senegal, the characterization of the new epidemiological profile of this disease is crucial for public health decision makers. SaTScan™ software using the Kulldorf method of retrospective space-time permutation and the Bernoulli purely spatial model was used to identify malaria clusters using confirmed malaria cases in 74 villages. ArcMAp was used to map malaria hotspots. Logistic regression was used to investigate risk factors for malaria hotspots in Keur Soce health and demographic surveillance site. A total of 1,614 individuals in 440 randomly selected households were enrolled. The overall malaria prevalence was 12%. The malaria prevalence during the study period varied from less than 2% to more than 25% from one village to another. The results showed also that rooms located between 50 m to 100 m away from livestock holding place [adjusted O.R = 0.7, P = 0.044, 95% C.I (1.02 - 7.42)], bed net use [adjusted O.R = 1.2, P = 0.024, 95% C.I (1.02 -1.48)], are good predictors for malaria hotspots in the Keur Soce health and demographic surveillance site. The socio economic status of the household also predicted on hotspots patterns. The less poor household are 30% less likely to be classified as malaria hotspots area compared to the poorest household [adjusted O.R = 0.7, P = 0.014, 95% C.I (0.47 - 0.91)]. The study investigated risk factors for malaria hotspots in small communities in the Keur Soce site. The result showed considerable variation of malaria

  8. Mesoscale Biotransformations of Uranium: Identifying Sites and Strategies where Reductive Immobilization is Practical

    International Nuclear Information System (INIS)

    Tetsu K. Tokunaga; Jiamin Wan; Terry C. Hazen; Mary K. Firestone; Eoin Brodie; Yongman Kim; Rebecca Daly

    2006-01-01

    Bioreduction of U in contaminated sediments is an attractive strategy because of its low cost, and because of short-term studies supporting its feasibility. However, any in-situ immobilization approach for U will require assurance of either permanent fixation, or of very low release rates into the biosphere. Our previous long-term (2 years) laboratory experiments have shown that organic carbon (OC) based U(VI) bioreduction to UO2 can be transient even under sustained reducing (methanogenic) conditions. The biogeochemical processes underlying this finding urgently need to be understood. The current research is designed to identify mechanisms responsible for anaerobic U oxidation, and identify conditions that will support long-term stability of bioreduced U. We are investigating: (1) effects of OC concentration and supply rate on remobilization of bioreduced U, (2) the roles of Fe- and Mn-oxides as potential U oxidants in sediments, and (3) the role of microorganisms in U reoxidation, and (4) influences of pH on U(IV)/U(VI) redox equilibrium

  9. Identifying functional transcription factor binding sites in yeast by considering their positional preference in the promoters.

    Directory of Open Access Journals (Sweden)

    Fu-Jou Lai

    Full Text Available Transcription factor binding site (TFBS identification plays an important role in deciphering gene regulatory codes. With comprehensive knowledge of TFBSs, one can understand molecular mechanisms of gene regulation. In the recent decades, various computational approaches have been proposed to predict TFBSs in the genome. The TFBS dataset of a TF generated by each algorithm is a ranked list of predicted TFBSs of that TF, where top ranked TFBSs are statistically significant ones. However, whether these statistically significant TFBSs are functional (i.e. biologically relevant is still unknown. Here we develop a post-processor, called the functional propensity calculator (FPC, to assign a functional propensity to each TFBS in the existing computationally predicted TFBS datasets. It is known that functional TFBSs reveal strong positional preference towards the transcriptional start site (TSS. This motivates us to take TFBS position relative to the TSS as the key idea in building our FPC. Based on our calculated functional propensities, the TFBSs of a TF in the original TFBS dataset could be reordered, where top ranked TFBSs are now the ones with high functional propensities. To validate the biological significance of our results, we perform three published statistical tests to assess the enrichment of Gene Ontology (GO terms, the enrichment of physical protein-protein interactions, and the tendency of being co-expressed. The top ranked TFBSs in our reordered TFBS dataset outperform the top ranked TFBSs in the original TFBS dataset, justifying the effectiveness of our post-processor in extracting functional TFBSs from the original TFBS dataset. More importantly, assigning functional propensities to putative TFBSs enables biologists to easily identify which TFBSs in the promoter of interest are likely to be biologically relevant and are good candidates to do further detailed experimental investigation. The FPC is implemented as a web tool at http://santiago.ee.ncku.edu.tw/FPC/.

  10. A spatial modeling approach to identify potential butternut restoration sites in Mammoth Cave National Park

    Science.gov (United States)

    Thompson, L.M.; Van Manen, F.T.; Schlarbaum, S.E.; DePoy, M.

    2006-01-01

    Incorporation of disease resistance is nearly complete for several important North American hardwood species threatened by exotic fungal diseases. The next important step toward species restoration would be to develop reliable tools to delineate ideal restoration sites on a landscape scale. We integrated spatial modeling and remote sensing techniques to delineate potential restoration sites for Butternut (Juglans cinerea L.) trees, a hardwood species being decimated by an exotic fungus, in Mammoth Cave National Park (MCNP), Kentucky. We first developed a multivariate habitat model to determine optimum Butternut habitats within MCNP. Habitat characteristics of 54 known Butternut locations were used in combination with eight topographic and land use data layers to calculate an index of habitat suitability based on Mahalanobis distance (D2). We used a bootstrapping technique to test the reliability of model predictions. Based on a threshold value for the D2 statistic, 75.9% of the Butternut locations were correctly classified, indicating that the habitat model performed well. Because Butternut seedlings require extensive amounts of sunlight to become established, we used canopy cover data to refine our delineation of favorable areas for Butternut restoration. Areas with the most favorable conditions to establish Butternut seedlings were limited to 291.6 ha. Our study provides a useful reference on the amount and location of favorable Butternut habitat in MCNP and can be used to identify priority areas for future Butternut restoration. Given the availability of relevant habitat layers and accurate location records, our approach can be applied to other tree species and areas. ?? 2006 Society for Ecological Restoration International.

  11. Rigorous Screening Technology for Identifying Suitable CO2 Storage Sites II

    Energy Technology Data Exchange (ETDEWEB)

    George J. Koperna Jr.; Vello A. Kuuskraa; David E. Riestenberg; Aiysha Sultana; Tyler Van Leeuwen

    2009-06-01

    This report serves as the final technical report and users manual for the 'Rigorous Screening Technology for Identifying Suitable CO2 Storage Sites II SBIR project. Advanced Resources International has developed a screening tool by which users can technically screen, assess the storage capacity and quantify the costs of CO2 storage in four types of CO2 storage reservoirs. These include CO2-enhanced oil recovery reservoirs, depleted oil and gas fields (non-enhanced oil recovery candidates), deep coal seems that are amenable to CO2-enhanced methane recovery, and saline reservoirs. The screening function assessed whether the reservoir could likely serve as a safe, long-term CO2 storage reservoir. The storage capacity assessment uses rigorous reservoir simulation models to determine the timing, ultimate storage capacity, and potential for enhanced hydrocarbon recovery. Finally, the economic assessment function determines both the field-level and pipeline (transportation) costs for CO2 sequestration in a given reservoir. The screening tool has been peer reviewed at an Electrical Power Research Institute (EPRI) technical meeting in March 2009. A number of useful observations and recommendations emerged from the Workshop on the costs of CO2 transport and storage that could be readily incorporated into a commercial version of the Screening Tool in a Phase III SBIR.

  12. Dipeptide frequency/bias analysis identifies conserved sites of nonrandomness shared by cysteine-rich motifs.

    Science.gov (United States)

    Campion, S R; Ameen, A S; Lai, L; King, J M; Munzenmaier, T N

    2001-08-15

    This report describes the application of a simple computational tool, AAPAIR.TAB, for the systematic analysis of the cysteine-rich EGF, Sushi, and Laminin motif/sequence families at the two-amino acid level. Automated dipeptide frequency/bias analysis detects preferences in the distribution of amino acids in established protein families, by determining which "ordered dipeptides" occur most frequently in comprehensive motif-specific sequence data sets. Graphic display of the dipeptide frequency/bias data revealed family-specific preferences for certain dipeptides, but more importantly detected a shared preference for employment of the ordered dipeptides Gly-Tyr (GY) and Gly-Phe (GF) in all three protein families. The dipeptide Asn-Gly (NG) also exhibited high-frequency and bias in the EGF and Sushi motif families, whereas Asn-Thr (NT) was distinguished in the Laminin family. Evaluation of the distribution of dipeptides identified by frequency/bias analysis subsequently revealed the highly restricted localization of the G(F/Y) and N(G/T) sequence elements at two separate sites of extreme conservation in the consensus sequence of all three sequence families. The similar employment of the high-frequency/bias dipeptides in three distinct protein sequence families was further correlated with the concurrence of these shared molecular determinants at similar positions within the distinctive scaffolds of three structurally divergent, but similarly employed, motif modules.

  13. Provocative Endoscopy to Identify Bleeding Site in Upper Gastrointestinal Bleeding: A Novel Approach in Transarterial Embolization.

    Science.gov (United States)

    Kamo, Minobu; Fuwa, Sokun; Fukuda, Katsuyuki; Fujita, Yoshiyuki; Kurihara, Yasuyuki

    2016-07-01

    This report describes a novel approach to endoscopically induce bleeding by removing a clot from the bleeding site during angiography for upper gastrointestinal (UGI) hemorrhage. This procedure enabled accurate identification of the bleeding site, allowing for successful targeted embolization despite a negative initial angiogram. Provocative endoscopy may be a feasible and useful option for angiography of obscure bleeding sites in patients with UGI arterial hemorrhage. Copyright © 2016 SIR. Published by Elsevier Inc. All rights reserved.

  14. Identifying the most productive breeding sites for malaria mosquitoes in The Gambia

    NARCIS (Netherlands)

    Fillinger, U.; Sombroek, H.; Majambere, S.; Loon, van E.; Takken, W.; Lindsay, S.W.

    2009-01-01

    Background: Ideally larval control activities should be targeted at sites that generate the most adult vectors, thereby reducing operational costs. Despite the plethora of potential mosquito breeding sites found in the floodplains of the Gambia River, about 150 km from its mouth, during the rainy

  15. Application of Geophysical Techniques in Identifying UNE Signatures at Semipalatinsk Test Site (for OSI Purposes)

    Science.gov (United States)

    Belyashov, A.; Shaitorov, V.; Yefremov, M.

    2014-03-01

    This article describes geological and geophysical studies of an underground nuclear explosion area in one of the boreholes at the Semipalatinsk test site in Kazakhstan. During these studies, the typical elements of mechanical impact of the underground explosion on the host medium—fracturing of rock, spall zones, faults, cracks, etc., were observed. This information supplements to the database of underground nuclear explosion phenomenology and can be applied in fulfilling on-site inspection tasks under the Comprehensive Nuclear-Test-Ban Treaty.

  16. Identifying the Tunneling Site in Strong-Field Ionization of H_{2}^{+}.

    Science.gov (United States)

    Liu, Kunlong; Barth, Ingo

    2017-12-15

    The tunneling site of the electron in a molecule exposed to a strong laser field determines the initial position of the ionizing electron and, as a result, has a large impact on the subsequent ultrafast electron dynamics on the polyatomic Coulomb potential. Here, the tunneling site of the electron of H_{2}^{+} ionized by a strong circularly polarized (CP) laser pulse is studied by numerically solving the time-dependent Schrödinger equation. We show that the electron removed from the down-field site is directly driven away by the CP field and the lateral photoelectron momentum distribution (LPMD) exhibits a Gaussian-like distribution, whereas the corresponding LPMD of the electron removed from the up-field site differs from the Gaussian shape due to the Coulomb focusing and scattering by the down-field core. Our current study presents the direct evidence clarifying a long-standing controversy over the tunneling site in H_{2}^{+} and raises the important role of the tunneling site in strong-field molecular ionization.

  17. Biological data warehousing system for identifying transcriptional regulatory sites from gene expressions of microarray data.

    Science.gov (United States)

    Tsou, Ann-Ping; Sun, Yi-Ming; Liu, Chia-Lin; Huang, Hsien-Da; Horng, Jorng-Tzong; Tsai, Meng-Feng; Liu, Baw-Juine

    2006-07-01

    Identification of transcriptional regulatory sites plays an important role in the investigation of gene regulation. For this propose, we designed and implemented a data warehouse to integrate multiple heterogeneous biological data sources with data types such as text-file, XML, image, MySQL database model, and Oracle database model. The utility of the biological data warehouse in predicting transcriptional regulatory sites of coregulated genes was explored using a synexpression group derived from a microarray study. Both of the binding sites of known transcription factors and predicted over-represented (OR) oligonucleotides were demonstrated for the gene group. The potential biological roles of both known nucleotides and one OR nucleotide were demonstrated using bioassays. Therefore, the results from the wet-lab experiments reinforce the power and utility of the data warehouse as an approach to the genome-wide search for important transcription regulatory elements that are the key to many complex biological systems.

  18. Web-based Tool Identifies and Quantifies Potential Cost Savings Measures at the Hanford Site

    International Nuclear Information System (INIS)

    Renevitz, Marisa J.; Peschong, Jon C.; Charboneau, Briant L.; Simpson, Brett C.

    2014-01-01

    The Technical Improvement system is an approachable web-based tool that is available to Hanford DOE staff, site contractors, and general support service contractors as part of the baseline optimization effort underway at the Hanford Site. Finding and implementing technical improvements are a large part of DOE's cost savings efforts. The Technical Improvement dashboard is a key tool for brainstorming and monitoring the progress of submitted baseline optimization and potential cost/schedule efficiencies. The dashboard is accessible to users over the Hanford Local Area Network (HLAN) and provides a highly visual and straightforward status to management on the ideas provided, alleviating the need for resource intensive weekly and monthly reviews

  19. Superfund TIO videos. Set A. Identifying PRPS. Removal process: Removal site evaluation. Part 2. Audio-Visual

    International Nuclear Information System (INIS)

    1990-01-01

    The videotape is divided into three sections. Section 1 details the liability of Potentially Responsible Parties (PRPs) and describes the four classes of PRPs: current owners and operators, former owners and operators, generators, and transporters (if they selected the site). Section 2 lists the goals of the Potentially Responsible Party (PRP) search and explains how to identify key players during the PRP search. How to plan and conduct the PRP search is also outlined. Section 3 outlines the steps involved in conducting a removal site evaluation. A discussion of when to conduct a removal preliminary assessment, a removal site inspection, and an Engineering Evaluation/Cost Analysis (EE/AC) also is covered

  20. FANCD2 binding identifies conserved fragile sites at large transcribed genes in avian cells

    DEFF Research Database (Denmark)

    Pentzold, Constanze; Shah, Shiraz Ali; Hansen, Niels Richard

    2018-01-01

    Common Chromosomal Fragile Sites (CFSs) are specific genomic regions prone to form breaks on metaphase chromosomes in response to replication stress. Moreover, CFSs are mutational hotspots in cancer genomes, showing that the mutational mechanisms that operate at CFSs are highly active in cancer c...

  1. Neuropeptide Y binding sites in rat brain identified with purified neuropeptide Y-I125

    International Nuclear Information System (INIS)

    Walker, M.W.; Miller, R.J.

    1986-01-01

    Neuropeptide Y (NPY) is a widely distributed neuronally localized peptide with 36 amino acids, 5 of which are tyrosines. The authors wished to investigate the properties of specific receptors for NPY. They therefore labeled the tyrosines with I125 using chloramine T and then purified the peptide using HPLC. A single mono-iodinated species of NPY which yielded > 85% specific binding in rat forebrain synaptosomes was selected as the ligand for all subsequent experiments. A time course of binding showed that equilibrium conditions were reached in 60 minutes at 21 0 C. Scatchard plots revealed a single class of binding sites with a Kd and a Bmax of 3 x 10-10 M and 28 pmol/mg, respectively. Competition binding with unlabeled NPY showed 50% displacement of bound ligand at 1 x 10-10 M NPY. Competition binding with rat pancreatic polypeptide (RPP), a homologous peptide possessing little NPY-like activity, showed 50% displacement of bound ligand at 2 x 10 -7 M RPP. No binding was observed on F-11 or PC12 neuronal cell lines, or on HSWP fibroblast cells. They conclude that NPY-I125 purified to homogeneity with HPLC is a highly selective ligand for NPY receptor sites. They are currently investigating such sites in brain, gut, and other tissues

  2. Guide for Identifying and Converting High-Potential Petroleum Brownfield Sites to Alternative Fuel Stations

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, C.; Hettinger, D.; Mosey, G.

    2011-05-01

    Former gasoline stations that are now classified as brownfields can be good sites to sell alternative fuels because they are in locations that are convenient to vehicles and they may be seeking a new source of income. However, their success as alternative fueling stations is highly dependent on location-specific criteria. First, this report outlines what these criteria are, how to prioritize them, and then applies that assessment framework to five of the most popular alternative fuels--electricity, natural gas, hydrogen, ethanol, and biodiesel. The second part of this report delves into the criteria and tools used to assess an alternative fuel retail site at the local level. It does this through two case studies of converting former gasoline stations in the Seattle-Eugene area into electric charge stations. The third part of this report addresses steps to be taken after the specific site has been selected. This includes choosing and installing the recharging equipment, which includes steps to take in the permitting process and key players to include.

  3. Gradient temperature Raman spectroscopy identifies flexible sites in proline and alanine peptides

    Science.gov (United States)

    Continuous thermo dynamic Raman spectroscopy (TDRS) applies the temperature gradients utilized in differential scanning calorimetry (DSC) to Raman spectroscopy, providing a straightforward technique to identify molecular rearrangements that occur just prior to phase transitions. Herein we apply TDRS...

  4. COSMID: A Web-based Tool for Identifying and Validating CRISPR/Cas Off-target Sites

    Directory of Open Access Journals (Sweden)

    Thomas J Cradick

    2014-01-01

    Full Text Available Precise genome editing using engineered nucleases can significantly facilitate biological studies and disease treatment. In particular, clustered regularly interspaced short palindromic repeats (CRISPR with CRISPR-associated (Cas proteins are a potentially powerful tool for modifying a genome by targeted cleavage of DNA sequences complementary to designed guide strand RNAs. Although CRISPR/Cas systems can have on-target cleavage rates close to the transfection rates, they may also have relatively high off-target cleavage at similar genomic sites that contain one or more base pair mismatches, and insertions or deletions relative to the guide strand. We have developed a bioinformatics-based tool, COSMID (CRISPR Off-target Sites with Mismatches, Insertions, and Deletions that searches genomes for potential off-target sites (http://crispr.bme.gatech.edu. Based on the user-supplied guide strand and input parameters, COSMID identifies potential off-target sites with the specified number of mismatched bases and insertions or deletions when compared with the guide strand. For each site, amplification primers optimal for the chosen application are also given as output. This ranked-list of potential off-target sites assists the choice and evaluation of intended target sites, thus helping the design of CRISPR/Cas systems with minimal off-target effects, as well as the identification and quantification of CRISPR/Cas induced off-target cleavage in cells.

  5. A preliminary guidebook for identifying stratigraphic contacts at the Nevada Test Site

    International Nuclear Information System (INIS)

    Pawloski, G.A.; McKague, H.L.; Wagoner, J.L.; McKinnis, W.B.

    1992-01-01

    Lithologic variation, regional depositional trends, and the lack of written guidelines have resulted in inconsistencies in the recognition of stratigraphic contacts in drill holes at the Nevada Test Site (NTS). Stratigraphic identification, based on mineralogy of discrete samples, can be augmented by geophysical logs and downhole movies to more accurately and consistently locate contacts between units. Criteria are established for locating the base of the Pahute Mesa ash-flow tuff, the top of the Ammonia Tanks ash-flow tuff, the top of the Ammonia Tanks bedded tuff, and the top and the base of the Rainier Mesa Tuff

  6. A Study Identifying Causes of Construction Waste Production and Applying Safety Management on Construction Site

    Directory of Open Access Journals (Sweden)

    Ali Asghar Najafpoor

    2014-09-01

    Full Text Available Background and purpose: In a recent century, the amount of construction waste has increased significantly. Although the building industry has a considerable role in the development of a society, it is regarded as an environmentally destructive. Source reduction is the highest goal in the waste management hierarchy and is in priority. It also has economic benefits by reducing costs associated with transportation, disposal or recycling of wastes. The present study is aimed to identify activities generating the wastes in design, transportation and storage and procurement of building materials. Materials and Methods: This was questionnaire survey. A total of 94 professionals in the construction industry were attended in this study. To determine the validity and reliability of the instrument, content validity method and Cronbach’s alpha coefficient (0.79 were used. Data were analyzed using SPSS for Windows. Frequencies, percentage, mean and standard deviation were determined in this research. Results: The results showed that handling and storage have been chosen as the most causative factor of waste production in construction activity. Improper material storage was identified major factor in producing waste in handling and storage phase. Usage of low-quality material in design stage and material price changes in procurement were recognized as major causes of waste production in these stages. Conclusion: All studied phases in this research were identified as causative factors in producing of waste. Identifying causes of construction waste production will help us decide better how to control this sort of wastes.

  7. Radiation port cutaneous metastases: Reports of two patients whose recurrent visceral cancers presented as skin lesions at the site of previous radiation and literature review

    Directory of Open Access Journals (Sweden)

    Brian Spencer Hoyt

    2014-01-01

    Full Text Available Radiation therapy is associated with a variety of complications, including the development of primary skin cancers in the radiated region. However, it is rare for patients with visceral cancers who are treated with radiation therapy to subsequently develop cutaneous metastasis within the radiation port. We describe two patients with internal malignancies who developed cutaneous metastases within their radiation ports following radiotherapy. In addition, we used PubMed to perform an extensive literature review and identify additional reports of cutaneous metastasis within a radiation port. We excluded patients who developed melanoma or primary skin cancers in the radiation port. We also excluded patients with non-solid organ malignancies. Herein, we summarize the characteristics of 23 additional patients who experienced radiation port cutaneous metastases and explore possible mechanisms for the occurrence of radiation port cutaneous metastases.

  8. Identifying opportune landing sites in degraded visual environments with terrain and cultural databases

    Science.gov (United States)

    Moody, Marc; Fisher, Robert; Little, J. Kristin

    2014-06-01

    Boeing has developed a degraded visual environment navigational aid that is flying on the Boeing AH-6 light attack helicopter. The navigational aid is a two dimensional software digital map underlay generated by the Boeing™ Geospatial Embedded Mapping Software (GEMS) and fully integrated with the operational flight program. The page format on the aircraft's multi function displays (MFD) is termed the Approach page. The existing work utilizes Digital Terrain Elevation Data (DTED) and OpenGL ES 2.0 graphics capabilities to compute the pertinent graphics underlay entirely on the graphics processor unit (GPU) within the AH-6 mission computer. The next release will incorporate cultural databases containing Digital Vertical Obstructions (DVO) to warn the crew of towers, buildings, and power lines when choosing an opportune landing site. Future IRAD will include Light Detection and Ranging (LIDAR) point cloud generating sensors to provide 2D and 3D synthetic vision on the final approach to the landing zone. Collision detection with respect to terrain, cultural, and point cloud datasets may be used to further augment the crew warning system. The techniques for creating the digital map underlay leverage the GPU almost entirely, making this solution viable on most embedded mission computing systems with an OpenGL ES 2.0 capable GPU. This paper focuses on the AH-6 crew interface process for determining a landing zone and flying the aircraft to it.

  9. A bioinformatics approach for identifying transgene insertion sites using whole genome sequencing data.

    Science.gov (United States)

    Park, Doori; Park, Su-Hyun; Ban, Yong Wook; Kim, Youn Shic; Park, Kyoung-Cheul; Kim, Nam-Soo; Kim, Ju-Kon; Choi, Ik-Young

    2017-08-15

    Genetically modified crops (GM crops) have been developed to improve the agricultural traits of modern crop cultivars. Safety assessments of GM crops are of paramount importance in research at developmental stages and before releasing transgenic plants into the marketplace. Sequencing technology is developing rapidly, with higher output and labor efficiencies, and will eventually replace existing methods for the molecular characterization of genetically modified organisms. To detect the transgenic insertion locations in the three GM rice gnomes, Illumina sequencing reads are mapped and classified to the rice genome and plasmid sequence. The both mapped reads are classified to characterize the junction site between plant and transgene sequence by sequence alignment. Herein, we present a next generation sequencing (NGS)-based molecular characterization method, using transgenic rice plants SNU-Bt9-5, SNU-Bt9-30, and SNU-Bt9-109. Specifically, using bioinformatics tools, we detected the precise insertion locations and copy numbers of transfer DNA, genetic rearrangements, and the absence of backbone sequences, which were equivalent to results obtained from Southern blot analyses. NGS methods have been suggested as an effective means of characterizing and detecting transgenic insertion locations in genomes. Our results demonstrate the use of a combination of NGS technology and bioinformatics approaches that offers cost- and time-effective methods for assessing the safety of transgenic plants.

  10. FIGIFIGO as a tool to characterize and identify planetary analogue sites

    Science.gov (United States)

    Gritsevich, M.; Peltoniemi, J.; Hakala, T.; Muinonen, K.

    2014-07-01

    We present an overview of the Finnish Geodetic Institute's field goniospectrometer (FIGIFIGO) and highlight its usability to study extraterrestrial analogues on the Earth. The design concept of this custom-made instrument has been proved to have a number of advantages, such as a well-adopted user-friendly interface, a high level of automation, and excellent suitability for field measurements within a wide range of weather conditions. It is perfect for collection of reference data on a given target in natural undisturbed (and well-recorded for further data interpretation) conditions. The instrument communicates via a controlled computer with an implemented simple and user-friendly interface. This allows users to easily set up optional parameters at the beginning of the measurement series. Thus a number of details may be modified, such as the initial position of the sensor, the range and speed of further automated zenith turns, and length of the turnable arm holding the selected optics (including an option for a computer-turned linear polarizer) above the target. The assembly and operation of the instrument are fast and efficient in both laboratory and field conditions. It is battery powered and easily portable, including possible transportation by plane, car, boat, or sledge. The system includes a sky camera to detect the goniometer orientation and a pyranometer to monitor the actual illumination conditions. A fine-tune mirror is used for spatial correction of the optics footprint. Recent calibration of the system has significantly increased the measurement robustness and data reliability, and has provided the operators with information on how to operate the instrument in the most efficient and accurate way. Measurement campaigns are organized frequently and significant amount of reference data has been already collected. The identification of new planetary analogue sites and characterization of known ones using FIGIFIGO could offer new possibilities and provide

  11. Identifying sites of replication initiation in yeast chromosomes: looking for origins in all the right places.

    Science.gov (United States)

    van Brabant, A J; Hunt, S Y; Fangman, W L; Brewer, B J

    1998-06-01

    DNA fragments that contain an active origin of replication generate bubble-shaped replication intermediates with diverging forks. We describe two methods that use two-dimensional (2-D) agarose gel electrophoresis along with DNA sequence information to identify replication origins in natural and artificial Saccharomyces cerevisiae chromosomes. The first method uses 2-D gels of overlapping DNA fragments to locate an active chromosomal replication origin within a region known to confer autonomous replication on a plasmid. A variant form of 2-D gels can be used to determine the direction of fork movement, and the second method uses this technique to find restriction fragments that are replicated by diverging forks, indicating that a bidirectional replication origin is located between the two fragments. Either of these two methods can be applied to the analysis of any genomic region for which there is DNA sequence information or an adequate restriction map.

  12. Small molecule inhibitors of the LEDGF site of human immunodeficiency virus integrase identified by fragment screening and structure based design.

    Directory of Open Access Journals (Sweden)

    Thomas S Peat

    Full Text Available A fragment-based screen against human immunodeficiency virus type 1 (HIV integrase led to a number of compounds that bound to the lens epithelium derived growth factor (LEDGF binding site of the integrase catalytic core domain. We determined the crystallographic structures of complexes of the HIV integrase catalytic core domain for 10 of these compounds and quantitated the binding by surface plasmon resonance. We demonstrate that the compounds inhibit the interaction of LEDGF with HIV integrase in a proximity AlphaScreen assay, an assay for the LEDGF enhancement of HIV integrase strand transfer and in a cell based assay. The compounds identified represent a potential framework for the development of a new series of HIV integrase inhibitors that do not bind to the catalytic site of the enzyme.

  13. Exome Sequencing Identified a Splice Site Mutation in FHL1 that Causes Uruguay Syndrome, an X-Linked Disorder With Skeletal Muscle Hypertrophy and Premature Cardiac Death.

    Science.gov (United States)

    Xue, Yuan; Schoser, Benedikt; Rao, Aliz R; Quadrelli, Roberto; Vaglio, Alicia; Rupp, Verena; Beichler, Christine; Nelson, Stanley F; Schapacher-Tilp, Gudrun; Windpassinger, Christian; Wilcox, William R

    2016-04-01

    Previously, we reported a rare X-linked disorder, Uruguay syndrome in a single family. The main features are pugilistic facies, skeletal deformities, and muscular hypertrophy despite a lack of exercise and cardiac ventricular hypertrophy leading to premature death. An ≈19 Mb critical region on X chromosome was identified through identity-by-descent analysis of 3 affected males. Exome sequencing was conducted on one affected male to identify the disease-causing gene and variant. A splice site variant (c.502-2A>G) in the FHL1 gene was highly suspicious among other candidate genes and variants. FHL1A is the predominant isoform of FHL1 in cardiac and skeletal muscle. Sequencing cDNA showed the splice site variant led to skipping of exons 6 of the FHL1A isoform, equivalent to the FHL1C isoform. Targeted analysis showed that this splice site variant cosegregated with disease in the family. Western blot and immunohistochemical analysis of muscle from the proband showed a significant decrease in protein expression of FHL1A. Real-time polymerase chain reaction analysis of different isoforms of FHL1 demonstrated that the FHL1C is markedly increased. Mutations in the FHL1 gene have been reported in disorders with skeletal and cardiac myopathy but none has the skeletal or facial phenotype seen in patients with Uruguay syndrome. Our data suggest that a novel FHL1 splice site variant results in the absence of FHL1A and the abundance of FHL1C, which may contribute to the complex and severe phenotype. Mutation screening of the FHL1 gene should be considered for patients with uncharacterized myopathies and cardiomyopathies. © 2016 American Heart Association, Inc.

  14. GIS and Multi Criteria Decision Method Based Approach of Identifying Appropriate Landfill Sites for the City Of Chittagong

    Directory of Open Access Journals (Sweden)

    M. Ali Ashraf

    2015-02-01

    were identified initially. Out of these sites four were found to be most appropriate and suitable for use as landfill. DOI: http://dx.doi.org/10.3126/ije.v4i1.12174International Journal of Environment Volume-4, Issue-1, Dec-Feb 2014/15, page: 1-15  

  15. Using the Textpresso Site-Specific Recombinases Web server to identify Cre expressing mouse strains and floxed alleles.

    Science.gov (United States)

    Condie, Brian G; Urbanski, William M

    2014-01-01

    Effective tools for searching the biomedical literature are essential for identifying reagents or mouse strains as well as for effective experimental design and informed interpretation of experimental results. We have built the Textpresso Site Specific Recombinases (Textpresso SSR) Web server to enable researchers who use mice to perform in-depth searches of a rapidly growing and complex part of the mouse literature. Our Textpresso Web server provides an interface for searching the full text of most of the peer-reviewed publications that report the characterization or use of mouse strains that express Cre or Flp recombinase. The database also contains most of the publications that describe the characterization or analysis of strains carrying conditional alleles or transgenes that can be inactivated or activated by site-specific recombinases such as Cre or Flp. Textpresso SSR complements the existing online databases that catalog Cre and Flp expression patterns by providing a unique online interface for the in-depth text mining of the site specific recombinase literature.

  16. A Prospective Comparison of 18F-FDG PET/CT and CT as Diagnostic Tools to Identify the Primary Tumor Site in Patients with Extracervical Carcinoma of Unknown Primary Site

    DEFF Research Database (Denmark)

    Moller, Anne Kirstine H; Loft, Annika; Berthelsen, Anne K

    2012-01-01

    that the same set of criteria were used for classification of patients, that is, either as CUP patients or patients with a suggested primary tumor site. The independently obtained suggestions of primary tumor sites using PET/CT and CT were correlated with the SR to reach a consensus regarding true-positive (TP......), true-negative, false-negative, and false-positive results.Results. SR identified a primary tumor site in 66 CUP patients (48.9%). PET/CT identified 38 TP primary tumor sites and CT identified 43 TP primary tumor sites. No statistically significant differences were observed between (18)F-FDG PET...

  17. Identifying strategic sites for Green-Infrastructures (GI) to manage stormwater in a miscellaneous use urban African watershed

    Science.gov (United States)

    Selker, J. S.; Kahsai, S. K.

    2017-12-01

    Green Infrastructure (GI) or Low impact development (LID), is a land use planning and design approach with the objective of mitigating land development impacts to the environment, and is ever more looked to as a way to lessen runoff and pollutant loading to receiving water bodies. Broad-scale approaches for siting GI/LID have been developed for agricultural watersheds, but are rare for urban watersheds, largely due to greater land use complexity. And it is even more challenging when it comes to Urban Africa due to the combination of poor data quality, rapid and unplanned development, and civic institutions unable to reliably carry out regular maintenance. We present a spacio-temporal simulation-based approach to identify an optimal prioritization of sites for GI/LID based on DEM, land use and land cover. Optimization used is a multi-objective optimization tool along with an urban storm water management model (SWMM) to identify the most cost-effective combination of LID/GI. This was applied to an urban watershed in NW Kampala, Lubigi Catchment (notorious for being heavily flooded every year), with a miscellaneous use watershed in Uganda, as a case-study to demonstrate the approach.

  18. Genome-wide screens for in vivo Tinman binding sites identify cardiac enhancers with diverse functional architectures.

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    Hong Jin

    Full Text Available The NK homeodomain factor Tinman is a crucial regulator of early mesoderm patterning and, together with the GATA factor Pannier and the Dorsocross T-box factors, serves as one of the key cardiogenic factors during specification and differentiation of heart cells. Although the basic framework of regulatory interactions driving heart development has been worked out, only about a dozen genes involved in heart development have been designated as direct Tinman target genes to date, and detailed information about the functional architectures of their cardiac enhancers is lacking. We have used immunoprecipitation of chromatin (ChIP from embryos at two different stages of early cardiogenesis to obtain a global overview of the sequences bound by Tinman in vivo and their linked genes. Our data from the analysis of ~50 sequences with high Tinman occupancy show that the majority of such sequences act as enhancers in various mesodermal tissues in which Tinman is active. All of the dorsal mesodermal and cardiac enhancers, but not some of the others, require tinman function. The cardiac enhancers feature diverse arrangements of binding motifs for Tinman, Pannier, and Dorsocross. By employing these cardiac and non-cardiac enhancers in machine learning approaches, we identify a novel motif, termed CEE, as a classifier for cardiac enhancers. In vivo assays for the requirement of the binding motifs of Tinman, Pannier, and Dorsocross, as well as the CEE motifs in a set of cardiac enhancers, show that the Tinman sites are essential in all but one of the tested enhancers; although on occasion they can be functionally redundant with Dorsocross sites. The enhancers differ widely with respect to their requirement for Pannier, Dorsocross, and CEE sites, which we ascribe to their different position in the regulatory circuitry, their distinct temporal and spatial activities during cardiogenesis, and functional redundancies among different factor binding sites.

  19. Selection of Inhibitor-Resistant Viral Potassium Channels Identifies a Selectivity Filter Site that Affects Barium and Amantadine Block

    Science.gov (United States)

    Fujiwara, Yuichiro; Arrigoni, Cristina; Domigan, Courtney; Ferrara, Giuseppina; Pantoja, Carlos; Thiel, Gerhard; Moroni, Anna; Minor, Daniel L.

    2009-01-01

    Background Understanding the interactions between ion channels and blockers remains an important goal that has implications for delineating the basic mechanisms of ion channel function and for the discovery and development of ion channel directed drugs. Methodology/Principal Findings We used genetic selection methods to probe the interaction of two ion channel blockers, barium and amantadine, with the miniature viral potassium channel Kcv. Selection for Kcv mutants that were resistant to either blocker identified a mutant bearing multiple changes that was resistant to both. Implementation of a PCR shuffling and backcrossing procedure uncovered that the blocker resistance could be attributed to a single change, T63S, at a position that is likely to form the binding site for the inner ion in the selectivity filter (site 4). A combination of electrophysiological and biochemical assays revealed a distinct difference in the ability of the mutant channel to interact with the blockers. Studies of the analogous mutation in the mammalian inward rectifier Kir2.1 show that the T→S mutation affects barium block as well as the stability of the conductive state. Comparison of the effects of similar barium resistant mutations in Kcv and Kir2.1 shows that neighboring amino acids in the Kcv selectivity filter affect blocker binding. Conclusions/Significance The data support the idea that permeant ions have an integral role in stabilizing potassium channel structure, suggest that both barium and amantadine act at a similar site, and demonstrate how genetic selections can be used to map blocker binding sites and reveal mechanistic features. PMID:19834614

  20. Site-Mutation of Hydrophobic Core Residues Synchronically Poise Super Interleukin 2 for Signaling: Identifying Distant Structural Effects through Affordable Computations

    Directory of Open Access Journals (Sweden)

    Longcan Mei

    2018-03-01

    Full Text Available A superkine variant of interleukin-2 with six site mutations away from the binding interface developed from the yeast display technique has been previously characterized as undergoing a distal structure alteration which is responsible for its super-potency and provides an elegant case study with which to get insight about how to utilize allosteric effect to achieve desirable protein functions. By examining the dynamic network and the allosteric pathways related to those mutated residues using various computational approaches, we found that nanosecond time scale all-atom molecular dynamics simulations can identify the dynamic network as efficient as an ensemble algorithm. The differentiated pathways for the six core residues form a dynamic network that outlines the area of structure alteration. The results offer potentials of using affordable computing power to predict allosteric structure of mutants in knowledge-based mutagenesis.

  1. A GIS-based approach for identifying potential runoff harvesting sites in the Thukela River basin, South Africa

    Science.gov (United States)

    de Winnaar, G.; Jewitt, G. P. W.; Horan, M.

    Water scarce countries such as South Africa are subject to various hydrological constraints which can often be attributed to poor rainfall partitioning, particularly within resource poor farming communities that are reliant on rainfed agriculture. Recent initiatives to address this have shifted focus to explore more efficient alternatives to water supply and the recognition of numerous opportunities to implement runoff harvesting as a means to supplement water availability. However, increasing the implementation of runoff harvesting, without encountering unintended impacts on downstream hydrological and ecological systems, requires better understanding of the hydrologic and environmental impacts at catchment scale. In this paper the representation of spatial variations in landscape characteristics such as soil, land use, rainfall and slope information is shown to be an important step in identifying potential runoff harvesting sites, after which modelling the hydrological response in catchments where extensive runoff harvesting is being considered can be performed and likely impacts assessed. Geographic information systems (GIS) was utilised as an integrating tool to store, analyse and manage spatial information and when linked to hydrological response models, provided a rational means to facilitate decision making by providing catchment level identification, planning and assessment of runoff harvesting sites as illustrated by a case study at the Potshini catchment, a small sub-catchment in the Thukela River basin, South Africa. Through the linked GIS, potential runoff harvesting sites are identified relative to areas that concentrate runoff and where the stored water will be appropriately distributed. Based on GIS analysis it was found that 17% percent of the Potshini catchment area has a high potential for generating surface runoff, whereas an analysis of all factors which influence the location of such systems, shows that 18% is highly suitable for runoff

  2. An evaluation of applicability of seismic refraction method in identifying shallow archaeological features A case study at archaeological site

    Science.gov (United States)

    Jahangardi, Morteza; Hafezi Moghaddas, Naser; Keivan Hosseini, Sayyed; Garazhian, Omran

    2015-04-01

    We applied the seismic refraction method at archaeological site, Tepe Damghani located in Sabzevar, NE of Iran, in order to determine the structures of archaeological interests. This pre-historical site has special conditions with respect to geographical location and geomorphological setting, so it is an urban archaeological site, and in recent years it has been used as an agricultural field. In spring and summer of 2012, the third season of archaeological excavation was carried out. Test trenches of excavations in this site revealed that cultural layers were often disturbed adversely due to human activities such as farming and road construction in recent years. Conditions of archaeological cultural layers in southern and eastern parts of Tepe are slightly better, for instance, in test trench 3×3 m²1S03, third test trench excavated in the southern part of Tepe, an adobe in situ architectural structure was discovered that likely belongs to cultural features of a complex with 5 graves. After conclusion of the third season of archaeological excavation, all of the test trenches were filled with the same soil of excavated test trenches. Seismic refraction method was applied with12 channels of P geophones in three lines with a geophone interval of 0.5 meter and a 1.5 meter distance between profiles on test trench 1S03. The goal of this operation was evaluation of applicability of seismic method in identification of archaeological features, especially adobe wall structures. Processing of seismic data was done with the seismic software, SiesImager. Results were presented in the form of seismic section for every profile, so that identification of adobe wall structures was achieved hardly. This could be due to that adobe wall had been built with the same materials of the natural surrounding earth. Thus, there is a low contrast and it has an inappropriate effect on seismic processing and identifying of archaeological features. Hence the result could be that application of

  3. TSSer: an automated method to identify transcription start sites in prokaryotic genomes from differential RNA sequencing data.

    Science.gov (United States)

    Jorjani, Hadi; Zavolan, Mihaela

    2014-04-01

    Accurate identification of transcription start sites (TSSs) is an essential step in the analysis of transcription regulatory networks. In higher eukaryotes, the capped analysis of gene expression technology enabled comprehensive annotation of TSSs in genomes such as those of mice and humans. In bacteria, an equivalent approach, termed differential RNA sequencing (dRNA-seq), has recently been proposed, but the application of this approach to a large number of genomes is hindered by the paucity of computational analysis methods. With few exceptions, when the method has been used, annotation of TSSs has been largely done manually. In this work, we present a computational method called 'TSSer' that enables the automatic inference of TSSs from dRNA-seq data. The method rests on a probabilistic framework for identifying both genomic positions that are preferentially enriched in the dRNA-seq data as well as preferentially captured relative to neighboring genomic regions. Evaluating our approach for TSS calling on several publicly available datasets, we find that TSSer achieves high consistency with the curated lists of annotated TSSs, but identifies many additional TSSs. Therefore, TSSer can accelerate genome-wide identification of TSSs in bacterial genomes and can aid in further characterization of bacterial transcription regulatory networks. TSSer is freely available under GPL license at http://www.clipz.unibas.ch/TSSer/index.php

  4. Genetic Characterization of a Novel HIV-1 Circulating Recombinant Form (CRF74_01B) Identified among Intravenous Drug Users in Malaysia: Recombination History and Phylogenetic Linkage with Previously Defined Recombinant Lineages.

    Science.gov (United States)

    Cheong, Hui Ting; Chow, Wei Zhen; Takebe, Yutaka; Chook, Jack Bee; Chan, Kok Gan; Al-Darraji, Haider Abdulrazzaq Abed; Koh, Clayton; Kamarulzaman, Adeeba; Tee, Kok Keng

    2015-01-01

    In many parts of Southeast Asia, the HIV-1 epidemic has been driven by the sharing of needles and equipment among intravenous drug users (IDUs). Over the last few decades, many studies have proven time and again that the diversity of HIV-1 epidemics can often be linked to the route of infection transmission. That said, the diversity and complexity of HIV-1 molecular epidemics in the region have been increasing at an alarming rate, due in part to the high tendency of the viral RNA to recombine. This scenario was exemplified by the discovery of numerous circulating recombinant forms (CRFs), especially in Thailand and Malaysia. In this study, we characterized a novel CRF designated CRF74_01B, which was identified in six epidemiologically unlinked IDUs in Kuala Lumpur, Malaysia. The near-full length genomes were composed of CRF01_AE and subtype B', with eight breakpoints dispersed in the gag-pol and nef regions. Remarkably, this CRF shared four and two recombination hotspots with the previously described CRF33_01B and the less prevalent CRF53_01B, respectively. Genealogy-based Bayesian phylogenetic analysis of CRF74_01B genomic regions showed that it is closely related to both CRF33_01B and CRF53_01B. This observation suggests that CRF74_01B was probably a direct descendent from specific lineages of CRF33_01B, CRF53_01B and subtype B' that could have emerged in the mid-1990s. Additionally, it illustrated the active recombination processes between prevalent HIV-1 subtypes and recombinants in Malaysia. In summary, we report a novel HIV-1 genotype designated CRF74_01B among IDUs in Kuala Lumpur, Malaysia. The characterization of the novel CRF74_01B is of considerable significance towards the understanding of the genetic diversity and population dynamics of HIV-1 circulating in the region.

  5. Genetic Characterization of a Novel HIV-1 Circulating Recombinant Form (CRF74_01B Identified among Intravenous Drug Users in Malaysia: Recombination History and Phylogenetic Linkage with Previously Defined Recombinant Lineages.

    Directory of Open Access Journals (Sweden)

    Hui Ting Cheong

    Full Text Available In many parts of Southeast Asia, the HIV-1 epidemic has been driven by the sharing of needles and equipment among intravenous drug users (IDUs. Over the last few decades, many studies have proven time and again that the diversity of HIV-1 epidemics can often be linked to the route of infection transmission. That said, the diversity and complexity of HIV-1 molecular epidemics in the region have been increasing at an alarming rate, due in part to the high tendency of the viral RNA to recombine. This scenario was exemplified by the discovery of numerous circulating recombinant forms (CRFs, especially in Thailand and Malaysia. In this study, we characterized a novel CRF designated CRF74_01B, which was identified in six epidemiologically unlinked IDUs in Kuala Lumpur, Malaysia. The near-full length genomes were composed of CRF01_AE and subtype B', with eight breakpoints dispersed in the gag-pol and nef regions. Remarkably, this CRF shared four and two recombination hotspots with the previously described CRF33_01B and the less prevalent CRF53_01B, respectively. Genealogy-based Bayesian phylogenetic analysis of CRF74_01B genomic regions showed that it is closely related to both CRF33_01B and CRF53_01B. This observation suggests that CRF74_01B was probably a direct descendent from specific lineages of CRF33_01B, CRF53_01B and subtype B' that could have emerged in the mid-1990s. Additionally, it illustrated the active recombination processes between prevalent HIV-1 subtypes and recombinants in Malaysia. In summary, we report a novel HIV-1 genotype designated CRF74_01B among IDUs in Kuala Lumpur, Malaysia. The characterization of the novel CRF74_01B is of considerable significance towards the understanding of the genetic diversity and population dynamics of HIV-1 circulating in the region.

  6. Dominant mutations in S. cerevisiae PMS1 identify the Mlh1-Pms1 endonuclease active site and an exonuclease 1-independent mismatch repair pathway.

    Directory of Open Access Journals (Sweden)

    Catherine E Smith

    2013-10-01

    Full Text Available Lynch syndrome (hereditary nonpolypsis colorectal cancer or HNPCC is a common cancer predisposition syndrome. Predisposition to cancer in this syndrome results from increased accumulation of mutations due to defective mismatch repair (MMR caused by a mutation in one of the mismatch repair genes MLH1, MSH2, MSH6 or PMS2/scPMS1. To better understand the function of Mlh1-Pms1 in MMR, we used Saccharomyces cerevisiae to identify six pms1 mutations (pms1-G683E, pms1-C817R, pms1-C848S, pms1-H850R, pms1-H703A and pms1-E707A that were weakly dominant in wild-type cells, which surprisingly caused a strong MMR defect when present on low copy plasmids in an exo1Δ mutant. Molecular modeling showed these mutations caused amino acid substitutions in the metal coordination pocket of the Pms1 endonuclease active site and biochemical studies showed that they inactivated the endonuclease activity. This model of Mlh1-Pms1 suggested that the Mlh1-FERC motif contributes to the endonuclease active site. Consistent with this, the mlh1-E767stp mutation caused both MMR and endonuclease defects similar to those caused by the dominant pms1 mutations whereas mutations affecting the predicted metal coordinating residue Mlh1-C769 had no effect. These studies establish that the Mlh1-Pms1 endonuclease is required for MMR in a previously uncharacterized Exo1-independent MMR pathway.

  7. Dominant mutations in S. cerevisiae PMS1 identify the Mlh1-Pms1 endonuclease active site and an exonuclease 1-independent mismatch repair pathway.

    Science.gov (United States)

    Smith, Catherine E; Mendillo, Marc L; Bowen, Nikki; Hombauer, Hans; Campbell, Christopher S; Desai, Arshad; Putnam, Christopher D; Kolodner, Richard D

    2013-10-01

    Lynch syndrome (hereditary nonpolypsis colorectal cancer or HNPCC) is a common cancer predisposition syndrome. Predisposition to cancer in this syndrome results from increased accumulation of mutations due to defective mismatch repair (MMR) caused by a mutation in one of the mismatch repair genes MLH1, MSH2, MSH6 or PMS2/scPMS1. To better understand the function of Mlh1-Pms1 in MMR, we used Saccharomyces cerevisiae to identify six pms1 mutations (pms1-G683E, pms1-C817R, pms1-C848S, pms1-H850R, pms1-H703A and pms1-E707A) that were weakly dominant in wild-type cells, which surprisingly caused a strong MMR defect when present on low copy plasmids in an exo1Δ mutant. Molecular modeling showed these mutations caused amino acid substitutions in the metal coordination pocket of the Pms1 endonuclease active site and biochemical studies showed that they inactivated the endonuclease activity. This model of Mlh1-Pms1 suggested that the Mlh1-FERC motif contributes to the endonuclease active site. Consistent with this, the mlh1-E767stp mutation caused both MMR and endonuclease defects similar to those caused by the dominant pms1 mutations whereas mutations affecting the predicted metal coordinating residue Mlh1-C769 had no effect. These studies establish that the Mlh1-Pms1 endonuclease is required for MMR in a previously uncharacterized Exo1-independent MMR pathway.

  8. SVM-based prediction of propeptide cleavage sites in spider toxins identifies toxin innovation in an Australian tarantula.

    Directory of Open Access Journals (Sweden)

    Emily S W Wong

    Full Text Available Spider neurotoxins are commonly used as pharmacological tools and are a popular source of novel compounds with therapeutic and agrochemical potential. Since venom peptides are inherently toxic, the host spider must employ strategies to avoid adverse effects prior to venom use. It is partly for this reason that most spider toxins encode a protective proregion that upon enzymatic cleavage is excised from the mature peptide. In order to identify the mature toxin sequence directly from toxin transcripts, without resorting to protein sequencing, the propeptide cleavage site in the toxin precursor must be predicted bioinformatically. We evaluated different machine learning strategies (support vector machines, hidden Markov model and decision tree and developed an algorithm (SpiderP for prediction of propeptide cleavage sites in spider toxins. Our strategy uses a support vector machine (SVM framework that combines both local and global sequence information. Our method is superior or comparable to current tools for prediction of propeptide sequences in spider toxins. Evaluation of the SVM method on an independent test set of known toxin sequences yielded 96% sensitivity and 100% specificity. Furthermore, we sequenced five novel peptides (not used to train the final predictor from the venom of the Australian tarantula Selenotypus plumipes to test the accuracy of the predictor and found 80% sensitivity and 99.6% 8-mer specificity. Finally, we used the predictor together with homology information to predict and characterize seven groups of novel toxins from the deeply sequenced venom gland transcriptome of S. plumipes, which revealed structural complexity and innovations in the evolution of the toxins. The precursor prediction tool (SpiderP is freely available on ArachnoServer (http://www.arachnoserver.org/spiderP.html, a web portal to a comprehensive relational database of spider toxins. All training data, test data, and scripts used are available from

  9. Identifying and Further Understanding the Role of Bacteria and Archaea in a Basic Mine Drainage Remediation Site in Tanoma, PA

    Science.gov (United States)

    Sharp, G.; Mount, G.

    2017-12-01

    Acid mine drainage pollutes over 3000 miles of streams and ground water in Pennsylvania alone, and in response many solutions have been developed to counteract the effects of acidic mine drainage. It is estimated by USGS that restoring these watersheds would cost 5 billion-15 billion in total. As economic conditions place limits on expenditures, cost effective means of remediation will be of critical importance. One such method is passive bioremediation, and in the case of metal contamination, self-sustaining oxygenation. Our location of interest is the Tanoma Acid Mine Drainage engineered wetland near Tanoma, Pennsylvania. It is estimated that up to 5,000 gallons per minute is currently being discharged into the site. While most local remediation sites are acidic (pH bioremediation in more neutral pH setting (pH of 5.5-7.5). In this study, we look to further understand biologic, chemical, and hydrologic controls that contribute to the efficiency of the wetland. Our research will focus on the spatial and temporal distribution of biomass through the wetland system as well as changes in water and soil chemistry. Local biofilm (Leptothrix discophora ) are an important part of the remediation process, using iron from the water as an energy source. The bacteria reduce the iron content of the water, precipitating it onto the pond bed as Terraced Iron Formations (TIF). Terraces iron formations (TIF's) are correlated with localized biofilm-archaea densities where archaea thrive in iron rich sediments. By determining bacteria densities in the wetland through gram stain analysis, we can further understand their role in terraced iron formation creation, find localized TIF's that occur, and correlate methane production due to archaea in that location. Mapping TIF locations and identifying bacteria densities will help determine the bioremediation effects on the overall efficiency of iron reduction throughout the Tanoma AMD passive remediation system.

  10. Multi-species comparative analysis of the equine ACE gene identifies a highly conserved potential transcription factor binding site in intron 16.

    Science.gov (United States)

    Hamilton, Natasha A; Tammen, Imke; Raadsma, Herman W

    2013-01-01

    Angiotensin converting enzyme (ACE) is essential for control of blood pressure. The human ACE gene contains an intronic Alu indel (I/D) polymorphism that has been associated with variation in serum enzyme levels, although the functional mechanism has not been identified. The polymorphism has also been associated with cardiovascular disease, type II diabetes, renal disease and elite athleticism. We have characterized the ACE gene in horses of breeds selected for differing physical abilities. The equine gene has a similar structure to that of all known mammalian ACE genes. Nine common single nucleotide polymorphisms (SNPs) discovered in pooled DNA were found to be inherited in nine haplotypes. Three of these SNPs were located in intron 16, homologous to that containing the Alu polymorphism in the human. A highly conserved 18 bp sequence, also within that intron, was identified as being a potential binding site for the transcription factors Oct-1, HFH-1 and HNF-3β, and lies within a larger area of higher than normal homology. This putative regulatory element may contribute to regulation of the documented inter-individual variation in human circulating enzyme levels, for which a functional mechanism is yet to be defined. Two equine SNPs occurred within the conserved area in intron 16, although neither of them disrupted the putative binding site. We propose a possible regulatory mechanism of the ACE gene in mammalian species which was previously unknown. This advance will allow further analysis leading to a better understanding of the mechanisms underpinning the associations seen between the human Alu polymorphism and enzyme levels, cardiovascular disease states and elite athleticism.

  11. Multi-species comparative analysis of the equine ACE gene identifies a highly conserved potential transcription factor binding site in intron 16.

    Directory of Open Access Journals (Sweden)

    Natasha A Hamilton

    Full Text Available Angiotensin converting enzyme (ACE is essential for control of blood pressure. The human ACE gene contains an intronic Alu indel (I/D polymorphism that has been associated with variation in serum enzyme levels, although the functional mechanism has not been identified. The polymorphism has also been associated with cardiovascular disease, type II diabetes, renal disease and elite athleticism. We have characterized the ACE gene in horses of breeds selected for differing physical abilities. The equine gene has a similar structure to that of all known mammalian ACE genes. Nine common single nucleotide polymorphisms (SNPs discovered in pooled DNA were found to be inherited in nine haplotypes. Three of these SNPs were located in intron 16, homologous to that containing the Alu polymorphism in the human. A highly conserved 18 bp sequence, also within that intron, was identified as being a potential binding site for the transcription factors Oct-1, HFH-1 and HNF-3β, and lies within a larger area of higher than normal homology. This putative regulatory element may contribute to regulation of the documented inter-individual variation in human circulating enzyme levels, for which a functional mechanism is yet to be defined. Two equine SNPs occurred within the conserved area in intron 16, although neither of them disrupted the putative binding site. We propose a possible regulatory mechanism of the ACE gene in mammalian species which was previously unknown. This advance will allow further analysis leading to a better understanding of the mechanisms underpinning the associations seen between the human Alu polymorphism and enzyme levels, cardiovascular disease states and elite athleticism.

  12. A 1.4-Billion Pixel Map of the Seafloor: BOEM's Mission to Visualize Dynamic Geology and Identify Natural Seep Sites in the Gulf of Mexico

    Science.gov (United States)

    Kramer, K.; Shedd, W. W.

    2017-12-01

    In May, 2017, the U.S. Department of the Interior's Bureau of Ocean Energy Management (BOEM) published a high-resolution seafloor map of the northern Gulf of Mexico region. The new map, derived from 3-D seismic surveys, provides the scientific community with enhanced resolution and reveals previously undiscovered and poorly resolved geologic features of the continental slope, salt minibasin province, abyssal plain, Mississippi Fan, and the Florida Shelf and Escarpment. It becomes an even more powerful scientific tool when paired with BOEM's public database of 35,000 seafloor features, identifying natural hydrocarbon seeps, hard grounds, mud volcanoes, sediment flows, pockmarks, slumps, and many others. BOEM has mapped the Gulf of Mexico seafloor since 1998 in a regulatory mission to identify natural oil and gas seeps and protect the coral and chemosynthetic communities growing at those sites. The nineteen-year mapping effort, still ongoing, resulted in the creation of the 1.4-billion pixel map and the seafloor features database. With these tools and continual collaboration with academia, professional scientific institutions, and the offshore energy industry, BOEM will continue to incorporate new data to update and expand these two resources on a regular basis. They can be downloaded for free from BOEM's website at https://www.boem.gov/Gulf-of-Mexico-Deepwater-Bathymetry/ and https://www.boem.gov/Seismic-Water-Bottom-Anomalies-Map-Gallery/.

  13. Isthmus sites identified by Ripple Mapping are usually anatomically stable: A novel method to guide atrial substrate ablation?

    Science.gov (United States)

    Luther, Vishal; Qureshi, Norman; Lim, Phang Boon; Koa-Wing, Michael; Jamil-Copley, Shahnaz; Ng, Fu Siong; Whinnett, Zachary; Davies, D Wyn; Peters, Nicholas S; Kanagaratnam, Prapa; Linton, Nick

    2018-03-01

    Postablation reentrant ATs depend upon conducting isthmuses bordered by scar. Bipolar voltage maps highlight scar as sites of low voltage, but the voltage amplitude of an electrogram depends upon the myocardial activation sequence. Furthermore, a voltage threshold that defines atrial scar is unknown. We used Ripple Mapping (RM) to test whether these isthmuses were anatomically fixed between different activation vectors and atrial rates. We studied post-AF ablation ATs where >1 rhythm was mapped. Multipolar catheters were used with CARTO Confidense for high-density mapping. RM visualized the pattern of activation, and the voltage threshold below which no activation was seen. Isthmuses were characterized at this threshold between maps for each patient. Ten patients were studied (Map 1 was AT1; Map 2: sinus 1/10, LA paced 2/10, AT2 with reverse CS activation 3/10; AT2 CL difference 50 ± 30 ms). Point density was similar between maps (Map 1: 2,589 ± 1,330; Map 2: 2,214 ± 1,384; P  =  0.31). RM activation threshold was 0.16 ± 0.08 mV. Thirty-one isthmuses were identified in Map 1 (median 3 per map; width 27 ± 15 mm; 7 anterior; 6 roof; 8 mitral; 9 septal; 1 posterior). Importantly, 7 of 31 (23%) isthmuses were unexpectedly identified within regions without prior ablation. AT1 was treated following ablation of 11/31 (35%) isthmuses. Of the remaining 20 isthmuses, 14 of 16 isthmuses (88%) were consistent between the two maps (four were inadequately mapped). Wavefront collision caused variation in low voltage distribution in 2 of 16 (12%). The distribution of isthmuses and nonconducting tissue within the ablated left atrium, as defined by RM, appear concordant between rhythms. This could guide a substrate ablative approach. © 2018 Wiley Periodicals, Inc.

  14. Novel colchicine-site binders with a cyclohexanedione scaffold identified through a ligand-based virtual screening approach.

    Science.gov (United States)

    Canela, María-Dolores; Pérez-Pérez, María-Jesús; Noppen, Sam; Sáez-Calvo, Gonzalo; Díaz, J Fernando; Camarasa, María-José; Liekens, Sandra; Priego, Eva-María

    2014-05-22

    Vascular disrupting agents (VDAs) constitute an innovative anticancer therapy that targets the tumor endothelium, leading to tumor necrosis. Our approach for the identification of new VDAs has relied on a ligand 3-D shape similarity virtual screening (VS) approach using the ROCS program as the VS tool and as query colchicine and TN-16, which both bind the α,β-tubulin dimer. One of the hits identified, using TN-16 as query, has been explored by the synthesis of its structural analogues, leading to 2-(1-((2-methoxyphenyl)amino)ethylidene)-5-phenylcyclohexane-1,3-dione (compound 16c) with an IC50 = 0.09 ± 0.01 μM in HMEC-1 and BAEC, being 100-fold more potent than the initial hit. Compound 16c caused cell cycle arrest in the G2/M phase and interacted with the colchicine-binding site in tubulin, as confirmed by a competition assay with N,N'-ethylenebis(iodoacetamide) and by fluorescence spectroscopy. Moreover, 16c destroyed an established endothelial tubular network at 1 μM and inhibited the migration and invasion of human breast carcinoma cells at 0.4 μM. In conclusion, our approach has led to a new chemotype of promising antiproliferative compounds with antimitotic and potential VDA properties.

  15. Monoclonal antibody OKB7, which identifies the 14OKd complement receptor type 2 (CR/sub 2/), also identifies a 72Kd secreted fragment of CR/sub 2/ that contains the C3d-binding site

    Energy Technology Data Exchange (ETDEWEB)

    Myones, B.L.; Ross, G.D.

    1986-03-05

    CR/sub 2/ is a 140-145Kd glycoprotein expressed on B lymphocytes which binds both C3d and Epstein-Barr virus (EBV). OKB7, an IgG/sub 2a/ monoclonal antibody to CR/sub 2/, blocks C3d and EBV binding, while HB-5, another monoclonal IgG/sub 2a/ anti-CR/sub 2/, does not. A 72Kd C3d-binding glycoprotein (gp72), isolated from Raji cell media, was previously thought to be CR/sub 2/ because a polyclonal rabbit anti-gp72 inhibited EC3d rosettes. ELISA assay demonstrated that OKB7, but not HB-5, bound to purified gp72 fixed to microtiter wells. Insoluble and soluble gp72 blocked Raji cell uptake of /sup 125/I-labeled OKB7, but not labeled anti-B2 or HB-5. Rabbit anti-gp72 immunoprecipitated bands at 140Kd and 72Kd from /sup 125/I-labelled and solubilized B cell membranes. Culture media from Raji cells grown in the presence /sup 3/H-labeled amino acids was sequentially immunoprecipitated by irrelevant antibody, OKB7, and HB-5. A single 72Kd radiolabeled band was demonstrated only with OKB7, and this was identical to that produced by the immunoprecipitation of /sup 125/I-labeled gp72 with rabbit anti-gp72. Thus, OKB7, which identifies the 140Kd CR/sub 2/ molecule, also identifies a 72Kd shed fragment of CR/sub 2/ isolated from Raji cell media, which contains the C3d-binding site.

  16. Monoclonal antibody OKB7, which identifies the 14OKd complement receptor type 2 (CR2), also identifies a 72Kd secreted fragment of CR2 that contains the C3d-binding site

    International Nuclear Information System (INIS)

    Myones, B.L.; Ross, G.D.

    1986-01-01

    CR 2 is a 140-145Kd glycoprotein expressed on B lymphocytes which binds both C3d and Epstein-Barr virus (EBV). OKB7, an IgG/sub 2a/ monoclonal antibody to CR 2 , blocks C3d and EBV binding, while HB-5, another monoclonal IgG/sub 2a/ anti-CR 2 , does not. A 72Kd C3d-binding glycoprotein (gp72), isolated from Raji cell media, was previously thought to be CR 2 because a polyclonal rabbit anti-gp72 inhibited EC3d rosettes. ELISA assay demonstrated that OKB7, but not HB-5, bound to purified gp72 fixed to microtiter wells. Insoluble and soluble gp72 blocked Raji cell uptake of 125 I-labeled OKB7, but not labeled anti-B2 or HB-5. Rabbit anti-gp72 immunoprecipitated bands at 140Kd and 72Kd from 125 I-labelled and solubilized B cell membranes. Culture media from Raji cells grown in the presence 3 H-labeled amino acids was sequentially immunoprecipitated by irrelevant antibody, OKB7, and HB-5. A single 72Kd radiolabeled band was demonstrated only with OKB7, and this was identical to that produced by the immunoprecipitation of 125 I-labeled gp72 with rabbit anti-gp72. Thus, OKB7, which identifies the 140Kd CR 2 molecule, also identifies a 72Kd shed fragment of CR 2 isolated from Raji cell media, which contains the C3d-binding site

  17. Laparoscopy After Previous Laparotomy

    Directory of Open Access Journals (Sweden)

    Zulfo Godinjak

    2006-11-01

    Full Text Available Following the abdominal surgery, extensive adhesions often occur and they can cause difficulties during laparoscopic operations. However, previous laparotomy is not considered to be a contraindication for laparoscopy. The aim of this study is to present that an insertion of Veres needle in the region of umbilicus is a safe method for creating a pneumoperitoneum for laparoscopic operations after previous laparotomy. In the last three years, we have performed 144 laparoscopic operations in patients that previously underwent one or two laparotomies. Pathology of digestive system, genital organs, Cesarean Section or abdominal war injuries were the most common causes of previouslaparotomy. During those operations or during entering into abdominal cavity we have not experienced any complications, while in 7 patients we performed conversion to laparotomy following the diagnostic laparoscopy. In all patients an insertion of Veres needle and trocar insertion in the umbilical region was performed, namely a technique of closed laparoscopy. Not even in one patient adhesions in the region of umbilicus were found, and no abdominal organs were injured.

  18. Simulations of hydrogen sorption in rht-MOF-1: identifying the binding sites through explicit polarization and quantum rotation calculations

    KAUST Repository

    Pham, Tony

    2014-01-01

    Grand canonical Monte Carlo (GCMC) simulations of hydrogen sorption were performed in rht-MOF-1, a metal-organic framework (MOF) that consists of isophthalate groups joined by copper paddlewheel clusters and Cu3O trimers through tetrazolate moeities. This is a charged rht-MOF that contains extra-framework nitrate counterions within the material. For the simulations performed herein, excellent agreement with experiment was achieved for the simulated hydrogen sorption isotherms and calculated isosteric heat of adsorption, Qst, values only when using a polarizable potential. Thermodynamic agreement is demonstrated via comparing to experimental isotherms and binding sites are revealed by combining simulation and inelastic neutron scattering (INS) data. Simulations involving explicit many-body polarization interactions assisted in the determination of the binding sites in rht-MOF-1 through the distribution of the induced dipoles that led to strong adsorbate interactions. Four distinct hydrogen sorption sites were determined from the polarization distribution: the nitrate ions located in the corners of the truncated tetrahedral cages, the Cu2+ ions of the paddlewheels that project into the truncated tetrahedral and truncated octahedral cages (Cu1 ions), the Cu2+ ions of the Cu3O trimers (Cu3 ions), and the sides of the paddlewheels in the cuboctahedral cage. The simulations revealed that the initial sorption sites for hydrogen in rht-MOF-1 are the nitrate ions; this site corresponds to the high initial Qst value for hydrogen (9.5 kJ mol-1) in the MOF. The radial distribution functions, g(r), about the Cu2+ ions at various loadings revealed that the Cu1 ions are the preferred open-metal sorption sites for hydrogen at low loading, while the Cu3 ions become occupied at higher loadings. The validation of the aforementioned sorption sites in rht-MOF-1 was confirmed by calculating the two-dimensional quantum rotational levels about each site and comparing the levels to the

  19. RED: A Java-MySQL Software for Identifying and Visualizing RNA Editing Sites Using Rule-Based and Statistical Filters.

    Directory of Open Access Journals (Sweden)

    Yongmei Sun

    Full Text Available RNA editing is one of the post- or co-transcriptional processes that can lead to amino acid substitutions in protein sequences, alternative pre-mRNA splicing, and changes in gene expression levels. Although several methods have been suggested to identify RNA editing sites, there remains challenges to be addressed in distinguishing true RNA editing sites from its counterparts on genome and technical artifacts. In addition, there lacks a software framework to identify and visualize potential RNA editing sites. Here, we presented a software - 'RED' (RNA Editing sites Detector - for the identification of RNA editing sites by integrating multiple rule-based and statistical filters. The potential RNA editing sites can be visualized at the genome and the site levels by graphical user interface (GUI. To improve performance, we used MySQL database management system (DBMS for high-throughput data storage and query. We demonstrated the validity and utility of RED by identifying the presence and absence of C→U RNA-editing sites experimentally validated, in comparison with REDItools, a command line tool to perform high-throughput investigation of RNA editing. In an analysis of a sample data-set with 28 experimentally validated C→U RNA editing sites, RED had sensitivity and specificity of 0.64 and 0.5. In comparison, REDItools had a better sensitivity (0.75 but similar specificity (0.5. RED is an easy-to-use, platform-independent Java-based software, and can be applied to RNA-seq data without or with DNA sequencing data. The package is freely available under the GPLv3 license at http://github.com/REDetector/RED or https://sourceforge.net/projects/redetector.

  20. RED: A Java-MySQL Software for Identifying and Visualizing RNA Editing Sites Using Rule-Based and Statistical Filters.

    Science.gov (United States)

    Sun, Yongmei; Li, Xing; Wu, Di; Pan, Qi; Ji, Yuefeng; Ren, Hong; Ding, Keyue

    2016-01-01

    RNA editing is one of the post- or co-transcriptional processes that can lead to amino acid substitutions in protein sequences, alternative pre-mRNA splicing, and changes in gene expression levels. Although several methods have been suggested to identify RNA editing sites, there remains challenges to be addressed in distinguishing true RNA editing sites from its counterparts on genome and technical artifacts. In addition, there lacks a software framework to identify and visualize potential RNA editing sites. Here, we presented a software - 'RED' (RNA Editing sites Detector) - for the identification of RNA editing sites by integrating multiple rule-based and statistical filters. The potential RNA editing sites can be visualized at the genome and the site levels by graphical user interface (GUI). To improve performance, we used MySQL database management system (DBMS) for high-throughput data storage and query. We demonstrated the validity and utility of RED by identifying the presence and absence of C→U RNA-editing sites experimentally validated, in comparison with REDItools, a command line tool to perform high-throughput investigation of RNA editing. In an analysis of a sample data-set with 28 experimentally validated C→U RNA editing sites, RED had sensitivity and specificity of 0.64 and 0.5. In comparison, REDItools had a better sensitivity (0.75) but similar specificity (0.5). RED is an easy-to-use, platform-independent Java-based software, and can be applied to RNA-seq data without or with DNA sequencing data. The package is freely available under the GPLv3 license at http://github.com/REDetector/RED or https://sourceforge.net/projects/redetector.

  1. Towards identifying the active sites on RuO2(110) in catalyzing oxygen evolution  

    DEFF Research Database (Denmark)

    Rao, Reshma R.; Kolb, Manuel J.; Halck, Niels Bendtsen

    2017-01-01

    While the surface atomic structure of RuO2 has been well studied in ultra high vacuum, much less is known about the interaction between water and RuO2 in aqueous solution. In this work, in situ surface X-ray scattering measurements combined with density functional theory (DFT) were used to determ......While the surface atomic structure of RuO2 has been well studied in ultra high vacuum, much less is known about the interaction between water and RuO2 in aqueous solution. In this work, in situ surface X-ray scattering measurements combined with density functional theory (DFT) were used...... on the coordinatively unsaturated Ru sites (CUS) and hydrogen adsorbed to the bridging oxygen sites. At potentials relevant to the oxygen evolution reaction (OER), an –OO species on the Ru CUS sites was detected, which was stabilized by a neighboring –OH group on the Ru CUS or bridge site. Combining potential...

  2. Pairwise comparisons of ten porcine tissues identify differential transcriptional regulation at the gene, isoform, promoter and transcription start site level

    DEFF Research Database (Denmark)

    Farajzadeh, Leila; Hornshøj, Henrik; Momeni, Jamal

    2013-01-01

    , isoform, and transcription start site (TSS), and promoter level showed that several of the genes differed at all four levels. Interestingly, these genes were mainly annotated to the "electron transport chain" and neuronal differentiation, emphasizing that "tissue important" genes are regulated at several...

  3. Applying the 5 WHYs to Identify Root Causes to Non-completions in On-Site Construction

    DEFF Research Database (Denmark)

    Lindhard, Søren Munch

    2014-01-01

    from mistakes. A central part of the control framework Last Planner System is to identify not completed activities to identify root causes and to learn. One tool to investigate root causes is the 5 WHYs approach. The 5 WHYs approach has been applied in a case study research to analysis the root cause...

  4. Model outputs for each hotspot site to identify the likely environmental, economic and social effects of proposed remediation strategies

    DEFF Research Database (Denmark)

    Fleskens, Luuk; Irvine, Brian; Kirkby, Mike

    2012-01-01

    Portuguese sites) a fire severity index under current conditions and under different technologies. The DESMICE model is informed by WB3 WOCAT database records, economic WB4 experimental results, additionally requested data on spatial variability of costs and benefits, and secondary data. It applies spatially...... multiple stakeholders in very different contexts into the modelling process, in order to enhance both the realism and relevance of outputs for policy and practice; b) site-selection modelling is being applied to land degradation mitigation to enable landscape-scale assessments of the most economically....... Biophysical models (e.g. PESERA) should be able to separate immediate and gradual aspects. Ongoing degradation in the without case is not yet implicitly considered. Analysis of robustness to climatic variability and prices is also essential. Finally, factors such as attitude towards conservation and risk...

  5. Pairwise comparisons of ten porcine tissues identify differential transcriptional regulation at the gene, isoform, promoter and transcription start site level

    International Nuclear Information System (INIS)

    Farajzadeh, Leila; Hornshøj, Henrik; Momeni, Jamal; Thomsen, Bo; Larsen, Knud; Hedegaard, Jakob; Bendixen, Christian; Madsen, Lone Bruhn

    2013-01-01

    Highlights: •Transcriptome sequencing yielded 223 mill porcine RNA-seq reads, and 59,000 transcribed locations. •Establishment of unique transcription profiles for ten porcine tissues including four brain tissues. •Comparison of transcription profiles at gene, isoform, promoter and transcription start site level. •Highlights a high level of regulation of neuro-related genes at both gene, isoform, and TSS level. •Our results emphasize the pig as a valuable animal model with respect to human biological issues. -- Abstract: The transcriptome is the absolute set of transcripts in a tissue or cell at the time of sampling. In this study RNA-Seq is employed to enable the differential analysis of the transcriptome profile for ten porcine tissues in order to evaluate differences between the tissues at the gene and isoform expression level, together with an analysis of variation in transcription start sites, promoter usage, and splicing. Totally, 223 million RNA fragments were sequenced leading to the identification of 59,930 transcribed gene locations and 290,936 transcript variants using Cufflinks with similarity to approximately 13,899 annotated human genes. Pairwise analysis of tissues for differential expression at the gene level showed that the smallest differences were between tissues originating from the porcine brain. Interestingly, the relative level of differential expression at the isoform level did generally not vary between tissue contrasts. Furthermore, analysis of differential promoter usage between tissues, revealed a proportionally higher variation between cerebellum (CBE) versus frontal cortex and cerebellum versus hypothalamus (HYP) than in the remaining comparisons. In addition, the comparison of differential transcription start sites showed that the number of these sites is generally increased in comparisons including hypothalamus in contrast to other pairwise assessments. A comprehensive analysis of one of the tissue contrasts, i

  6. Post-genome wide association studies and functional analyses identify association of MPP7 gene variants with site-specific bone mineral density.

    Science.gov (United States)

    Xiao, Su-Mei; Kung, Annie Wai Chee; Gao, Yi; Lau, Kam-Shing; Ma, Alvin; Zhang, Zhen-Lin; Liu, Jian-Min; Xia, Wiebo; He, Jin-Wei; Zhao, Lin; Nie, Min; Fu, Wei-Zhen; Zhang, Min-Jia; Sun, Jing; Kwan, Johnny S H; Tso, Gloria Hoi Wan; Dai, Zhi-Jie; Cheung, Ching-Lung; Bow, Cora H; Leung, Anskar Yu Hung; Tan, Kathryn Choon Beng; Sham, Pak Chung

    2012-04-01

    Our previous genome-wide association study (GWAS) in a Hong Kong Southern Chinese population with extreme bone mineral density (BMD) scores revealed suggestive association with MPP7, which ranked second after JAG1 as a candidate gene for BMD. To follow-up this suggestive signal, we replicated the top single-nucleotide polymorphism rs4317882 of MPP7 in three additional independent Asian-descent samples (n= 2684). The association of rs4317882 reached the genome-wide significance in the meta-analysis of all available subjects (P(meta)= 4.58 × 10(-8), n= 4204). Site heterogeneity was observed, with a larger effect on spine than hip BMD. Further functional studies in a zebrafish model revealed that vertebral bone mass was lower in an mpp7 knock-down model compared with the wide-type (P= 9.64 × 10(-4), n= 21). In addition, MPP7 was found to have constitutive expression in human bone-derived cells during osteogenesis. Immunostaining of murine MC3T3-E1 cells revealed that the Mpp7 protein is localized in the plasma membrane and intracytoplasmic compartment of osteoblasts. In an assessment of the function of identified variants, an electrophoretic mobility shift assay demonstrated the binding of transcriptional factor GATA2 to the risk allele 'A' but not the 'G' allele of rs4317882. An mRNA expression study in human peripheral blood mononuclear cells confirmed that the low BMD-related allele 'A' of rs4317882 was associated with lower MPP7 expression (P= 9.07 × 10(-3), n= 135). Our data suggest a genetic and functional association of MPP7 with BMD variation.

  7. Newly identified essential amino acid residues affecting ^8-sphingolipid desaturase activity revealed by site-directed mutagenesis

    Science.gov (United States)

    In order to identify amino acid residues crucial for the enzymatic activity of ^8-sphingolipid desaturases, a sequence comparison was performed among ^8-sphingolipid desaturases and ^6-fatty acid desaturase from various plants. In addition to the known conserved cytb5 (cytochrome b5) HPGG motif and...

  8. Partial digestion with restriction enzymes of ultraviolet-irradiated human genomic DNA: a method for identifying restriction site polymorphisms

    International Nuclear Information System (INIS)

    Nobile, C.; Romeo, G.

    1988-01-01

    A method for partial digestion of total human DNA with restriction enzymes has been developed on the basis of a principle already utilized by P.A. Whittaker and E. Southern for the analysis of phage lambda recombinants. Total human DNA irradiated with uv light of 254 nm is partially digested by restriction enzymes that recognize sequences containing adjacent thymidines because of TT dimer formation. The products resulting from partial digestion of specific genomic regions are detected in Southern blots by genomic-unique DNA probes with high reproducibility. This procedure is rapid and simple to perform because the same conditions of uv irradiation are used for different enzymes and probes. It is shown that restriction site polymorphisms occurring in the genomic regions analyzed are recognized by the allelic partial digest patterns they determine

  9. Diet of pumas (Puma concolor) in Sonora, Mexico, as determined by GPS kill sites and molecular identified scat, with comments on jaguar (Panthera onca) diet

    Science.gov (United States)

    Cassaigne, Ivonne; Medellin, Rodrigo A.; Thompson, Ron W.; Culver, Melanie; Ochoa, Alexander; Vargas, Karla; Childs, Jack L.; Sanderson, Jim; List, Rurik; Torres-Gomez, Armando

    2016-01-01

    We documented puma (Puma concolor) and jaguar (Panthera onca) prey consumption in northeastern Sonora, Mexico, by investigating global positioning system cluster sites (n = 220), and conducting molecular analyses of scat (n = 116) collected between 2011 and 2013. We used camera trap data (n = 8,976 camera days) to estimate relative abundances of pumas and jaguars. Deer (Odocoileus virginianus) was the most frequent prey for puma found at kill sites (67%) and identified from scat (74%), although based on relative numbers of prey consumed, deer represented 45% and lagomorphs 20% of the proportion of all individuals eaten. A variety of small prey (weighing Sonora.

  10. A strategy for interaction site prediction between phospho-binding modules and their partners identified from proteomic data.

    Science.gov (United States)

    Aucher, Willy; Becker, Emmanuelle; Ma, Emilie; Miron, Simona; Martel, Arnaud; Ochsenbein, Françoise; Marsolier-Kergoat, Marie-Claude; Guerois, Raphaël

    2010-12-01

    Small and large scale proteomic technologies are providing a wealth of potential interactions between proteins bearing phospho-recognition modules and their substrates. Resulting interaction maps reveal such a dense network of interactions that the functional dissection and understanding of these networks often require to break specific interactions while keeping the rest intact. Here, we developed a computational strategy, called STRIP, to predict the precise interaction site involved in an interaction with a phospho-recognition module. The method was validated by a two-hybrid screen carried out using the ForkHead Associated (FHA)1 domain of Rad53, a key protein of Saccharomyces cerevisiae DNA checkpoint, as a bait. In this screen we detected 11 partners, including Cdc7 and Cdc45, essential components of the DNA replication machinery. FHA domains are phospho-threonine binding modules and the threonines involved in both interactions could be predicted using the STRIP strategy. The threonines T484 and T189 in Cdc7 and Cdc45, respectively, were mutated and loss of binding could be monitored experimentally with the full-length proteins. The method was further tested for the analysis of 63 known Rad53 binding partners and provided several key insights regarding the threonines likely involved in these interactions. The STRIP method relies on a combination of conservation, phosphorylation likelihood, and binding specificity criteria and can be accessed via a web interface at http://biodev.extra.cea.fr/strip/.

  11. A Strategy for Interaction Site Prediction between Phospho-binding Modules and their Partners Identified from Proteomic Data*

    Science.gov (United States)

    Aucher, Willy; Becker, Emmanuelle; Ma, Emilie; Miron, Simona; Martel, Arnaud; Ochsenbein, Françoise; Marsolier-Kergoat, Marie-Claude; Guerois, Raphaël

    2010-01-01

    Small and large scale proteomic technologies are providing a wealth of potential interactions between proteins bearing phospho-recognition modules and their substrates. Resulting interaction maps reveal such a dense network of interactions that the functional dissection and understanding of these networks often require to break specific interactions while keeping the rest intact. Here, we developed a computational strategy, called STRIP, to predict the precise interaction site involved in an interaction with a phospho-recognition module. The method was validated by a two-hybrid screen carried out using the ForkHead Associated (FHA)1 domain of Rad53, a key protein of Saccharomyces cerevisiae DNA checkpoint, as a bait. In this screen we detected 11 partners, including Cdc7 and Cdc45, essential components of the DNA replication machinery. FHA domains are phospho-threonine binding modules and the threonines involved in both interactions could be predicted using the STRIP strategy. The threonines T484 and T189 in Cdc7 and Cdc45, respectively, were mutated and loss of binding could be monitored experimentally with the full-length proteins. The method was further tested for the analysis of 63 known Rad53 binding partners and provided several key insights regarding the threonines likely involved in these interactions. The STRIP method relies on a combination of conservation, phosphorylation likelihood, and binding specificity criteria and can be accessed via a web interface at http://biodev.extra.cea.fr/strip/. PMID:20733106

  12. Surgical site infection prevention: a survey to identify the gap between evidence and practice in University of Toronto teaching hospitals.

    Science.gov (United States)

    Eskicioglu, Cagla; Gagliardi, Anna R; Fenech, Darlene S; Forbes, Shawn S; McKenzie, Marg; McLeod, Robin S; Nathens, Avery B

    2012-08-01

    A gap exists between the best evidence and practice with regards to surgical site infection (SSI) prevention. Awareness of evidence is the first step in knowledge translation. A web-based survey was distributed to 59 general surgeons and 68 residents at University of Toronto teaching hospitals. Five domains pertaining to SSI prevention with questions addressing knowledge of prevention strategies, efficacy of antibiotics, strategies for changing practice and barriers to implementation of SSI prevention strategies were investigated. Seventy-six individuals (60%) responded. More than 90% of respondents stated there was evidence for antibiotic prophylaxis and perioperative normothermia and reported use of these strategies. There was a discrepancy in the perceived evidence for and the self-reported use of perioperative hyperoxia, omission of hair removal and bowel preparation. Eighty-three percent of respondents felt that consulting published guidelines is important in making decisions regarding antibiotics. There was also a discrepancy between what respondents felt were important strategies to ensure timely administration of antibiotics and what strategies were in place. Checklists, standardized orders, protocols and formal surveillance programs were rated most highly by 75%-90% of respondents, but less than 50% stated that these strategies were in place at their institutions. Broad-reaching initiatives that increase surgeon and trainee awareness and implementation of multifaceted hospital strategies that engage residents and attending surgeons are needed to change practice.

  13. Application of multiple tracers (SF6 and chloride) to identify the transport by characteristics of contaminant at two separate contaminated sites

    Science.gov (United States)

    Lee, K. K.; Lee, S. S.; Kim, H. H.; Koh, E. H.; Kim, M. O.; Lee, K.; Kim, H. J.

    2016-12-01

    Multiple tracers were applied for source and pathway detection at two different sites. CO2 gas injected in the subsurface for a shallow-depth CO2 injection and leak test can be regarded as a potential contaminant source. Therefore, it is necessary to identify the migration pattern of CO2 gas. Also, at a DNAPL contaminated site, it is important to figure out the characteristics of plume evolution from the source zone. In this study, multiple tracers (SF6 and chloride) were used to evaluate the applicability of volatile and non-volatile tracers and to identify the characteristics of contaminant transport at each CO2 injection and leak test site and DNAPL contaminated site. Firstly, at the CO2 test site, multiple tracers were used to perform the single well push-drift-pull tracer test at total 3 specific depth zones. As results of tests, volatile and non-volatile tracers showed different mass recovery percentage. Most of chloride mass was recovered but less than half of SF6 mass was recovered due to volatile property. This means that only gaseous SF6 leak out to unsaturated zone. However, breakthrough curves of both tracers indicated similar peak time, effective porosity, and regional groundwater velocity. Also, at both contaminated sites, natural gradient tracer tests were performed with multiple tracers. With the results of natural gradient tracer test, it was possible to confirm the applicability of multiple tracers and to understand the contaminant transport in highly heterogeneous aquifer systems through the long-term monitoring of tracers. Acknowledgement: financial support was provided by the R&D Project on Environmental Management of Geologic CO2 Storage)" from the KEITI (Project Number: 2014001810003) and Korea Ministry of Environment as "The GAIA project (2014000540010)".

  14. SCS-CN and GIS-based approach for identifying potential water harvesting sites in the Kali Watershed, Mahi River Basin, India

    Science.gov (United States)

    Ramakrishnan, D.; Bandyopadhyay, A.; Kusuma, K. N.

    2009-08-01

    The Kali sub-watershed is situated in the semi-arid region of Gujarat, India and forms a part of the Mahi River Watershed. This watershed receives an average annual rainfall of 900mm mainly between July and September. Due to high runoff potential, evapo-transpiration and poor infiltration, drought like situation prevails in this area from December to June almost every year. In this paper, augmentation of water resource is proposed by construction of runoff harvesting structures like check dam, percolation pond, farm pond, well and subsurface dyke. The site suitability for different water harvesting structures is determined by considering spatially varying parameters like runoff potential, slope, fracture pattern and micro-watershed area. GIS is utilised as a tool to store, analyse and integrate spatial and attribute information pertaining to runoff, slope, drainage and fracture. The runoff derived by SCS-CN method is a function of runoff potential which can be expressed in terms of runoff coefficient (ratio between the runoff and rainfall) which can be classified into three classes, viz., high (>40%), moderate (20-40%) and low (<20%). In addition to IMSD, FAO specifications for water harvesting/recharging structures, parameters such as effective storage, rock mass permeability are herein considered to augment effective storage. Using the overlay and decision tree concepts in GIS, potential water harvesting sites are identified. The derived sites are field investigated for suitability and implementation. In all, the accuracy of the site selection at implementation level varies from 80-100%.

  15. A triad of lys12, lys41, arg78 spatial domain, a novel identified heparin binding site on tat protein, facilitates tat-driven cell adhesion.

    Directory of Open Access Journals (Sweden)

    Jing Ai

    Full Text Available Tat protein, released by HIV-infected cells, has a battery of important biological effects leading to distinct AIDS-associated pathologies. Cell surface heparan sulfate protoglycans (HSPGs have been accepted as endogenous Tat receptors, and the Tat basic domain has been identified as the heparin binding site. However, findings that deletion or substitution of the basic domain inhibits but does not completely eliminate Tat-heparin interactions suggest that the basic domain is not the sole Tat heparin binding site. In the current study, an approach integrating computational modeling, mutagenesis, biophysical and cell-based assays was used to elucidate a novel, high affinity heparin-binding site: a Lys12, Lys41, Arg78 (KKR spatial domain. This domain was also found to facilitate Tat-driven β1 integrin activation, producing subsequent SLK cell adhesion in an HSPG-dependent manner, but was not involved in Tat internalization. The identification of this new heparin binding site may foster further insight into the nature of Tat-heparin interactions and subsequent biological functions, facilitating the rational design of new therapeutics against Tat-mediated pathological events.

  16. Computational Characterization of Small Molecules Binding to the Human XPF Active Site and Virtual Screening to Identify Potential New DNA Repair Inhibitors Targeting the ERCC1-XPF Endonuclease

    Directory of Open Access Journals (Sweden)

    Francesco Gentile

    2018-04-01

    Full Text Available The DNA excision repair protein ERCC-1-DNA repair endonuclease XPF (ERCC1-XPF is a heterodimeric endonuclease essential for the nucleotide excision repair (NER DNA repair pathway. Although its activity is required to maintain genome integrity in healthy cells, ERCC1-XPF can counteract the effect of DNA-damaging therapies such as platinum-based chemotherapy in cancer cells. Therefore, a promising approach to enhance the effect of these therapies is to combine their use with small molecules, which can inhibit the repair mechanisms in cancer cells. Currently, there are no structures available for the catalytic site of the human ERCC1-XPF, which performs the metal-mediated cleavage of a DNA damaged strand at 5′. We adopted a homology modeling strategy to build a structural model of the human XPF nuclease domain which contained the active site and to extract dominant conformations of the domain using molecular dynamics simulations followed by clustering of the trajectory. We investigated the binding modes of known small molecule inhibitors targeting the active site to build a pharmacophore model. We then performed a virtual screening of the ZINC Is Not Commercial 15 (ZINC15 database to identify new ERCC1-XPF endonuclease inhibitors. Our work provides structural insights regarding the binding mode of small molecules targeting the ERCC1-XPF active site that can be used to rationally optimize such compounds. We also propose a set of new potential DNA repair inhibitors to be considered for combination cancer therapy strategies.

  17. Initial direct comparison of 99mTc-TOC and 99mTc-TATE in identifying sites of disease in patients with proven GEP NETs.

    Science.gov (United States)

    Cwikla, Jaroslaw B; Mikolajczak, Renata; Pawlak, Dariusz; Buscombe, John R; Nasierowska-Guttmejer, Anna; Bator, Andrzej; Maecke, Helmut R; Walecki, Jerzy

    2008-07-01

    The imaging of neuroendocrine tumors has become one of the most significant areas in nuclear oncology. In an attempt to provide high-quality imaging and possible sensitivity at a reduced cost, time, and radiation dose, several (99m)Tc agents have been proposed. The aim of this initial study was to compare the tumor uptake and biodistribution of 2 new 6-hydrazinopyridine-3-carboxylic acid (HYNIC)-derivatized Tyr(3)-octreotide analogs, (99m)Tc-[HYNIC,Tyr(3)]octreotide ((99m)Tc-TOC) and (99m)Tc-[HYNIC,Tyr(3),Thr(8)]octreotide ((99m)Tc-TATE), in patients with somatostatin receptor-expressing tumors. Each of 12 patients with proven gastrointestinal pancreatic neuroendocrine tumors received a mean activity of 520 MBq of (99m)Tc-TOC and (99m)Tc-TATE. Scintigraphy with both tracers was performed 3-4 h after their injection using standard whole-body and SPECT imaging. The images were reviewed subjectively by 2 readers, who reported tumor uptake lesion by lesion. Both radiotracers demonstrated concordance between the results in 7 patients (58%). In total, 110 sites of disease were identified with (99m)Tc-TOC, compared with 115 with (99m)Tc-TATE. There was 1 case in which (99m)Tc-TOC identified sites of disease not seen on (99m)Tc-TATE imaging but 4 cases in which some sites of disease were seen with (99m)Tc-TATE and not (99m)Tc-TOC. In this initial study, both tracers seem to show similar sites of tumor, with (99m)Tc-TATE having a slight edge in the total number of lesions seen, especially in lymph node metastases.

  18. Rhodium(II) Proximity-Labeling Identifies a Novel Target Site on STAT3 for Inhibitors with Potent Anti-Leukemia Activity.

    Science.gov (United States)

    Minus, Matthew B; Liu, Wei; Vohidov, Farrukh; Kasembeli, Moses M; Long, Xin; Krueger, Michael J; Stevens, Alexandra; Kolosov, Mikhail I; Tweardy, David J; Sison, Edward Allan R; Redell, Michele S; Ball, Zachary T

    2015-10-26

    Nearly 40 % of children with acute myeloid leukemia (AML) suffer relapse arising from chemoresistance, often involving upregulation of the oncoprotein STAT3 (signal transducer and activator of transcription 3). Herein, rhodium(II)-catalyzed, proximity-driven modification identifies the STAT3 coiled-coil domain (CCD) as a novel ligand-binding site, and we describe a new naphthalene sulfonamide inhibitor that targets the CCD, blocks STAT3 function, and halts its disease-promoting effects in vitro, in tumor growth models, and in a leukemia mouse model, validating this new therapeutic target for resistant AML. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Use of Anisotropy, 3D Segmented Atlas, and Computational Analysis to Identify Gray Matter Subcortical Lesions Common to Concussive Injury from Different Sites on the Cortex.

    Directory of Open Access Journals (Sweden)

    Praveen Kulkarni

    Full Text Available Traumatic brain injury (TBI can occur anywhere along the cortical mantel. While the cortical contusions may be random and disparate in their locations, the clinical outcomes are often similar and difficult to explain. Thus a question that arises is, do concussions at different sites on the cortex affect similar subcortical brain regions? To address this question we used a fluid percussion model to concuss the right caudal or rostral cortices in rats. Five days later, diffusion tensor MRI data were acquired for indices of anisotropy (IA for use in a novel method of analysis to detect changes in gray matter microarchitecture. IA values from over 20,000 voxels were registered into a 3D segmented, annotated rat atlas covering 150 brain areas. Comparisons between left and right hemispheres revealed a small population of subcortical sites with altered IA values. Rostral and caudal concussions were of striking similarity in the impacted subcortical locations, particularly the central nucleus of the amygdala, laterodorsal thalamus, and hippocampal complex. Subsequent immunohistochemical analysis of these sites showed significant neuroinflammation. This study presents three significant findings that advance our understanding and evaluation of TBI: 1 the introduction of a new method to identify highly localized disturbances in discrete gray matter, subcortical brain nuclei without postmortem histology, 2 the use of this method to demonstrate that separate injuries to the rostral and caudal cortex produce the same subcortical, disturbances, and 3 the central nucleus of the amygdala, critical in the regulation of emotion, is vulnerable to concussion.

  20. Identifying the Infection Control Areas Requiring Modifications in Thoracic Surgery Units: Results of a Two-Year Surveillance of Surgical Site Infections in Hospitals in Southern Poland.

    Science.gov (United States)

    Dubiel, Grzegorz; Rogoziński, Paweł; Żaloudik, Elżbieta; Bruliński, Krzysztof; Różańska, Anna; Wójkowska-Mach, Jadwiga

    2017-10-01

    Surgical site infection (SSI) is considered to be a priority in infection control. The objective of this study is the analysis of results of active targeted surveillance conducted over a two-year period in the Department of Thoracic Surgery at the Pulmonology and Thoracic Surgery Center in Bystra, in southern Poland. The retrospective analysis was carried out on the basis of results of active monitoring of SSI in the 45-bed Department of Thoracic Surgery at the Pulmonology and Thoracic Surgery Center in Bystra between April 1, 2014 and April 30, 2016. Surgical site infections were identified based on the definitions of the European Centre for Disease Prevention and Control (ECDC) taking into account the time of symptom onset, specifically, whether the symptoms occurred within 30 d after the surgical procedure. Detection of SSI relied on daily inspection of incisions by a trained nurse, analysis of medical and nursing entries in the computer system, and analysis of all results of microbiologic tests taken in the unit and in the operating room. In the study period, data were collected regarding 1,387 treatment procedures meeting the registration criteria. Forty cases of SSI were detected yielding an incidence rate of 3%. Most cases (55%) were found in the course of hospitalization and 45% were detected after the patient's discharge. The SSIs were classified as follows: superficial, 37.5%; deep infections, 7.5%; and organ/space infection, 55%. Among patients who were diagnosed with SSI, most were male (77.5%). For patients with an American Society of Anesthesiologists (ASA) score I-II the incidence rate was 2%; ASA score III or more, 3.7%. The incidence rate varied from 0.3% in clean surgical site to 6.5% in clean-contaminated site. The study validated the usefulness of targeted surveillance in monitoring SSIs in patients hospitalized in thoracic surgery departments. Surgical site infection surveillance identified areas of care requiring modifications, namely

  1. Previously unknown species of Aspergillus.

    Science.gov (United States)

    Gautier, M; Normand, A-C; Ranque, S

    2016-08-01

    The use of multi-locus DNA sequence analysis has led to the description of previously unknown 'cryptic' Aspergillus species, whereas classical morphology-based identification of Aspergillus remains limited to the section or species-complex level. The current literature highlights two main features concerning these 'cryptic' Aspergillus species. First, the prevalence of such species in clinical samples is relatively high compared with emergent filamentous fungal taxa such as Mucorales, Scedosporium or Fusarium. Second, it is clearly important to identify these species in the clinical laboratory because of the high frequency of antifungal drug-resistant isolates of such Aspergillus species. Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) has recently been shown to enable the identification of filamentous fungi with an accuracy similar to that of DNA sequence-based methods. As MALDI-TOF MS is well suited to the routine clinical laboratory workflow, it facilitates the identification of these 'cryptic' Aspergillus species at the routine mycology bench. The rapid establishment of enhanced filamentous fungi identification facilities will lead to a better understanding of the epidemiology and clinical importance of these emerging Aspergillus species. Based on routine MALDI-TOF MS-based identification results, we provide original insights into the key interpretation issues of a positive Aspergillus culture from a clinical sample. Which ubiquitous species that are frequently isolated from air samples are rarely involved in human invasive disease? Can both the species and the type of biological sample indicate Aspergillus carriage, colonization or infection in a patient? Highly accurate routine filamentous fungi identification is central to enhance the understanding of these previously unknown Aspergillus species, with a vital impact on further improved patient care. Copyright © 2016 European Society of Clinical Microbiology and

  2. In Silico Analysis of Gene Expression Network Components Underlying Pigmentation Phenotypes in the Python Identified Evolutionarily Conserved Clusters of Transcription Factor Binding Sites

    Directory of Open Access Journals (Sweden)

    Kristopher J. L. Irizarry

    2016-01-01

    Full Text Available Color variation provides the opportunity to investigate the genetic basis of evolution and selection. Reptiles are less studied than mammals. Comparative genomics approaches allow for knowledge gained in one species to be leveraged for use in another species. We describe a comparative vertebrate analysis of conserved regulatory modules in pythons aimed at assessing bioinformatics evidence that transcription factors important in mammalian pigmentation phenotypes may also be important in python pigmentation phenotypes. We identified 23 python orthologs of mammalian genes associated with variation in coat color phenotypes for which we assessed the extent of pairwise protein sequence identity between pythons and mouse, dog, horse, cow, chicken, anole lizard, and garter snake. We next identified a set of melanocyte/pigment associated transcription factors (CREB, FOXD3, LEF-1, MITF, POU3F2, and USF-1 that exhibit relatively conserved sequence similarity within their DNA binding regions across species based on orthologous alignments across multiple species. Finally, we identified 27 evolutionarily conserved clusters of transcription factor binding sites within ~200-nucleotide intervals of the 1500-nucleotide upstream regions of AIM1, DCT, MC1R, MITF, MLANA, OA1, PMEL, RAB27A, and TYR from Python bivittatus. Our results provide insight into pigment phenotypes in pythons.

  3. Mass spectrometry and site-directed mutagenesis identify several autophosphorylated residues required for the activity of PrkC, a Ser/Thr kinase from Bacillus subtilis

    DEFF Research Database (Denmark)

    Madec, Edwige; Stensballe, Allan; Kjellström, Sven

    2003-01-01

    We have shown recently that PrkC, which is involved in developmental processes in Bacillus subtilis, is a Ser/Thr kinase with features of the receptor kinase family of eukaryotic Hanks kinases. In this study, we expressed and purified from Escherichia coli the cytoplasmic domain of PrkC containing...... the kinase and a short juxtamembrane region. This fragment, which we designate PrkCc, undergoes autophosphorylation in E.coli. PrkCc is further autophosphorylated in vitro, apparently through a trans-kinase, intermolecular reaction. PrkC also displays kinase activity with myelin basic protein. Using high...... mass accuracy electrospray tandem mass spectrometry (LC-MS/MS) and nanoelectrospray tandem mass spectrometry, we identified seven phosphorylated threonine and one serine residue in PrkCc. All the corresponding residues were replaced by systematic site-directed mutagenesis and the purified mutant...

  4. Structure-guided approach identifies a novel class of HIV-1 ribonuclease H inhibitors: binding mode insights through magnesium complexation and site-directed mutagenesis studies

    DEFF Research Database (Denmark)

    Poongavanam, Vasanthanathan; Corona, Angela; Steinmann, Casper

    2018-01-01

    is a long and expensive process that can be speeded up by in silico methods. In the present study, a structure-guided screening is coupled with a similarity-based search on the Specs database to identify a new class of HIV-1 RNase H inhibitors. Out of the 45 compounds selected for experimental testing, 15...... inhibited the RNase H function below 100 μM with three hits exhibiting IC50 values active compound, AA, inhibits HIV-1 RNase H with an IC50 of 5.1 μM and exhibits a Mg-independent mode of inhibition. Site-directed mutagenesis studies provide valuable insight into the binding mode of newly...

  5. Radiation Therapy Deficiencies Identified During On-Site Dosimetry Visits by the Imaging and Radiation Oncology Core Houston Quality Assurance Center.

    Science.gov (United States)

    Kry, Stephen F; Dromgoole, Lainy; Alvarez, Paola; Leif, Jessica; Molineu, Andrea; Taylor, Paige; Followill, David S

    2017-12-01

    To review the dosimetric, mechanical, and programmatic deficiencies most frequently observed during on-site visits of radiation therapy facilities by the Imaging and Radiation Oncology Core Quality Assurance Center in Houston (IROC Houston). The findings of IROC Houston between 2000 and 2014, including 409 institutions and 1020 linear accelerators (linacs), were compiled. On-site evaluations by IROC Houston include verification of absolute calibration (tolerance of ±3%), relative dosimetric review (tolerances of ±2% between treatment planning system [TPS] calculation and measurement), mechanical evaluation (including multileaf collimator and kilovoltage-megavoltage isocenter evaluation against Task Group [TG]-142 tolerances), and general programmatic review (including institutional quality assurance program vs TG-40 and TG-142). An average of 3.1 deficiencies was identified at each institution visited, a number that has decreased slightly with time. The most common errors are tabulated and include TG-40/TG-142 compliance (82% of institutions were deficient), small field size output factors (59% of institutions had errors ≥3%), and wedge factors (33% of institutions had errors ≥3%). Dosimetric errors of ≥10%, including in beam calibration, were seen at many institutions. There is substantial room for improvement of both dosimetric and programmatic issues in radiation therapy, which should be a high priority for the medical physics community. Particularly relevant was suboptimal beam modeling in the TPS and a corresponding failure to detect these errors by not including TPS data in the linac quality assurance process. Copyright © 2017 Elsevier Inc. All rights reserved.

  6. Quantitative in vivo analyses reveal calcium-dependent phosphorylation sites and identifies a novel component of the Toxoplasma invasion motor complex.

    Directory of Open Access Journals (Sweden)

    Thomas Nebl

    2011-09-01

    Full Text Available Apicomplexan parasites depend on the invasion of host cells for survival and proliferation. Calcium-dependent signaling pathways appear to be essential for micronemal release and gliding motility, yet the target of activated kinases remains largely unknown. We have characterized calcium-dependent phosphorylation events during Toxoplasma host cell invasion. Stimulation of live tachyzoites with Ca²⁺-mobilizing drugs leads to phosphorylation of numerous parasite proteins, as shown by differential 2-DE display of ³²[P]-labeled protein extracts. Multi-dimensional Protein Identification Technology (MudPIT identified ∼546 phosphorylation sites on over 300 Toxoplasma proteins, including 10 sites on the actomyosin invasion motor. Using a Stable Isotope of Amino Acids in Culture (SILAC-based quantitative LC-MS/MS analyses we monitored changes in the abundance and phosphorylation of the invasion motor complex and defined Ca²⁺-dependent phosphorylation patterns on three of its components--GAP45, MLC1 and MyoA. Furthermore, calcium-dependent phosphorylation of six residues across GAP45, MLC1 and MyoA is correlated with invasion motor activity. By analyzing proteins that appear to associate more strongly with the invasion motor upon calcium stimulation we have also identified a novel 15-kDa Calmodulin-like protein that likely represents the MyoA Essential Light Chain of the Toxoplasma invasion motor. This suggests that invasion motor activity could be regulated not only by phosphorylation but also by the direct binding of calcium ions to this new component.

  7. Identifying key controls on the behavior of an acidic-U(VI) plume in the Savannah River Site using reactive transport modeling.

    Science.gov (United States)

    Bea, Sergio A; Wainwright, Haruko; Spycher, Nicolas; Faybishenko, Boris; Hubbard, Susan S; Denham, Miles E

    2013-08-01

    Acidic low-level waste radioactive waste solutions were discharged to three unlined seepage basins at the F-Area of the Department of Energy (DOE) Savannah River Site (SRS), South Carolina, USA, from 1955 through 1989. Despite many years of active remediation, the groundwater remains acidic and contaminated with significant levels of U(VI) and other radionuclides. Monitored Natural Attenuation (MNA) is a desired closure strategy for the site, based on the premise that regional flow of clean background groundwater will eventually neutralize the groundwater acidity, immobilizing U(VI) through adsorption. An in situ treatment system is currently in place to accelerate this in the downgradient portion of the plume and similar measures could be taken upgradient if necessary. Understanding the long-term pH and U(VI) adsorption behavior at the site is critical to assess feasibility of MNA along with the in-situ remediation treatments. This paper presents a reactive transport (RT) model and uncertainty quantification (UQ) analyses to explore key controls on the U(VI)-plume evolution and long-term mobility at this site. Two-dimensional numerical RT simulations are run including the saturated and unsaturated (vadose) zones, U(VI) and H(+) adsorption (surface complexation) onto sediments, dissolution and precipitation of Al and Fe minerals, and key hydrodynamic processes are considered. UQ techniques are applied using a new open-source tool that is part of the developing ASCEM reactive transport modeling and analysis framework to: (1) identify the complex physical and geochemical processes that control the U(VI) plume migration in the pH range where the plume is highly mobile, (2) evaluate those physical and geochemical parameters that are most controlling, and (3) predict the future plume evolution constrained by historical, chemical and hydrological data. The RT simulation results show a good agreement with the observed historical pH and concentrations of U(VI), nitrates

  8. The Kavirondo Escarpment: a previously unrecognized site of high ...

    African Journals Online (AJOL)

    Despite only a limited effort there, we report several new atlas square occurrences, presence of the local and poorly known Rock Cisticola Cisticola emini and a significant range extension for the Stone Partridge Ptilopachus petrosus. Our short visits indicate high avian species richness is associated with the escarpment and ...

  9. The Kavirondo Escarpment: a previously unrecognized site of high ...

    African Journals Online (AJOL)

    west, and comprises the northern fault line escarpment of the Kavirondo Rift Valley. (Baker et al. 1972). ... Darker shading represents higher elevations and contours shown are for 1400 m .... Kavirondo Escarpment represents a 50 km north-easterly extension of range and only ... Grey-winged Robin Sheppardia polioptera.

  10. Antigenic Fingerprinting following Primary RSV Infection in Young Children Identifies Novel Antigenic Sites and Reveals Unlinked Evolution of Human Antibody Repertoires to Fusion and Attachment Glycoproteins.

    Directory of Open Access Journals (Sweden)

    Sandra Fuentes

    2016-04-01

    Full Text Available Respiratory Syncytial Virus (RSV is the major cause of pneumonia among infants. Here we elucidated the antibody repertoire following primary RSV infection and traced its evolution through adolescence and adulthood. Whole genome-fragment phage display libraries (GFPDL expressing linear and conformational epitopes in the RSV fusion protein (F and attachment protein (G were used for unbiased epitope profiling of infant sera prior to and following RSV infection. F-GFPDL analyses demonstrated modest changes in the anti-F epitope repertoires post-RSV infection, while G-GFPDL analyses revealed 100-fold increase in number of bound phages. The G-reactive epitopes spanned the N- and C-terminus of the G ectodomain, along with increased reactivity to the central conserved domain (CCD. Panels of F and G antigenic sites were synthesized to evaluate sera from young children (<2 yr, adolescents (14-18 yr and adults (30-45 yr in SPR real-time kinetics assays. A steady increase in RSV-F epitope repertoires from young children to adults was observed using peptides and F proteins. Importantly, several novel epitopes were identified in pre-fusion F and an immunodominant epitope in the F-p27. In all age groups, antibody binding to pre-fusion F was 2-3 folds higher than to post-fusion form. For RSV-G, antibody responses were high following early RSV infection in children, but declined significantly in adults, using either G proteins or peptides. This study identified unlinked evolution of anti-F and anti G responses and supportive evidence for immune pressure driven evolution of RSV-G. These findings could help development of effective countermeasures including vaccines.

  11. Use of a scenario-development procedure to identify potentially disruptive scenarios, Greater Confinement Disposal facility, Area 5, Nevada Test Site

    International Nuclear Information System (INIS)

    Guzowski, R.V.; Sandia National Labs., Albuquerque, NM

    1994-01-01

    The Greater Confinement Disposal (GCD) facility includes four boreholes that contain transuranic (TRLT) waste. Presence of the TRU waste means that this facility must comply with the US Environmental Protection Agency's Environmental Radiation Protection Standards for Management and Disposal of Spent Nuclear Fuel, High-Level and Transuranic Waste-Final Rule 40 CFR Part 191. To comply with the Containment Requirements of this rule, all potentially disruptive events and processes, and by implication all potentially disruptive combinations of events and processes (scenarios), must be identified for possible inclusion in performance assessments. Screening of the FEPs identified four events for scenario development: exploratory drilling for natural resources, drilling withdrawal wells, irrigation, and subsidence. Recent environmental-isotope analyses of the vadose zone suggest that radionuclide transport from the boreholes to the water table by infiltration is not a feasible transport mechanism within the time frame of regulatory concern. For this reason, the event of drilling withdrawal wells was merged with exploratory drilling for resources. The descriptions of the remaining three events were modified slightly to aid in estimation of event probabilities and consequence analyses. The three events are: exploratory drilling for resources penetrates a TRU borehole, irrigation occurs at the Radioactive Waste Management Site (RWMS), and subsidence occurs at the RWMS. Use of a logic diagram with these three events resulted in the construction of eight scenarios, including base-case (undisturbed) conditions. Screening these scenarios at this stage of scenario development was beyond the scope of this task. Based on the implementation assumptions, this scenario-development procedure produced a comprehensive set of mutually exclusive scenarios that are reproducible and auditable for use in GCD performance assessments

  12. Can osseous landmarks in the distal medial humerus be used to identify the attachment sites of ligaments and tendons: paleopathologic-anatomic imaging study in cadavers

    Energy Technology Data Exchange (ETDEWEB)

    Buck, Florian M. [Veterans Administration Medical Center, Department of Radiology, San Diego, CA (United States); Institut fuer Diagnostische Radiologie, Uniklinik Balgrist, Zurich (Switzerland); Zoner, Cristiane S.; Cardoso, Fabiano; Gheno, Ramon; Nico, Marcelo A.C.; Trudell, Debra J.; Resnick, Donald [Veterans Administration Medical Center, Department of Radiology, San Diego, CA (United States); Randall, Tori D. [San Diego Museum of Man, Physical Anthropology, San Diego, CA (United States)

    2010-09-15

    To describe osseous landmarks that allow identification of the attachments of the ligaments and tendons in the distal medial aspect of the humerus. Reliable osseous landmarks in the distal medial aspect of the humerus were identified in 34 well-preserved specimens from a paleopathologic collection. These osseous landmarks were then sought in magnetic resonance (MR) images of ten cadaveric elbow specimens so that the ease of their visualization and optimal imaging plane could be assessed. To assign these osseous landmarks to specific attachments of the tendons and ligaments in the distal medial humerus, we cut the specimens in slices and photographed and examined them. Subsequently, the prevalence of these osseous landmarks as well as the attachment sites of the tendons and ligaments in this location was determined. We determined ten reliable osseous landmarks in the distal medial aspect of the humerus, their prevalence and ease of identification, and their relationship to the attachments of the tendons and ligaments at the medial distal humerus. It is possible to use osseous landmarks at the distal medial humerus to facilitate identification of the different attachments of tendons and ligaments when MR images of the elbow are assessed. (orig.)

  13. Energy infrastructure of the United States and projected siting needs: Scoping ideas, identifying issues and options. Draft report of the Department of Energy Working Group on Energy Facility Siting to the Secretary

    Energy Technology Data Exchange (ETDEWEB)

    1993-12-01

    A Department of Energy (DOE) Working Group on Energy Facility Siting, chaired by the Policy Office with membership from the major program and staff offices of the Department, reviewed data regarding energy service needs, infrastructure requirements, and constraints to siting. The Working Group found that the expeditious siting of energy facilities has important economic, energy, and environmental implications for key Administration priorities.

  14. High FDG uptake areas on pre-radiotherapy PET/CT identify preferential sites of local relapse after chemoradiotherapy for locally advanced oesophageal cancer

    Energy Technology Data Exchange (ETDEWEB)

    Calais, Jeremie; Lemarignier, Charles; Vera, Pierre [Henri Becquerel Cancer Center and Rouen University Hospital, Nuclear Medicine Department, Rouen (France); University of Rouen, QuantIF-LITIS (Equipe d' Accueil 4108-FR CNRS 3638), Faculty of Medicine, Rouen (France); Dubray, Bernard [University of Rouen, QuantIF-LITIS (Equipe d' Accueil 4108-FR CNRS 3638), Faculty of Medicine, Rouen (France); Centre Henri Becquerel and Rouen University Hospital, Department of Radiotherapy and Medical Physics, Rouen (France); Nkhali, Lamyaa; Thureau, Sebastien; Modzelewski, Romain; Gardin, Isabelle [Henri Becquerel Cancer Center and Rouen University Hospital, Nuclear Medicine Department, Rouen (France); University of Rouen, QuantIF-LITIS (Equipe d' Accueil 4108-FR CNRS 3638), Faculty of Medicine, Rouen (France); Centre Henri Becquerel and Rouen University Hospital, Department of Radiotherapy and Medical Physics, Rouen (France); Di Fiore, Frederic [Rouen University Hospital, Department of Gastroenterology, Rouen (France); Rouen University Hospital, Department of Oncology, Henri Becquerel Cancer Center, IRON, Rouen (France); Michel, Pierre [Rouen University Hospital, Department of Gastroenterology, Rouen (France)

    2015-05-01

    The high failure rates in the radiotherapy (RT) target volume suggest that patients with locally advanced oesophageal cancer (LAOC) would benefit from increased total RT doses. High 2-deoxy-2-[{sup 18}F]fluoro-D-glucose (FDG) uptake (hotspot) on pre-RT FDG positron emission tomography (PET)/CT has been reported to identify intra-tumour sites at increased risk of relapse after RT in non-small cell lung cancer and in rectal cancer. Our aim was to confirm these observations in patients with LAOC and to determine the optimal maximum standardized uptake value (SUV{sub max}) threshold to delineate smaller RT target volumes that would facilitate RT dose escalation without impaired tolerance. The study included 98 consecutive patients with LAOC treated by chemoradiotherapy (CRT). All patients underwent FDG PET/CT at initial staging and during systematic follow-up in a single institution. FDG PET/CT acquisitions were coregistered on the initial CT scan. Various subvolumes within the initial tumour (30, 40, 50, 60, 70, 80 and 90 % SUV{sub max} thresholds) and in the subsequent local recurrence (LR, 40 and 90 % SUV{sub max} thresholds) were pasted on the initial CT scan and compared[Dice, Jaccard, overlap fraction (OF), common volume/baseline volume, common volume/recurrent volume]. Thirty-five patients had LR. The initial metabolic tumour volume was significantly higher in LR tumours than in the locally controlled tumours (mean 25.4 vs 14.2 cc; p = 0.002). The subvolumes delineated on initial PET/CT with a 30-60 % SUV{sub max} threshold were in good agreement with the recurrent volume at 40 % SUV{sub max} (OF = 0.60-0.80). The subvolumes delineated on initial PET/CT with a 30-60 % SUV{sub max} threshold were in good to excellent agreement with the core volume (90 % SUV{sub max}) of the relapse (common volume/recurrent volume and OF indices 0.61-0.89). High FDG uptake on pretreatment PET/CT identifies tumour subvolumes that are at greater risk of recurrence after CRT in

  15. The Decline of Laparoendoscopic Single-Site Surgery: A Survey of the Endourological Society to Identify Shortcomings and Guidance for Future Directions.

    Science.gov (United States)

    Sorokin, Igor; Canvasser, Noah E; Irwin, Brian; Autorino, Riccardo; Liatsikos, Evangelos N; Cadeddu, Jeffrey A; Rane, Abhay

    2017-10-01

    To analyze the most recent temporal trends in the adoption of urologic laparoendoscopic single-site (LESS), to identify the perceived limitations associated with its decline, and to determine factors that might revive the role of LESS in the field of minimally invasive urologic surgery. A 15 question survey was created and sent to members of the Endourological Society in September 2016. Only members who performed LESS procedures in practice were asked to respond. In total, 106 urologists responded to the survey. Most of the respondents were from the United States (35%) and worked in an academic hospital (84.9%). Standard LESS was the most popular approach (78.1%), while 14.3% used robotics, and 7.6% used both. 2009 marked the most popular year to perform the initial (27.6%) and the majority (20%) of LESS procedures. The most common LESS procedure was a radical/simple nephrectomy (51%) followed by pyeloplasty (17.3%). In the past 12 months, 60% of respondents had performed no LESS procedures. Compared to conventional laparoscopy, respondents only believed cosmesis to be better, however, this enthusiasm waned over time. Worsening shifts in enthusiasm for LESS also occurred with patient desire, marketability, cost, safety, and robotic adaptability. The highest rated factor to help LESS regain popularity was a new robotic platform. The decline of LESS is apparent, with few urologists continuing to perform procedures attributed to multiple factors. The availability of a purpose-built robotic platform and better instrumentation might translate into a renewed future interest of LESS.

  16. Analysis of 30 putative BRCA1 splicing mutations in hereditary breast and ovarian cancer families identifies exonic splice site mutations that escape in silico prediction.

    Directory of Open Access Journals (Sweden)

    Barbara Wappenschmidt

    Full Text Available Screening for pathogenic mutations in breast and ovarian cancer genes such as BRCA1/2, CHEK2 and RAD51C is common practice for individuals from high-risk families. However, test results may be ambiguous due to the presence of unclassified variants (UCV in the concurrent absence of clearly cancer-predisposing mutations. Especially the presence of intronic or exonic variants within these genes that possibly affect proper pre-mRNA processing poses a challenge as their functional implications are not immediately apparent. Therefore, it appears necessary to characterize potential splicing UCV and to develop appropriate classification tools. We investigated 30 distinct BRCA1 variants, both intronic and exonic, regarding their spliceogenic potential by commonly used in silico prediction algorithms (HSF, MaxEntScan along with in vitro transcript analyses. A total of 25 variants were identified spliceogenic, either causing/enhancing exon skipping or activation of cryptic splice sites, or both. Except from a single intronic variant causing minor effects on BRCA1 pre-mRNA processing in our analyses, 23 out of 24 intronic variants were correctly predicted by MaxEntScan, while HSF was less accurate in this cohort. Among the 6 exonic variants analyzed, 4 severely impair correct pre-mRNA processing, while the remaining two have partial effects. In contrast to the intronic alterations investigated, only half of the spliceogenic exonic variants were correctly predicted by HSF and/or MaxEntScan. These data support the idea that exonic splicing mutations are commonly disease-causing and concurrently prone to escape in silico prediction, hence necessitating experimental in vitro splicing analysis.

  17. Comparative assessment of environmental and socio-economic impacts of disposal of radioactive waste by shallow burial at sites identified by Nirex

    International Nuclear Information System (INIS)

    Gordon, A.E.M.; Morrow, A.J.; Watson, S.R.

    1987-09-01

    This case study tested two methodologies, comparative assessment and multi-attribute value analysis, on repository site selection. Problems affecting their application stemmed from incomplete baseline and proposed project data and from the impacts being essentially indistinguishable between sites. The latter meant that initial screening was not possible and subsequent screening became arbitrary. The large number of impacts which had to be retained made handling difficult and meaningful rating under comparative assessment was virtually impossible without introducing implicit weightings and adjusting the scale. Multi-attribute value analysis, whilst the more data demanding of the two methodologies, has a greater capability for handling the impacts. Clearly, the limitations on what data can realistically be collected must be taken into account when the evaluation methodology is designed. Ideally a draft methodology should be applied to one site and modified as need be before used for the formal assessment. (author)

  18. TargetM6A: Identifying N6-Methyladenosine Sites From RNA Sequences via Position-Specific Nucleotide Propensities and a Support Vector Machine.

    Science.gov (United States)

    Li, Guang-Qing; Liu, Zi; Shen, Hong-Bin; Yu, Dong-Jun

    2016-10-01

    As one of the most ubiquitous post-transcriptional modifications of RNA, N 6 -methyladenosine ( [Formula: see text]) plays an essential role in many vital biological processes. The identification of [Formula: see text] sites in RNAs is significantly important for both basic biomedical research and practical drug development. In this study, we designed a computational-based method, called TargetM6A, to rapidly and accurately target [Formula: see text] sites solely from the primary RNA sequences. Two new features, i.e., position-specific nucleotide/dinucleotide propensities (PSNP/PSDP), are introduced and combined with the traditional nucleotide composition (NC) feature to formulate RNA sequences. The extracted features are further optimized to obtain a much more compact and discriminative feature subset by applying an incremental feature selection (IFS) procedure. Based on the optimized feature subset, we trained TargetM6A on the training dataset with a support vector machine (SVM) as the prediction engine. We compared the proposed TargetM6A method with existing methods for predicting [Formula: see text] sites by performing stringent jackknife tests and independent validation tests on benchmark datasets. The experimental results show that the proposed TargetM6A method outperformed the existing methods for predicting [Formula: see text] sites and remarkably improved the prediction performances, with MCC = 0.526 and AUC = 0.818. We also provided a user-friendly web server for TargetM6A, which is publicly accessible for academic use at http://csbio.njust.edu.cn/bioinf/TargetM6A.

  19. Hydrous ferric oxide: evaluation of Cd-HFO surface complexation models combining Cd(K) EXAFS data, potentiometric titration results, and surface site structures identified from mineralogical knowledge.

    Science.gov (United States)

    Spadini, Lorenzo; Schindler, Paul W; Charlet, Laurent; Manceau, Alain; Vala Ragnarsdottir, K

    2003-10-01

    The surface properties of ferrihydrite were studied by combining wet chemical data, Cd(K) EXAFS data, and a surface structure and protonation model of the ferrihydrite surface. Acid-base titration experiments and Cd(II)-ferrihydrite sorption experiments were performed within 3titration data could be adequately modeled by triple bond Fe- OH(2)(+1/2)-H(+)triple bond Fe-OH(-1/2),logk((int))=-8.29, assuming the existence of a unique intrinsic microscopic constant, logk((int)), and consequently the existence of a single significant type of acid-base reactive functional groups. The surface structure model indicates that these groups are terminal water groups. The Cd(II) data were modeled assuming the existence of a single reactive site. The model fits the data set at low Cd(II) concentration and up to 50% surface coverage. At high coverage more Cd(II) ions than predicted are adsorbed, which is indicative of the existence of a second type of site of lower affinity. This agrees with the surface structure and protonation model developed, which indicates comparable concentrations of high- and low-affinity sites. The model further shows that for each class of low- and high-affinity sites there exists a variety of corresponding Cd surface complex structure, depending on the model crystal faces on which the complexes develop. Generally, high-affinity surface structures have surface coordinations of 3 and 4, as compared to 1 and 2 for low-affinity surface structures.

  20. Characterization of the Escherichia coli prsA1-encoded mutant phosphoribosylpyrophosphate synthetase identifies a divalent cation-nucleotide binding site

    DEFF Research Database (Denmark)

    Bower, Stanley G.; Harlow, Kenneth W.; Switzer, Robert L.

    1989-01-01

    : DLHAXQIQGFFDI/VPI/VD. There was little alteration in the Km for ribose 5-phosphate. The Km for ATP of the mutant enzyme was increased 27-fold when Mg2+ was the activating cation but only 5-fold when Mn2+ was used. Maximal velocities of the wild type and mutant enzymes were the same. The mutant enzyme has a 6......-fold lower affinity for Ca2+, as judged by the ability of Ca2+ to inhibit the reaction in the presence of 10 mM Mg2+. Wild type PRPP synthetase is subject to product inhibition by AMP, but AMP inhibition of the prsA1 mutant enzyme could not be detected. It has been previously proposed that a divalent...

  1. Mutational analysis of the EMCV 2A protein identifies a nuclear localization signal and an eIF4E binding site

    International Nuclear Information System (INIS)

    Groppo, Rachel; Brown, Bradley A.; Palmenberg, Ann C.

    2011-01-01

    Cardioviruses have a unique 2A protein (143 aa). During genome translation, the encephalomyocarditis virus (EMCV) 2A is released through a ribosome skipping event mitigated through C-terminal 2A sequences and by subsequent N-terminal reaction with viral 3C pro . Although viral replication is cytoplasmic, mature 2A accumulates in nucleoli shortly after infection. Some protein also transiently associates with cytoplasmic 40S ribosomal subunits, an activity contributing to inhibition of cellular cap-dependent translation. Cardiovirus sequences predict an eIF4E binding site (aa 126-134) and a nuclear localization signal (NLS, aa 91-102), within 2A, both of which are functional during EMCV infection. Point mutations preventing eIF4E:2A interactions gave small-plaque phenotype viruses, but still inhibited cellular cap-dependent translation. Deletions within the NLS motif relocalized 2A to the cytoplasm and abrogated the inhibition of cap-dependent translation. A fusion protein linking the 2A NLS to eGFP was sufficient to redirect the reporter to the nucleus but not into nucleoli.

  2. Sieve analysis of breakthrough HIV-1 sequences in HVTN 505 identifies vaccine pressure targeting the CD4 binding site of Env-gp120.

    Science.gov (United States)

    deCamp, Allan C; Rolland, Morgane; Edlefsen, Paul T; Sanders-Buell, Eric; Hall, Breana; Magaret, Craig A; Fiore-Gartland, Andrew J; Juraska, Michal; Carpp, Lindsay N; Karuna, Shelly T; Bose, Meera; LePore, Steven; Miller, Shana; O'Sullivan, Annemarie; Poltavee, Kultida; Bai, Hongjun; Dommaraju, Kalpana; Zhao, Hong; Wong, Kim; Chen, Lennie; Ahmed, Hasan; Goodman, Derrick; Tay, Matthew Z; Gottardo, Raphael; Koup, Richard A; Bailer, Robert; Mascola, John R; Graham, Barney S; Roederer, Mario; O'Connell, Robert J; Michael, Nelson L; Robb, Merlin L; Adams, Elizabeth; D'Souza, Patricia; Kublin, James; Corey, Lawrence; Geraghty, Daniel E; Frahm, Nicole; Tomaras, Georgia D; McElrath, M Juliana; Frenkel, Lisa; Styrchak, Sheila; Tovanabutra, Sodsai; Sobieszczyk, Magdalena E; Hammer, Scott M; Kim, Jerome H; Mullins, James I; Gilbert, Peter B

    2017-01-01

    Although the HVTN 505 DNA/recombinant adenovirus type 5 vector HIV-1 vaccine trial showed no overall efficacy, analysis of breakthrough HIV-1 sequences in participants can help determine whether vaccine-induced immune responses impacted viruses that caused infection. We analyzed 480 HIV-1 genomes sampled from 27 vaccine and 20 placebo recipients and found that intra-host HIV-1 diversity was significantly lower in vaccine recipients (P ≤ 0.04, Q-values ≤ 0.09) in Gag, Pol, Vif and envelope glycoprotein gp120 (Env-gp120). Furthermore, Env-gp120 sequences from vaccine recipients were significantly more distant from the subtype B vaccine insert than sequences from placebo recipients (P = 0.01, Q-value = 0.12). These vaccine effects were associated with signatures mapping to CD4 binding site and CD4-induced monoclonal antibody footprints. These results suggest either (i) no vaccine efficacy to block acquisition of any viral genotype but vaccine-accelerated Env evolution post-acquisition; or (ii) vaccine efficacy against HIV-1s with Env sequences closest to the vaccine insert combined with increased acquisition due to other factors, potentially including the vaccine vector.

  3. Tandem affinity purification of histones, coupled to mass spectrometry, identifies associated proteins and new sites of post-translational modification in Saccharomyces cerevisiae.

    Science.gov (United States)

    Valero, M Luz; Sendra, Ramon; Pamblanco, Mercè

    2016-03-16

    Histones and their post-translational modifications contribute to regulating fundamental biological processes in all eukaryotic cells. We have applied a conventional tandem affinity purification strategy to histones H3 and H4 of the yeast Saccharomyces cerevisiae. Mass spectrometry analysis of the co-purified proteins revealed multiple associated proteins, including core histones, which indicates that tagged histones may be incorporated to the nucleosome particle. Among the many other co-isolated proteins there are histone chaperones, elements of chromatin remodeling, of nucleosome assembly/disassembly, and of histone modification complexes. The histone chaperone Rtt106p, two members of chromatin assembly FACT complex and Psh1p, an ubiquitin ligase, were the most abundant proteins obtained with both H3-TAP and H4-TAP, regardless of the cell extraction medium stringency. Our mass spectrometry analyses have also revealed numerous novel post-translational modifications, including 30 new chemical modifications in histones, mainly by ubiquitination. We have discovered not only new sites of ubiquitination but that, besides lysine, also serine and threonine residues are targets of ubiquitination on yeast histones. Our results show the standard tandem affinity purification procedure is suitable for application to yeast histones, in order to isolate and characterize histone-binding proteins and post-translational modifications, avoiding the bias caused by histone purification from a chromatin-enriched fraction. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. Use of geographic information systems (GIS to identify adequate sites for cultivation of the seaweed Gracilaria birdiae in Rio Grande do Norte, Northeastern Brazil

    Directory of Open Access Journals (Sweden)

    Flavo E. S. de Sousa

    2012-06-01

    Full Text Available This study was designed to select potential areas for cultivation of the seaweed Gracilaria birdiae Plastino & E.C. Oliveira (Gracilariales, Rhodophyta on the coast of Rio Grande do Norte state, Brazil. The Geographic Information System (GIS and multi-criteria evaluation (MCE were used to identify the most suitable areas. The Analytical Hierarchical Process (AHP was applied to establish MCE weights, thereby generating viable areas for species cultivation. From a total of 3316.82 ha, around 53.67% (1780.06 ha were indicated as highly suitable areas, 40.93% (1357.58 ha as moderately suitable and 5.40% (179.18 ha as scarcely suitable for seaweed cultivation. Seven areas (1084.62 ha are located on the northern coast and 20 (2232.20 ha on the eastern coast. The results show that GIS can be used as an effective instrument for selecting seaweed cultivation areas.

  5. Combined serial analysis of gene expression and transcription factor binding site prediction identifies novel-candidate-target genes of Nr2e1 in neocortex development.

    Science.gov (United States)

    Schmouth, Jean-François; Arenillas, David; Corso-Díaz, Ximena; Xie, Yuan-Yun; Bohacec, Slavita; Banks, Kathleen G; Bonaguro, Russell J; Wong, Siaw H; Jones, Steven J M; Marra, Marco A; Simpson, Elizabeth M; Wasserman, Wyeth W

    2015-07-24

    Nr2e1 (nuclear receptor subfamily 2, group e, member 1) encodes a transcription factor important in neocortex development. Previous work has shown that nuclear receptors can have hundreds of target genes, and bind more than 300 co-interacting proteins. However, recognition of the critical role of Nr2e1 in neural stem cells and neocortex development is relatively recent, thus the molecular mechanisms involved for this nuclear receptor are only beginning to be understood. Serial analysis of gene expression (SAGE), has given researchers both qualitative and quantitative information pertaining to biological processes. Thus, in this work, six LongSAGE mouse libraries were generated from laser microdissected tissue samples of dorsal VZ/SVZ (ventricular zone and subventricular zone) from the telencephalon of wild-type (Wt) and Nr2e1-null embryos at the critical development ages E13.5, E15.5, and E17.5. We then used a novel approach, implementing multiple computational methods followed by biological validation to further our understanding of Nr2e1 in neocortex development. In this work, we have generated a list of 1279 genes that are differentially expressed in response to altered Nr2e1 expression during in vivo neocortex development. We have refined this list to 64 candidate direct-targets of NR2E1. Our data suggested distinct roles for Nr2e1 during different neocortex developmental stages. Most importantly, our results suggest a possible novel pathway by which Nr2e1 regulates neurogenesis, which includes Lhx2 as one of the candidate direct-target genes, and SOX9 as a co-interactor. In conclusion, we have provided new candidate interacting partners and numerous well-developed testable hypotheses for understanding the pathways by which Nr2e1 functions to regulate neocortex development.

  6. Global mapping of binding sites for Nrf2 identifies novel targets in cell survival response through ChIP-Seq profiling and network analysis

    Science.gov (United States)

    Malhotra, Deepti; Portales-Casamar, Elodie; Singh, Anju; Srivastava, Siddhartha; Arenillas, David; Happel, Christine; Shyr, Casper; Wakabayashi, Nobunao; Kensler, Thomas W.; Wasserman, Wyeth W.; Biswal, Shyam

    2010-01-01

    The Nrf2 (nuclear factor E2 p45-related factor 2) transcription factor responds to diverse oxidative and electrophilic environmental stresses by circumventing repression by Keap1, translocating to the nucleus, and activating cytoprotective genes. Nrf2 responses provide protection against chemical carcinogenesis, chronic inflammation, neurodegeneration, emphysema, asthma and sepsis in murine models. Nrf2 regulates the expression of a plethora of genes that detoxify oxidants and electrophiles and repair or remove damaged macromolecules, such as through proteasomal processing. However, many direct targets of Nrf2 remain undefined. Here, mouse embryonic fibroblasts (MEF) with either constitutive nuclear accumulation (Keap1−/−) or depletion (Nrf2−/−) of Nrf2 were utilized to perform chromatin-immunoprecipitation with parallel sequencing (ChIP-Seq) and global transcription profiling. This unique Nrf2 ChIP-Seq dataset is highly enriched for Nrf2-binding motifs. Integrating ChIP-Seq and microarray analyses, we identified 645 basal and 654 inducible direct targets of Nrf2, with 244 genes at the intersection. Modulated pathways in stress response and cell proliferation distinguish the inducible and basal programs. Results were confirmed in an in vivo stress model of cigarette smoke-exposed mice. This study reveals global circuitry of the Nrf2 stress response emphasizing Nrf2 as a central node in cell survival response. PMID:20460467

  7. Use of DOE site selection criteria for screening low-level waste disposal sites on the Oak Ridge Reservation

    International Nuclear Information System (INIS)

    Lee, D.W.; Ketelle, R.H.; Stinton, L.H.

    1983-09-01

    The proposed Department of Energy (DOE) site selection criteria were applied to the Oak Ridge Reservation, and the application was evaluated to determine the criteria's usefulness in the selection of a low-level waste disposal site. The application of the criteria required the development of a methodology to provide a framework for evaluation. The methodology is composed of site screening and site characterization stages. The site screening stage relies on reconnaissance data to identify a preferred site capable of satisfying the site selection criteria. The site characterization stage relies on a detailed site investigation to determine site acceptability. The site selection criteria were applied to the DOE Oak Ridge Reservation through the site screening stage. Results of this application were similar to those of a previous siting study on the Oak Ridge Reservation. The DOE site selection criteria when coupled with the methodology that was developed were easily applied and would be adaptable to any region of interest

  8. Identifying unstable sites on logging roads

    Science.gov (United States)

    R. M. Rice; J. Lewis

    1986-01-01

    Logging roads are an important source of forestry-related erosion. The amount of erosion on a forest road is determined by the interaction between how the road is constructed and maintained and the environment in which it is built. The roads in this study were constructed with large bulldozers, and most excavated material was sidecast. The roads studied were...

  9. Environmental Modeling, The Natural Filter Wetland Priority layers identify priority wetland restoration sites by subwatershed. Land use, hydrology, soil, and landscape characteristics were analyzed to rank opportunities with high nutrient removal potential., Published in 2014, Smaller than 1:100000 scale, Maryland Department of Natural Resources (DNR).

    Data.gov (United States)

    NSGIC Education | GIS Inventory — Environmental Modeling dataset current as of 2014. The Natural Filter Wetland Priority layers identify priority wetland restoration sites by subwatershed. Land use,...

  10. Ocean Disposal Site Monitoring

    Science.gov (United States)

    EPA is responsible for managing all designated ocean disposal sites. Surveys are conducted to identify appropriate locations for ocean disposal sites and to monitor the impacts of regulated dumping at the disposal sites.

  11. Promoting Your Web Site.

    Science.gov (United States)

    Raeder, Aggi

    1997-01-01

    Discussion of ways to promote sites on the World Wide Web focuses on how search engines work and how they retrieve and identify sites. Appropriate Web links for submitting new sites and for Internet marketing are included. (LRW)

  12. Exploring the influence of EGCG on the β-sheet-rich oligomers of human islet amyloid polypeptide (hIAPP1-37 and identifying its possible binding sites from molecular dynamics simulation.

    Directory of Open Access Journals (Sweden)

    Qianqian Wang

    Full Text Available EGCG possesses the ability of disaggregating the existing amyloid fibrils which were associated with many age-related degenerative diseases. However, the molecular mechanism of EGCG to disaggregate these fibrils is poorly known. In this work, to study the influence of EGCG on the full-length human islet amyloid polypeptide 1-37 (hIAPP1-37 oligomers, molecular dynamics simulations of hIAPP1-37 pentamer and decamer with EGCG were performed, respectively. The obtained results indicate that EGCG indeed destabilized the hIAPP1-37 oligomers. The nematic order parameter and secondary structure calculations coupled with the free-energy landscape indicate that EGCG broke the initial ordered pattern of two polymers, greatly reduced their β-sheet content and enlarged their conformational space. On this basis, three possible target sites were identified with the binding capacity order of S1>S2>S3. After a deeper analysis of each site, we found that S1 was the most possible site on which residues B-Ile26/Ala25, A-Phe23, B/C-Leu27 and E-Tyr37 played an important role for their binding. The proposal of this molecular mechanism can not only provide a prospective interaction figure between EGCG and β-sheet-rich fibrils of hIAPP1-37, but also is useful for further discovering other potential inhibitors.

  13. Identification of sumoylation sites in CCDC6, the first identified RET partner gene in papillary thyroid carcinoma, uncovers a mode of regulating CCDC6 function on CREB1 transcriptional activity.

    Directory of Open Access Journals (Sweden)

    Chiara Luise

    Full Text Available CCDC6 was originally identified in chimeric genes as caused by chromosomal translocation involving the RET protooncogene in some thyroid tumors. Recognised as a 65 kDa pro-apoptotic phosphoprotein, CCDC6 has been enrolled as an ATM substrate that contribute to protect genome integrity by modulating PP4c activity in response to genotoxic stress. Recently, CCDC6 has been identified as a repressor of CREB1-dependent transcription. Sumoylation has emerged as an important mechanism in transcriptional control. Here, we report the identification and characterization of three sites of sumoylation in CCDC6 (K74, K266 and K424 which are highly conserved in vertebrates. We demonstrate that the post-translational modifications by SUMO2 constrain most of the CCDC6 protein in the cytosol and affect its functional interaction with CREB1 with a decrease of CCDC6 repressive function on CREB1 transcriptional activity. Indeed, the impairment of functional outcome of sumoylated CCDC6 is obtained knocking down all three the sumoylation sites. Interestingly, in thyroid cells the SUMO2-mediated CCDC6 post-translational modifications are induced by Forskolin, a cAMP analog. Signal transduction via the cAMP pathway is known to be ubiquitous and represents a major line of communication between many organisms and their environment. We believe that CCDC6 could be an important player in the dynamics of cAMP signaling by fine regulating CREB1 transcriptional activity in normal and transformed thyroid cells.

  14. O-GlcNAcPRED-II: an integrated classification algorithm for identifying O-GlcNAcylation sites based on fuzzy undersampling and a K-means PCA oversampling technique.

    Science.gov (United States)

    Jia, Cangzhi; Zuo, Yun; Zou, Quan; Hancock, John

    2018-02-06

    Protein O-GlcNAcylation (O-GlcNAc) is an important post-translational modification of serine (S)/threonine (T) residues that involves multiple molecular and cellular processes. Recent studies have suggested that abnormal O-G1cNAcylation causes many diseases, such as cancer and various neurodegenerative diseases. With the available protein O-G1cNAcylation sites experimentally verified, it is highly desired to develop automated methods to rapidly and effectively identify O-G1cNAcylation sites. Although some computational methods have been proposed, their performance has been unsatisfactory, particularly in terms of prediction sensitivity. In this study, we developed an ensemble model O-GlcNAcPRED-II to identify potential O-G1cNAcylation sites. A K-means principal component analysis oversampling technique (KPCA) and fuzzy undersampling method (FUS) were first proposed and incorporated to reduce the proportion of the original positive and negative training samples. Then, rotation forest, a type of classifier-integrated system, was adopted to divide the eight types of feature space into several subsets using four sub-classifiers: random forest, k-nearest neighbour, naive Bayesian and support vector machine. We observed that O-GlcNAcPRED-II achieved a sensitivity of 81.05%, specificity of 95.91%, accuracy of 91.43% and Matthew's correlation coefficient of 0.7928 for five-fold cross-validation run 10 times. Additionally, the results obtained by O-GlcNAcPRED-II on two independent datasets also indicated that the proposed predictor outperformed five published prediction tools. http://121.42.167.206/OGlcPred/. cangzhijia@dlmu.edu.cn or zouquan@nclab.net. © The Author (2018). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  15. Preoperative screening: value of previous tests.

    Science.gov (United States)

    Macpherson, D S; Snow, R; Lofgren, R P

    1990-12-15

    To determine the frequency of tests done in the year before elective surgery that might substitute for preoperative screening tests and to determine the frequency of test results that change from a normal value to a value likely to alter perioperative management. Retrospective cohort analysis of computerized laboratory data (complete blood count, sodium, potassium, and creatinine levels, prothrombin time, and partial thromboplastin time). Urban tertiary care Veterans Affairs Hospital. Consecutive sample of 1109 patients who had elective surgery in 1988. At admission, 7549 preoperative tests were done, 47% of which duplicated tests performed in the previous year. Of 3096 previous results that were normal as defined by hospital reference range and done closest to the time of but before admission (median interval, 2 months), 13 (0.4%; 95% CI, 0.2% to 0.7%), repeat values were outside a range considered acceptable for surgery. Most of the abnormalities were predictable from the patient's history, and most were not noted in the medical record. Of 461 previous tests that were abnormal, 78 (17%; CI, 13% to 20%) repeat values at admission were outside a range considered acceptable for surgery (P less than 0.001, frequency of clinically important abnormalities of patients with normal previous results with those with abnormal previous results). Physicians evaluating patients preoperatively could safely substitute the previous test results analyzed in this study for preoperative screening tests if the previous tests are normal and no obvious indication for retesting is present.

  16. Automatic electromagnetic valve for previous vacuum

    International Nuclear Information System (INIS)

    Granados, C. E.; Martin, F.

    1959-01-01

    A valve which permits the maintenance of an installation vacuum when electric current fails is described. It also lets the air in the previous vacuum bomb to prevent the oil ascending in the vacuum tubes. (Author)

  17. Exome Sequencing Identifies a Novel LMNA Splice-Site Mutation and Multigenic Heterozygosity of Potential Modifiers in a Family with Sick Sinus Syndrome, Dilated Cardiomyopathy, and Sudden Cardiac Death.

    Directory of Open Access Journals (Sweden)

    Michael V Zaragoza

    Full Text Available The goals are to understand the primary genetic mechanisms that cause Sick Sinus Syndrome and to identify potential modifiers that may result in intrafamilial variability within a multigenerational family. The proband is a 63-year-old male with a family history of individuals (>10 with sinus node dysfunction, ventricular arrhythmia, cardiomyopathy, heart failure, and sudden death. We used exome sequencing of a single individual to identify a novel LMNA mutation and demonstrated the importance of Sanger validation and family studies when evaluating candidates. After initial single-gene studies were negative, we conducted exome sequencing for the proband which produced 9 gigabases of sequencing data. Bioinformatics analysis showed 94% of the reads mapped to the reference and identified 128,563 unique variants with 108,795 (85% located in 16,319 genes of 19,056 target genes. We discovered multiple variants in known arrhythmia, cardiomyopathy, or ion channel associated genes that may serve as potential modifiers in disease expression. To identify candidate mutations, we focused on ~2,000 variants located in 237 genes of 283 known arrhythmia, cardiomyopathy, or ion channel associated genes. We filtered the candidates to 41 variants in 33 genes using zygosity, protein impact, database searches, and clinical association. Only 21 of 41 (51% variants were validated by Sanger sequencing. We selected nine confirmed variants with minor allele frequencies G, a novel heterozygous splice-site mutation as the primary mutation with rare or novel variants in HCN4, MYBPC3, PKP4, TMPO, TTN, DMPK and KCNJ10 as potential modifiers and a mechanism consistent with haploinsufficiency.

  18. Hanford Site Development Plan

    Energy Technology Data Exchange (ETDEWEB)

    Rinne, C.A.; Curry, R.H.; Hagan, J.W.; Seiler, S.W.; Sommer, D.J. (Westinghouse Hanford Co., Richland, WA (USA)); Yancey, E.F. (Pacific Northwest Lab., Richland, WA (USA))

    1990-01-01

    The Hanford Site Development Plan (Site Development Plan) is intended to guide the short- and long-range development and use of the Hanford Site. All acquisition, development, and permanent facility use at the Hanford Site will conform to the approved plan. The Site Development Plan also serves as the base document for all subsequent studies that involve use of facilities at the Site. This revision is an update of a previous plan. The executive summary presents the highlights of the five major topics covered in the Site Development Plan: general site information, existing conditions, planning analysis, Master Plan, and Five-Year Plan. 56 refs., 67 figs., 31 tabs.

  19. Hanford Site Development Plan

    International Nuclear Information System (INIS)

    Rinne, C.A.; Curry, R.H.; Hagan, J.W.; Seiler, S.W.; Sommer, D.J.; Yancey, E.F.

    1990-01-01

    The Hanford Site Development Plan (Site Development Plan) is intended to guide the short- and long-range development and use of the Hanford Site. All acquisition, development, and permanent facility use at the Hanford Site will conform to the approved plan. The Site Development Plan also serves as the base document for all subsequent studies that involve use of facilities at the Site. This revision is an update of a previous plan. The executive summary presents the highlights of the five major topics covered in the Site Development Plan: general site information, existing conditions, planning analysis, Master Plan, and Five-Year Plan. 56 refs., 67 figs., 31 tabs

  20. 75 FR 42487 - Supplementary Identifying Information of Previously-Designated Individual, Foreign Narcotics...

    Science.gov (United States)

    2010-07-21

    ... State, and the Secretary of Homeland Security when designating and blocking the property and interests... in, or providing financial or technological support for or to, or providing goods or services in... Agustin, Colombia; DOB 19 Feb 1976; Citizen Colombia; Cedula No. 79928745 (Colombia); Passport AF392658...

  1. Previously identified patellar tendinopathy risk factors differ between elite and sub-elite volleyball players.

    Science.gov (United States)

    Janssen, I; Steele, J R; Munro, B J; Brown, N A T

    2015-06-01

    Patellar tendinopathy is the most common knee injury incurred in volleyball, with its prevalence in elite athletes more than three times that of their sub-elite counterparts. The purpose of this study was to determine whether patellar tendinopathy risk factors differed between elite and sub-elite male volleyball players. Nine elite and nine sub-elite male volleyball players performed a lateral stop-jump block movement. Maximum vertical jump, training history, muscle extensibility and strength, three-dimensional landing kinematics (250 Hz), along with lower limb neuromuscular activation patterns (1500 Hz), and patellar tendon loading were collected during each trial. Multivariate analyses of variance (P volleyball players. Interventions designed to reduce landing frequency and improve quadriceps extensibility are recommended to reduce patellar tendinopathy prevalence in volleyball players. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  2. Previously Identified Deficiencies Not Corrected in the General Fund Enterprise Business System Program

    Science.gov (United States)

    2011-06-15

    Army AAA Report No. A-2009-0226- FFM , “Examination of Federal Financial Management Improvement Act Compliance - Test Validation General Fund Enterprise...Business System Release 1.2,” September 30, 2009 AAA Report No. A-2009-0231- FFM , “General Fund Enterprise Business System - Federal Financial...Management Improvement Act Compliance Examination of Release 1.3 Functionality,” September 30, 2009 AAA Report No. A-2009-0232- FFM , “General Fund

  3. 77 FR 14594 - Additions to the Identifying Information for an Individual Previously Designated Pursuant to the...

    Science.gov (United States)

    2012-03-12

    ..., Distrito Federal, Mexico; c/o PARQUES TEMATICOS S.A., Medellin, Colombia; c/o PROMO RAIZ S.A., Medellin... GRANADA, S.A. DE C.V., Mexico City, Distrito Federal, Mexico; c/o PARQUES TEMATICOS S.A., Medellin...

  4. Preliminary Site Characterization Report, Rulsion Site, Colorado

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-08-01

    This report is a summary of environmental information gathered during a review of the documents pertaining to Project Rulison and interviews with personnel who worked on the project. Project Rulison was part of Operation Plowshare (a program designed to explore peaceful uses for nuclear devices). The project consisted of detonating a 43-kiloton nuclear device on September 10, 1969, in western Colorado to stimulate natural gas production. Following the detonation, a reentry well was drilled and several gas production tests were conducted. The reentry well was shut-in after the last gas production test and was held in standby condition until the general cleanup was undertaken in 1972. A final cleanup was conducted after the emplacement and testing wells were plugged in 1976. However, some surface radiologic contamination resulted from decontamination of the drilling equipment and fallout from the gas flaring during drilling operations. With the exception of the drilling effluent pond, all surface contamination at the Rulison Site was removed during the cleanup operations. All mudpits and other excavations were backfilled, and both upper and lower drilling pads were leveled and dressed. This report provides information regarding known or suspected areas of contamination, previous cleanup activities, analytical results, a review of the regulatory status, the site`s physical environment, and future recommendations for Project Ruhson. Based on this research, several potential areas of contamination have been identified. These include the drilling effluent pond and mudpits used during drilling operations. In addition, contamination could migrate in the gas horizon.

  5. 77 FR 70176 - Previous Participation Certification

    Science.gov (United States)

    2012-11-23

    ... participants' previous participation in government programs and ensure that the past record is acceptable prior... information is designed to be 100 percent automated and digital submission of all data and certifications is... government programs and ensure that the past record is acceptable prior to granting approval to participate...

  6. On the Tengiz petroleum deposit previous study

    International Nuclear Information System (INIS)

    Nysangaliev, A.N.; Kuspangaliev, T.K.

    1997-01-01

    Tengiz petroleum deposit previous study is described. Some consideration about structure of productive formation, specific characteristic properties of petroleum-bearing collectors are presented. Recommendation on their detail study and using of experience on exploration and development of petroleum deposit which have analogy on most important geological and industrial parameters are given. (author)

  7. Subsequent pregnancy outcome after previous foetal death

    NARCIS (Netherlands)

    Nijkamp, J. W.; Korteweg, F. J.; Holm, J. P.; Timmer, A.; Erwich, J. J. H. M.; van Pampus, M. G.

    Objective: A history of foetal death is a risk factor for complications and foetal death in subsequent pregnancies as most previous risk factors remain present and an underlying cause of death may recur. The purpose of this study was to evaluate subsequent pregnancy outcome after foetal death and to

  8. The job satisfaction of principals of previously disadvantaged schools

    African Journals Online (AJOL)

    The aim of this study was to identify influences on the job satisfaction of previously disadvantaged ..... I am still riding the cloud … I hope it lasts. .... as a way of creating a climate and culture in schools where individuals are willing to explore.

  9. Rapid fish stock depletion in previously unexploited seamounts: the ...

    African Journals Online (AJOL)

    Rapid fish stock depletion in previously unexploited seamounts: the case of Beryx splendens from the Sierra Leone Rise (Gulf of Guinea) ... A spectral analysis and red-noise spectra procedure (REDFIT) algorithm was used to identify the red-noise spectrum from the gaps in the observed time-series of catch per unit effort by ...

  10. The job satisfaction of principals of previously disadvantaged schools

    African Journals Online (AJOL)

    The aim of this study was to identify influences on the job satisfaction of previously disadvantaged school principals in North-West Province. Evans's theory of job satisfaction, morale and motivation was useful as a conceptual framework. A mixedmethods explanatory research design was important in discovering issues with ...

  11. Subsequent childbirth after a previous traumatic birth.

    Science.gov (United States)

    Beck, Cheryl Tatano; Watson, Sue

    2010-01-01

    Nine percent of new mothers in the United States who participated in the Listening to Mothers II Postpartum Survey screened positive for meeting the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition criteria for posttraumatic stress disorder after childbirth. Women who have had a traumatic birth experience report fewer subsequent children and a longer length of time before their second baby. Childbirth-related posttraumatic stress disorder impacts couples' physical relationship, communication, conflict, emotions, and bonding with their children. The purpose of this study was to describe the meaning of women's experiences of a subsequent childbirth after a previous traumatic birth. Phenomenology was the research design used. An international sample of 35 women participated in this Internet study. Women were asked, "Please describe in as much detail as you can remember your subsequent pregnancy, labor, and delivery following your previous traumatic birth." Colaizzi's phenomenological data analysis approach was used to analyze the stories of the 35 women. Data analysis yielded four themes: (a) riding the turbulent wave of panic during pregnancy; (b) strategizing: attempts to reclaim their body and complete the journey to motherhood; (c) bringing reverence to the birthing process and empowering women; and (d) still elusive: the longed-for healing birth experience. Subsequent childbirth after a previous birth trauma has the potential to either heal or retraumatize women. During pregnancy, women need permission and encouragement to grieve their prior traumatic births to help remove the burden of their invisible pain.

  12. Identification of sites within the Palo Duro Basin. Volume 1. Palo Duro Location A

    International Nuclear Information System (INIS)

    1984-11-01

    This three-volume document narrows to two sites for continued investigations for potential nuclear waste repository sites in the Palo Duro Basin of the Texas Panhandle. Volume 1 narrows a site previously identified in Deaf Smith County, Texas; Volume 2 narrows a site previously identified in Swisher County, Texas; and Volume 3 contains responses to comments received regarding the drafts of Volumes 1 and 2 (BMI/ONWI-531). These volumes discuss the methodology and logic used as well as the results that narrowed these sites. Each of the 10 site performance criteria was divided into descriptors related to site performance characteristics. Each descriptor was evaluated by a systematic logic to determine if it could be used as a discriminator. Then more- and less-preferred areas for groups of discriminators were defined and composite maps were prepared and evaluated to identify the sites

  13. Identification of sites within the Palo Duro Basin. Volume 2. Palo Duro Location B

    International Nuclear Information System (INIS)

    1984-11-01

    This three-volume document narrows to two sites for continued investigations for potential nuclear waste repository sites in the Palo Duro Basin of the Texas Panhandle. Volume 1 narrows a site previously identified in Deaf Smith County, Texas; Volume 2 narrows a site previously identified in Swisher County, Texas; and Volume 3 contains responses to comments received regarding the drafts of Volumes 1 and 2 (BMI/ONWI-531). These volumes discuss the methodology and logic used as well as the results that narrowed these sites. Each of the 10 site performance criteria was divided into descriptors related to site performance characteristics. Each descriptor was evaluated by a systematic logic to determine if it could be used as a discriminator. Then more- and less-preferred areas for groups of discriminators were defined and composite maps were prepared and evaluated to identify the sites

  14. Managing previously disposed waste to today's standards

    International Nuclear Information System (INIS)

    1990-01-01

    A Radioactive Waste Management Complex (RWMC) was established at the Idaho National Engineering Laboratory (INEL) in 1952 for controlled disposal of radioactive waste generated at the INEL. Between 1954 and 1970 waste characterized by long lived, alpha emitting radionuclides from the Rocky Flats Plant was also buried at this site. Migration of radionuclides and other hazardous substances from the buried Migration of radionuclides and other hazardous substances from the buried waste has recently been detected. A Buried Waste Program (BWP) was established to manage cleanup of the buried waste. This program has four objectives: (1) determine contaminant sources, (2) determine extent of contamination, (3) mitigate migration, and (4) recommend an alternative for long term management of the waste. Activities designed to meet these objectives have been under way since the inception of the program. The regulatory environment governing these activities is evolving. Pursuant to permitting activities under the Resource Conservation and Recovery Act (RCRA), the Department of Energy (DOE) and the Environmental Protection Agency (EPA) entered into a Consent Order Compliance Agreement (COCA) for cleanup of past practice disposal units at the INEL. Subsequent to identification of the RWMC as a release site, cleanup activities proceeded under dual regulatory coverage of RCRA and the Atomic Energy Act. DOE, EPA, and the State of Idaho are negotiating a RCRA/Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) Interagency Agreement (IAG) for management of waste disposal sites at the INEL as a result of the November 1989 listing of the INEL on the National Priority List (NPL). Decision making for selection of cleanup technology will be conducted under the CERCLA process supplemented as required to meet the requirements of the National Environmental Policy Act (NEPA). 7 figs

  15. Environmental Modeling, The Buffer Priority layers for Nitrogen Removal identify priority forest/grass buffer sites by subwatershed. Land use, hydrology, soil, and landscape characteristics were analyzed to rank opportunities with high nitrogen removal potential., Published in 2014, Smaller than 1:100000 scale, Maryland Department of Natural Resources (DNR).

    Data.gov (United States)

    NSGIC Education | GIS Inventory — Environmental Modeling dataset current as of 2014. The Buffer Priority layers for Nitrogen Removal identify priority forest/grass buffer sites by subwatershed. Land...

  16. Nuclear power plant site selection: a case study

    International Nuclear Information System (INIS)

    Lugasi, Y.; Mehrez, A.; Sinuany-Stern, Z.

    1985-01-01

    Selecting the site for a nuclear power plant involves the evaluation of numerous criteria and the professional judgment of various experts. The Israel Atomic Energy Commission has been concerned with the problem of selecting a site for a nuclear power station. Previous studies have been performed by the commission to identify potential sites. There were initial screenings where potential sites were chosen according to various minimal criteria and international standards. Only sites that met all the criteria were chosen. A study was made to find the most preferred site among the potential sites that met all the criteria. Two mathematical approaches were used: Keeney's multiattribute utility function and Saaty's eigenvalue prioritization technique. Both models ranked the same site as the most desirable; however, the models differed in their ranking of the other sites

  17. Drupal 7 Multilingual Sites

    CERN Document Server

    Pol, Kristen

    2012-01-01

    A practical book with plenty of screenshots to guide you through the many features of multilingual Drupal. A demo ecommerce site is provided if you want to practice on a sample site, although you can apply the techniques learnt in the book directly to your site too. Any Drupal users who know the basics of building a Drupal site and are familiar with the Drupal UI, will benefit from this book. No previous knowledge of localization or internationalization is required.

  18. Books average previous decade of economic misery.

    Science.gov (United States)

    Bentley, R Alexander; Acerbi, Alberto; Ormerod, Paul; Lampos, Vasileios

    2014-01-01

    For the 20(th) century since the Depression, we find a strong correlation between a 'literary misery index' derived from English language books and a moving average of the previous decade of the annual U.S. economic misery index, which is the sum of inflation and unemployment rates. We find a peak in the goodness of fit at 11 years for the moving average. The fit between the two misery indices holds when using different techniques to measure the literary misery index, and this fit is significantly better than other possible correlations with different emotion indices. To check the robustness of the results, we also analysed books written in German language and obtained very similar correlations with the German economic misery index. The results suggest that millions of books published every year average the authors' shared economic experiences over the past decade.

  19. Books Average Previous Decade of Economic Misery

    Science.gov (United States)

    Bentley, R. Alexander; Acerbi, Alberto; Ormerod, Paul; Lampos, Vasileios

    2014-01-01

    For the 20th century since the Depression, we find a strong correlation between a ‘literary misery index’ derived from English language books and a moving average of the previous decade of the annual U.S. economic misery index, which is the sum of inflation and unemployment rates. We find a peak in the goodness of fit at 11 years for the moving average. The fit between the two misery indices holds when using different techniques to measure the literary misery index, and this fit is significantly better than other possible correlations with different emotion indices. To check the robustness of the results, we also analysed books written in German language and obtained very similar correlations with the German economic misery index. The results suggest that millions of books published every year average the authors' shared economic experiences over the past decade. PMID:24416159

  20. Identifying Functional Neighborhoods within the Cell Nucleus: Proximity Analysis of Early S-Phase Replicating Chromatin Domains to Sites of Transcription, RNA Polymerase II, HP1γ, Matrin 3 and SAF-A

    Science.gov (United States)

    Malyavantham, Kishore S; Bhattacharya, Sambit; Barbeitos, Marcos; Mukherjee, Lopamudra; Xu, Jinhui; Fackelmayer, Frank O; Berezney, Ronald

    2009-01-01

    Higher order chromatin organization in concert with epigenetic regulation is a key process that determines gene expression at the global level. The organization of dynamic chromatin domains and their associated protein factors is intertwined with nuclear function to create higher levels of functional zones within the cell nucleus. As a step towards elucidating the organization and dynamics of these functional zones, we have investigated the spatial proximities among a constellation of functionally related sites that are found within euchromatic regions of the cell nucleus including: HP1γ, nascent transcript sites (TS), active DNA replicating sites in early S phase (PCNA) and RNA polymerase II sites. We report close associations among these different sites with proximity values specific for each combination. Analysis of matrin 3 and SAF-A sites demonstrates that these nuclear matrix proteins are highly proximal with the functionally related sites as well as to each other and display closely aligned and overlapping regions following application of the minimal spanning tree (MST) algorithm to visualize higher order network-like patterns. Our findings suggest that multiple factors within the nuclear microenvironment collectively form higher order combinatorial arrays of function. We propose a model for the organization of these functional neighborhoods which takes into account the proximity values of the individual sites and their spatial organization within the nuclear architecture. PMID:18618731

  1. Underestimation of Severity of Previous Whiplash Injuries

    Science.gov (United States)

    Naqui, SZH; Lovell, SJ; Lovell, ME

    2008-01-01

    INTRODUCTION We noted a report that more significant symptoms may be expressed after second whiplash injuries by a suggested cumulative effect, including degeneration. We wondered if patients were underestimating the severity of their earlier injury. PATIENTS AND METHODS We studied recent medicolegal reports, to assess subjects with a second whiplash injury. They had been asked whether their earlier injury was worse, the same or lesser in severity. RESULTS From the study cohort, 101 patients (87%) felt that they had fully recovered from their first injury and 15 (13%) had not. Seventy-six subjects considered their first injury of lesser severity, 24 worse and 16 the same. Of the 24 that felt the violence of their first accident was worse, only 8 had worse symptoms, and 16 felt their symptoms were mainly the same or less than their symptoms from their second injury. Statistical analysis of the data revealed that the proportion of those claiming a difference who said the previous injury was lesser was 76% (95% CI 66–84%). The observed proportion with a lesser injury was considerably higher than the 50% anticipated. CONCLUSIONS We feel that subjects may underestimate the severity of an earlier injury and associated symptoms. Reasons for this may include secondary gain rather than any proposed cumulative effect. PMID:18201501

  2. [Electronic cigarettes - effects on health. Previous reports].

    Science.gov (United States)

    Napierała, Marta; Kulza, Maksymilian; Wachowiak, Anna; Jabłecka, Katarzyna; Florek, Ewa

    2014-01-01

    Currently very popular in the market of tobacco products have gained electronic cigarettes (ang. E-cigarettes). These products are considered to be potentially less harmful in compared to traditional tobacco products. However, current reports indicate that the statements of the producers regarding to the composition of the e- liquids not always are sufficient, and consumers often do not have reliable information on the quality of the product used by them. This paper contain a review of previous reports on the composition of e-cigarettes and their impact on health. Most of the observed health effects was related to symptoms of the respiratory tract, mouth, throat, neurological complications and sensory organs. Particularly hazardous effects of the e-cigarettes were: pneumonia, congestive heart failure, confusion, convulsions, hypotension, aspiration pneumonia, face second-degree burns, blindness, chest pain and rapid heartbeat. In the literature there is no information relating to passive exposure by the aerosols released during e-cigarette smoking. Furthermore, the information regarding to the use of these products in the long term are not also available.

  3. Superfund and Toxic Release Inventory Sites - MDC_ContaminatedSite

    Data.gov (United States)

    NSGIC Local Govt | GIS Inventory — A point feature class of open DERM Contaminated sites - see phase code for status of site. Contaminated sites identifies properties where environmental contamination...

  4. SAFEGUARDS ENVELOPE: PREVIOUS WORK AND EXAMPLES

    International Nuclear Information System (INIS)

    Metcalf, Richard; Bevill, Aaron; Charlton, William; Bean, Robert

    2008-01-01

    The future expansion of nuclear power will require not just electricity production but fuel cycle facilities such as fuel fabrication and reprocessing plants. As large reprocessing facilities are built in various states, they must be built and operated in a manner to minimize the risk of nuclear proliferation. Process monitoring has returned to the spotlight as an added measure that can increase confidence in the safeguards of special nuclear material (SNM). Process monitoring can be demonstrated to lengthen the allowable inventory period by reducing accountancy requirements, and to reduce the false positive indications. The next logical step is the creation of a Safeguards Envelope, a set of operational parameters and models to maximize anomaly detection and inventory period by process monitoring while minimizing operator impact and false positive rates. A brief example of a rudimentary Safeguards Envelope is presented, and shown to detect synthetic diversions overlaying a measured processing plant data set. This demonstration Safeguards Envelope is shown to increase the confidence that no SNM has been diverted with minimal operator impact, even though it is based on an information sparse environment. While the foundation on which a full Safeguards Envelope can be built has been presented in historical demonstrations of process monitoring, several requirements remain yet unfulfilled. Future work will require reprocessing plant transient models, inclusion of 'non-traditional' operating data, and exploration of new methods of identifying subtle events in transient processes

  5. Olkiluoto site description 2006

    International Nuclear Information System (INIS)

    Andersson, J.; Ahokas, H.; Hudson, J.A.

    2007-03-01

    subjective criteria are used for identifying faults; Regarding the rock mechanics description, presented in Chapter 5, additional data have been assessed and the overall level of rock mechanics understanding has increased compared with previous model versions; A new hydrogeological model has been developed, which is presented in Chapter 6, which places more emphasis on the hydraulic data. Pressure anomalies are now stronger drivers for including hydraulic zones in the model and the number of explicit uncertain cases is greater; The hydrogeochemical description, presented in Chapter 7, is consistent with the previous model and there is an increased level of internal consistency in the hydrogeochemical understanding. Information on gases and understanding of their origin has increased significantly. Based on these descriptions, the report also makes a second set of predictions in Chapter 9 concerning the expected geology and rock mechanics properties to be found during the excavation of the ONKALO and also predicts the hydrogeological and hydrogeochemical impacts of these excavations. Two types of predictions are made: type A predictions, that use only the latest version of the overall Site Model; and type B predictions, that also use all the data from the tunnel, which are derived from activities, such as tunnel mapping and Pilot holes. The Site Descriptive Modelling involves uncertainties and it is necessary to assess the confidence in such modelling. This has been assessed through special protocols in a technical auditing exercise, which is presented in Chapter 10. These protocols investigate whether all data have been considered and understood; where the uncertainties lie and what the potential is for alternative interpretations; whether there is sufficient consistency between disciplines and consistency with the past evolution of the site; as well as comparisons with previous model versions. Chapter 11 concludes that, overall, the uncertainty and confidence assessment

  6. Corneal perforation after conductive keratoplasty with previous refractive surgery.

    Science.gov (United States)

    Kymionis, George D; Titze, Patrik; Markomanolakis, Marinos M; Aslanides, Ioannis M; Pallikaris, Ioannis G

    2003-12-01

    A 56-year-old woman had conductive keratoplasty (CK) for residual hyperopia and astigmatism. Three years before the procedure, the patient had arcuate keratotomy, followed by laser in situ keratomileusis 2 years later for high astigmatism correction in both eyes. During CK, a corneal perforation occurred in the right eye; during the postoperative examination, an iris perforation and anterior subcapsule opacification were seen beneath the perforation site. The perforation was managed with a bandage contact lens and an antibiotic-steroid ointment; it had a negative Seidel sign by the third day. The surgery in the left eye was uneventful. Three months after the procedure, the uncorrected visual acuity was 20/32 and the best corrected visual acuity 20/20 in both eyes with a significant improvement in corneal topography. Care must be taken to prevent CK-treated spots from coinciding with areas in the corneal stroma that might have been altered by previous refractive procedures.

  7. Retrospective analysis on malignant calcification previously misdiagnosed as benign on screening mammography

    International Nuclear Information System (INIS)

    Ha, Su Min; Cha, Joo Hee; Kim, Hak Hee; Shin, Hee Jung; Chae, Eun Young; Choi, Woo Jung

    2017-01-01

    The purpose of our study was to investigate the morphology and distribution of calcifications initially interpreted as benign or probably benign, but proven to be malignant by subsequent stereotactic biopsy, and to identify the reason for misinterpretation or underestimation at the initial diagnosis. Out of 567 women who underwent stereotactic biopsy for calcifications at our hospital between January 2012 and December 2014, 167 women were diagnosed with malignancy. Forty-six of these 167 women had previous mammography assessed as benign or probably benign which was changed to suspicious malignancy on follow-up mammography. Of these 46 women, three women with biopsy-proven benign calcifications at the site of subsequent cancer were excluded, and 43 patients were finally included. The calcifications (morphology, distribution, extent, associated findings) in the previous and follow-up mammography examinations were analyzed according to the Breast Imaging Reporting and Data System (BI-RADS) lexicon and assessment category. We classified the patients into two groups: 1) group A patients who were still retrospectively re-categorized as less than or equal to BI-RADS 3 and 2) group B patients who were re-categorized as equal to or higher than BI-RADS 4a and whose results should have prompted previous diagnostic assessment. In the follow-up mammography examinations, change in calcification morphology (n = 27, 63%) was the most frequent cause of assessment change. The most frequent previous mammographic findings of malignant calcification were amorphous morphology (n = 26, 60%) and grouped distribution (n = 36, 84%). The most frequent calcification findings at reassessment were amorphous morphology (n = 4, 9%), fine pleomorphic calcification (n = 30, 70%), grouped distribution (n = 23, 53%), and segmental calcification (n = 12, 28%). There were 33 (77%) patients in group A, and 10 patients (23%) in group B. Amorphous morphology and grouped distribution were the most frequent

  8. Retrospective analysis on malignant calcification previously misdiagnosed as benign on screening mammography

    Energy Technology Data Exchange (ETDEWEB)

    Ha, Su Min [Dept. of Radiology, Research Institute of Radiology, Chung Ang University Hospital, Seoul(Korea, Republic of); Cha, Joo Hee; Kim, Hak Hee; Shin, Hee Jung; Chae, Eun Young; Choi, Woo Jung [Dept. of Radiology, Research Institute of Radiology, Asan Medical Center, University of Ulsan College of Medicine, Seoul (Korea, Republic of)

    2017-04-15

    The purpose of our study was to investigate the morphology and distribution of calcifications initially interpreted as benign or probably benign, but proven to be malignant by subsequent stereotactic biopsy, and to identify the reason for misinterpretation or underestimation at the initial diagnosis. Out of 567 women who underwent stereotactic biopsy for calcifications at our hospital between January 2012 and December 2014, 167 women were diagnosed with malignancy. Forty-six of these 167 women had previous mammography assessed as benign or probably benign which was changed to suspicious malignancy on follow-up mammography. Of these 46 women, three women with biopsy-proven benign calcifications at the site of subsequent cancer were excluded, and 43 patients were finally included. The calcifications (morphology, distribution, extent, associated findings) in the previous and follow-up mammography examinations were analyzed according to the Breast Imaging Reporting and Data System (BI-RADS) lexicon and assessment category. We classified the patients into two groups: 1) group A patients who were still retrospectively re-categorized as less than or equal to BI-RADS 3 and 2) group B patients who were re-categorized as equal to or higher than BI-RADS 4a and whose results should have prompted previous diagnostic assessment. In the follow-up mammography examinations, change in calcification morphology (n = 27, 63%) was the most frequent cause of assessment change. The most frequent previous mammographic findings of malignant calcification were amorphous morphology (n = 26, 60%) and grouped distribution (n = 36, 84%). The most frequent calcification findings at reassessment were amorphous morphology (n = 4, 9%), fine pleomorphic calcification (n = 30, 70%), grouped distribution (n = 23, 53%), and segmental calcification (n = 12, 28%). There were 33 (77%) patients in group A, and 10 patients (23%) in group B. Amorphous morphology and grouped distribution were the most frequent

  9. Incidence of Acneform Lesions in Previously Chemically Damaged Persons-2004

    Directory of Open Access Journals (Sweden)

    N Dabiri

    2008-04-01

    Full Text Available ABSTRACT: Introduction & Objective: Chemical gas weapons especially nitrogen mustard which was used in Iraq-Iran war against Iranian troops have several harmful effects on skin. Some other chemical agents also can cause acne form lesions on skin. The purpose of this study was to compare the incidence of acneform in previously chemically damaged soldiers and non chemically damaged persons. Materials & Methods: In this descriptive and analytical study, 180 chemically damaged soldiers, who have been referred to dermatology clinic between 2000 – 2004, and forty non-chemically damaged people, were chosen randomly and examined for acneform lesions. SPSS software was used for statistic analysis of the data. Results: The mean age of the experimental group was 37.5 ± 5.2 and that of the control group was 38.7 ± 5.9 years. The mean percentage of chemical damage in cases was 31 percent and the time after the chemical damage was 15.2 ± 1.1 years. Ninety seven cases (53.9 percent of the subjects and 19 people (47.5 percent of the control group had some degree of acne. No significant correlation was found in incidence, degree of lesions, site of lesions and age of subjects between two groups. No significant correlation was noted between percentage of chemical damage and incidence and degree of lesions in case group. Conclusion: Incidence of acneform lesions among previously chemically injured peoples was not higher than the normal cases.

  10. Discovery of previously unidentified genomic disorders from the duplication architecture of the human genome.

    Science.gov (United States)

    Sharp, Andrew J; Hansen, Sierra; Selzer, Rebecca R; Cheng, Ze; Regan, Regina; Hurst, Jane A; Stewart, Helen; Price, Sue M; Blair, Edward; Hennekam, Raoul C; Fitzpatrick, Carrie A; Segraves, Rick; Richmond, Todd A; Guiver, Cheryl; Albertson, Donna G; Pinkel, Daniel; Eis, Peggy S; Schwartz, Stuart; Knight, Samantha J L; Eichler, Evan E

    2006-09-01

    Genomic disorders are characterized by the presence of flanking segmental duplications that predispose these regions to recurrent rearrangement. Based on the duplication architecture of the genome, we investigated 130 regions that we hypothesized as candidates for previously undescribed genomic disorders. We tested 290 individuals with mental retardation by BAC array comparative genomic hybridization and identified 16 pathogenic rearrangements, including de novo microdeletions of 17q21.31 found in four individuals. Using oligonucleotide arrays, we refined the breakpoints of this microdeletion, defining a 478-kb critical region containing six genes that were deleted in all four individuals. We mapped the breakpoints of this deletion and of four other pathogenic rearrangements in 1q21.1, 15q13, 15q24 and 17q12 to flanking segmental duplications, suggesting that these are also sites of recurrent rearrangement. In common with the 17q21.31 deletion, these breakpoint regions are sites of copy number polymorphism in controls, indicating that these may be inherently unstable genomic regions.

  11. Likelihood of Bone Recurrence in Prior Sites of Metastasis in Patients With High-Risk Neuroblastoma

    Energy Technology Data Exchange (ETDEWEB)

    Polishchuk, Alexei L. [Department of Radiation Oncology, University of California at San Francisco School of Medicine and UCSF Benioff Children' s Hospital, San Francisco, California (United States); Li, Richard [Division of Radiation Oncology, Dana Farber/Boston Children' s Cancer and Blood Disorders Center, Brigham and Women' s Hospital, Harvard Medical School, Boston, Massachusetts (United States); Hill-Kayser, Christine [Department of Radiation Oncology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania (United States); Little, Anthony [Division of Oncology, Children' s Hospital of Philadelphia, Philadelphia, Pennsylvania (United States); Hawkins, Randall A. [Department of Radiology, University of California at San Francisco School of Medicine and UCSF Benioff Children' s Hospital, San Francisco, California (United States); Hamilton, Jeffrey; Lau, Michael [Department of Radiation Oncology, University of California at San Francisco School of Medicine and UCSF Benioff Children' s Hospital, San Francisco, California (United States); Tran, Hung Chi [Division of Hematology/Oncology, Children' s Hospital of Los Angeles, Los Angeles, California (United States); Strahlendorf, Caron [Division of Hematology and Oncology, Department of Pediatrics, The University of British Columbia, Vancouver, British Columbia (Canada); Lemons, Richard S. [Division of Pediatric Hematology/Oncology, University of Utah School of Medicine, Salt Lake City, Utah (United States); Weinberg, Vivian [Department of Radiation Oncology, University of California at San Francisco School of Medicine and UCSF Benioff Children' s Hospital, San Francisco, California (United States); Matthay, Katherine K.; DuBois, Steven G. [Department of Pediatrics, University of California at San Francisco School of Medicine and UCSF Benioff Children' s Hospital, San Francisco, California (United States); and others

    2014-07-15

    Purpose/Objectives: Despite recent improvements in outcomes, 40% of children with high-risk neuroblastoma will experience relapse, facing a guarded prognosis for long-term cure. Whether recurrences are at new sites or sites of original disease may guide decision making during initial therapy. Methods and Materials: Eligible patients were retrospectively identified from institutional databases at first metastatic relapse of high-risk neuroblastoma. Included patients had disease involving metaiodobenzylguanidine (MIBG)-avid metastatic sites at diagnosis and first relapse, achieved a complete or partial response with no more than one residual MIBG-avid site before first relapse, and received no total body irradiation or therapy with {sup 131}I-MIBG before first relapse. Anatomically defined metastatic sites were tracked from diagnosis through first relapse to determine tendency of disease to recur at previously involved versus uninvolved sites and to assess whether this pattern was influenced by site irradiation. Results: Of 159 MIBG-avid metastatic sites identified among 43 patients at first relapse, 131 (82.4%) overlapped anatomically with the set of 525 sites present at diagnosis. This distribution was similar for bone sites, but patterns of relapse were more varied for the smaller subset of soft tissue metastases. Among all metastatic sites at diagnosis in our subsequently relapsed patient cohort, only 3 of 19 irradiated sites (15.8%) recurred as compared with 128 of 506 (25.3%) unirradiated sites. Conclusions: Metastatic bone relapse in neuroblastoma usually occurs at anatomic sites of previous disease. Metastatic sites identified at diagnosis that did not receive radiation during frontline therapy appeared to have a higher risk of involvement at first relapse relative to previously irradiated metastatic sites. These observations support the current paradigm of irradiating metastases that persist after induction chemotherapy in high-risk patients. Furthermore

  12. Accessibility and content of individualized adult reconstructive hip and knee/musculoskeletal oncology fellowship web sites

    Directory of Open Access Journals (Sweden)

    Bradley L. Young, MD

    2018-06-01

    Conclusions: Several programs participating in the combined Adult Reconstructive Hip and Knee/Musculoskeletal Oncology Fellowship Match did not have accessible web sites. Of the web sites that were accessible, none contained comprehensive information and the majority lacked information that has been previously identified as being important to perspective applicants.

  13. Internally readable identifying tag

    International Nuclear Information System (INIS)

    Jefferts, K.B.; Jefferts, E.R.

    1980-01-01

    A method of identifying non-metallic objects by means of X-ray equipment is described in detail. A small metal pin with a number of grooves cut in a pre-determined equi-spaced pattern is implanted into the non-metallic object and by decoding the groove patterns using X-ray equipment, the object is uniquely identified. A specific example of such an application is in studying the migratory habits of fish. The pin inserted into the snout of the fish is 0.010 inch in diameter, 0.040 inch in length with 8 possible positions for grooves if spaced 0.005 inch apart. With 6 of the groove positions available for data, the capacity is 2 6 or 64 combinations; clearly longer pins would increase the data capacity. This method of identification is a major advance over previous techniques which necessitated destruction of the fish in order to recover the identification tag. (UK)

  14. Thermophysical Properties of the Phoenix Mars Landing Site Study Regions

    Science.gov (United States)

    Putzig, N. E.; Mellon, M. T.; Golombek, M. P.; Arvidson, R. E.

    2006-03-01

    Analysis of Phoenix Mars study regions places 4 of 5 in a previously-identified duricrust-dominated thermophysical unit which also contains the Viking and Spirit landing sites. Extrapolation of lander-observed properties to the study regions may be complicated by surface heterogeneity.

  15. Second malignancies in high-dose areas of previous tumor radiotherapy

    Energy Technology Data Exchange (ETDEWEB)

    Welte, Birgitta; Suhr, Peter; Bottke, Dirk; Bartkowiak, Detlef; Wiegel, Thomas [Dept. of Radiotherapy and Radiation Oncology, Univ. of Ulm (Germany); Doerr, Wolfgang [Dept. of Radiotherapy and Radiation Oncology, Radiobiology Lab., Univ. of Technology Dresden (Germany); Trott, Klaus Ruediger [UCL Cancer Centre, Univ. Coll. London (United Kingdom)

    2010-03-15

    Purpose: To characterize second tumors that developed in or near the high-dose areas of a previous radiotherapy, regarding their frequency, entities, latency, and dose dependence. Patients and Methods: 9,995/15,449 tumor patients of the Radiation Oncology Department in Ulm, Germany, treated between 1981 and 2003, survived at least 1 year after radiotherapy. By long-term follow-up and review of treatment documentation, 100 of them were identified who developed an independent second cancer in or near the irradiated first tumor site. Results: Major primary malignancies were breast cancer (27%), lymphoma (24%), and pelvic gynecologic tumors (17%). Main second tumors were carcinomas of the upper (18%) and lower (12%) gastrointestinal tract, head and neck tumors (10%), lymphoma (10%), breast cancer (9%), sarcoma (9%), and lung cancer (8%). Overall median second tumor latency was 7.4 years (1-42 years). For colorectal cancer it was 3.5 and for leukemia 4.3 years, but for sarcoma 11.7 and for breast cancer 17.1 years. The relatively frequent second tumors of the upper gastrointestinal tract were associated with median radiation doses of 24 Gy. By contrast, second colorectal cancer and sarcoma developed after median doses of 50 Gy. Conclusion: The 5- and 15-year probability to develop a histopathologically independent second tumor in or near the irradiated first tumor site, i.e., after intermediate or high radiation doses, was 0.5% and 2.2%, respectively. To identify potentially radiogenic second malignancies, a follow-up far beyond 5 years is mandatory. The incidence and potential dose-response relationship intermediate will be analyzed by a case-case and a case-control study of the Ulm data. (orig.)

  16. Detection of secondary binding sites in proteins using fragment screening.

    Science.gov (United States)

    Ludlow, R Frederick; Verdonk, Marcel L; Saini, Harpreet K; Tickle, Ian J; Jhoti, Harren

    2015-12-29

    Proteins need to be tightly regulated as they control biological processes in most normal cellular functions. The precise mechanisms of regulation are rarely completely understood but can involve binding of endogenous ligands and/or partner proteins at specific locations on a protein that can modulate function. Often, these additional secondary binding sites appear separate to the primary binding site, which, for example for an enzyme, may bind a substrate. In previous work, we have uncovered several examples in which secondary binding sites were discovered on proteins using fragment screening approaches. In each case, we were able to establish that the newly identified secondary binding site was biologically relevant as it was able to modulate function by the binding of a small molecule. In this study, we investigate how often secondary binding sites are located on proteins by analyzing 24 protein targets for which we have performed a fragment screen using X-ray crystallography. Our analysis shows that, surprisingly, the majority of proteins contain secondary binding sites based on their ability to bind fragments. Furthermore, sequence analysis of these previously unknown sites indicate high conservation, which suggests that they may have a biological function, perhaps via an allosteric mechanism. Comparing the physicochemical properties of the secondary sites with known primary ligand binding sites also shows broad similarities indicating that many of the secondary sites may be druggable in nature with small molecules that could provide new opportunities to modulate potential therapeutic targets.

  17. Twelve previously unknown phage genera are ubiquitous in global oceans.

    Science.gov (United States)

    Holmfeldt, Karin; Solonenko, Natalie; Shah, Manesh; Corrier, Kristen; Riemann, Lasse; Verberkmoes, Nathan C; Sullivan, Matthew B

    2013-07-30

    Viruses are fundamental to ecosystems ranging from oceans to humans, yet our ability to study them is bottlenecked by the lack of ecologically relevant isolates, resulting in "unknowns" dominating culture-independent surveys. Here we present genomes from 31 phages infecting multiple strains of the aquatic bacterium Cellulophaga baltica (Bacteroidetes) to provide data for an underrepresented and environmentally abundant bacterial lineage. Comparative genomics delineated 12 phage groups that (i) each represent a new genus, and (ii) represent one novel and four well-known viral families. This diversity contrasts the few well-studied marine phage systems, but parallels the diversity of phages infecting human-associated bacteria. Although all 12 Cellulophaga phages represent new genera, the podoviruses and icosahedral, nontailed ssDNA phages were exceptional, with genomes up to twice as large as those previously observed for each phage type. Structural novelty was also substantial, requiring experimental phage proteomics to identify 83% of the structural proteins. The presence of uncommon nucleotide metabolism genes in four genera likely underscores the importance of scavenging nutrient-rich molecules as previously seen for phages in marine environments. Metagenomic recruitment analyses suggest that these particular Cellulophaga phages are rare and may represent a first glimpse into the phage side of the rare biosphere. However, these analyses also revealed that these phage genera are widespread, occurring in 94% of 137 investigated metagenomes. Together, this diverse and novel collection of phages identifies a small but ubiquitous fraction of unknown marine viral diversity and provides numerous environmentally relevant phage-host systems for experimental hypothesis testing.

  18. Proteomics Analysis Reveals Previously Uncharacterized Virulence Factors in Vibrio proteolyticus

    Directory of Open Access Journals (Sweden)

    Ann Ray

    2016-07-01

    Full Text Available Members of the genus Vibrio include many pathogens of humans and marine animals that share genetic information via horizontal gene transfer. Hence, the Vibrio pan-genome carries the potential to establish new pathogenic strains by sharing virulence determinants, many of which have yet to be characterized. Here, we investigated the virulence properties of Vibrio proteolyticus, a Gram-negative marine bacterium previously identified as part of the Vibrio consortium isolated from diseased corals. We found that V. proteolyticus causes actin cytoskeleton rearrangements followed by cell lysis in HeLa cells in a contact-independent manner. In search of the responsible virulence factor involved, we determined the V. proteolyticus secretome. This proteomics approach revealed various putative virulence factors, including active type VI secretion systems and effectors with virulence toxin domains; however, these type VI secretion systems were not responsible for the observed cytotoxic effects. Further examination of the V. proteolyticus secretome led us to hypothesize and subsequently demonstrate that a secreted hemolysin, belonging to a previously uncharacterized clan of the leukocidin superfamily, was the toxin responsible for the V. proteolyticus-mediated cytotoxicity in both HeLa cells and macrophages. Clearly, there remains an armory of yet-to-be-discovered virulence factors in the Vibrio pan-genome that will undoubtedly provide a wealth of knowledge on how a pathogen can manipulate host cells.

  19. Kidnapping Detection and Recognition in Previous Unknown Environment

    Directory of Open Access Journals (Sweden)

    Yang Tian

    2017-01-01

    Full Text Available An unaware event referred to as kidnapping makes the estimation result of localization incorrect. In a previous unknown environment, incorrect localization result causes incorrect mapping result in Simultaneous Localization and Mapping (SLAM by kidnapping. In this situation, the explored area and unexplored area are divided to make the kidnapping recovery difficult. To provide sufficient information on kidnapping, a framework to judge whether kidnapping has occurred and to identify the type of kidnapping with filter-based SLAM is proposed. The framework is called double kidnapping detection and recognition (DKDR by performing two checks before and after the “update” process with different metrics in real time. To explain one of the principles of DKDR, we describe a property of filter-based SLAM that corrects the mapping result of the environment using the current observations after the “update” process. Two classical filter-based SLAM algorithms, Extend Kalman Filter (EKF SLAM and Particle Filter (PF SLAM, are modified to show that DKDR can be simply and widely applied in existing filter-based SLAM algorithms. Furthermore, a technique to determine the adapted thresholds of metrics in real time without previous data is presented. Both simulated and experimental results demonstrate the validity and accuracy of the proposed method.

  20. Hanford Site Infrastructure Plan

    International Nuclear Information System (INIS)

    1990-01-01

    The Hanford Site Infrastructure Plan (HIP) has been prepared as an overview of the facilities, utilities, systems, and services that support all activities on the Hanford Site. Its purpose is three-fold: to examine in detail the existing condition of the Hanford Site's aging utility systems, transportation systems, Site services and general-purpose facilities; to evaluate the ability of these systems to meet present and forecasted Site missions; to identify maintenance and upgrade projects necessary to ensure continued safe and cost-effective support to Hanford Site programs well into the twenty-first century. The HIP is intended to be a dynamic document that will be updated accordingly as Site activities, conditions, and requirements change. 35 figs., 25 tabs

  1. High-Grade Leiomyosarcoma Arising in a Previously Replanted Limb

    Directory of Open Access Journals (Sweden)

    Tiffany J. Pan

    2015-01-01

    Full Text Available Sarcoma development has been associated with genetics, irradiation, viral infections, and immunodeficiency. Reports of sarcomas arising in the setting of prior trauma, as in burn scars or fracture sites, are rare. We report a case of a leiomyosarcoma arising in an arm that had previously been replanted at the level of the elbow joint following traumatic amputation when the patient was eight years old. He presented twenty-four years later with a 10.8 cm mass in the replanted arm located on the volar forearm. The tumor was completely resected and pathology examination showed a high-grade, subfascial spindle cell sarcoma diagnosed as a grade 3 leiomyosarcoma with stage pT2bNxMx. The patient underwent treatment with brachytherapy, reconstruction with a free flap, and subsequently chemotherapy. To the best of our knowledge, this is the first case report of leiomyosarcoma developing in a replanted extremity. Development of leiomyosarcoma in this case could be related to revascularization, scar formation, or chronic injury after replantation. The patient remains healthy without signs of recurrence at three-year follow-up.

  2. Site Features

    Data.gov (United States)

    U.S. Environmental Protection Agency — This dataset consists of various site features from multiple Superfund sites in U.S. EPA Region 8. These data were acquired from multiple sources at different times...

  3. Positive-Unlabeled Learning for Pupylation Sites Prediction

    Directory of Open Access Journals (Sweden)

    Ming Jiang

    2016-01-01

    Full Text Available Pupylation plays a key role in regulating various protein functions as a crucial posttranslational modification of prokaryotes. In order to understand the molecular mechanism of pupylation, it is important to identify pupylation substrates and sites accurately. Several computational methods have been developed to identify pupylation sites because the traditional experimental methods are time-consuming and labor-sensitive. With the existing computational methods, the experimentally annotated pupylation sites are used as the positive training set and the remaining nonannotated lysine residues as the negative training set to build classifiers to predict new pupylation sites from the unknown proteins. However, the remaining nonannotated lysine residues may contain pupylation sites which have not been experimentally validated yet. Unlike previous methods, in this study, the experimentally annotated pupylation sites were used as the positive training set whereas the remaining nonannotated lysine residues were used as the unlabeled training set. A novel method named PUL-PUP was proposed to predict pupylation sites by using positive-unlabeled learning technique. Our experimental results indicated that PUL-PUP outperforms the other methods significantly for the prediction of pupylation sites. As an application, PUL-PUP was also used to predict the most likely pupylation sites in nonannotated lysine sites.

  4. Site decontamination

    International Nuclear Information System (INIS)

    Bicker, A.E.

    1981-01-01

    Among the several DOE sites that have been radiologically decontaminated under the auspices of the Nevada Operations Office are three whose physical characteristics are unique. These are the Tatum Dome Test Site (TDTS) near Hattiesburg, Mississippi; a location of mountainous terrain (Pahute Mesa) on the Nevada Test Site; and the GNOME site near Carlsbad, New Mexico. In each case the contamination, the terrain, and the climate conditions were different. This presentation includes a brief description of each site, the methods used to perform radiological surveys, the logistics required to support the decontamination (including health physics and sample analysis), and the specific techniques used to reduce or remove the contamination

  5. Nevada Test Site Wetlands Assessment

    Energy Technology Data Exchange (ETDEWEB)

    D. J. Hansen

    1997-05-01

    This report identifies 16 Nevada Test Site (NTS) natural water sources that may be classified by the U.S. Army Corps of Engineers (USACE) as jurisdictional wetlands and identifies eight water sources that may be classified as waters of the United States. These water sources are rare, localized habitats on the NTS that are important to regional wildlife and to isolated populations of water tolerant plants and aquatic organisms. No field investigations on the NTS have been conducted in the past to identify those natural water sources which would be protected as rare habitats and which may fall under regulatory authority of the Clean Water Act (CWA) of 1997. This report identifies and summarizes previous studies of NTS natural water sources, and identifies the current DOE management practices related to the protection of NTS wetlands. This report also presents management goals specific for NTS wetlands that incorporate the intent of existing wetlands legislation, the principles of ecosystem management, and the interests of regional land managers and other stakeholders.

  6. The frequency of company-sponsored alcohol brand-related sites on Facebook™-2012.

    Science.gov (United States)

    Nhean, Siphannay; Nyborn, Justin; Hinchey, Danielle; Valerio, Heather; Kinzel, Kathryn; Siegel, Michael; Jernigan, David H

    2014-06-01

    This research provides an estimate of the frequency of company-sponsored alcohol brand-related sites on Facebook™. We conducted a systematic overview of the extent of alcohol brand-related sites on Facebook™ in 2012. We conducted a 2012 Facebook™ search for sites specifically related to 898 alcohol brands across 16 different alcoholic beverage types. Descriptive statistics were produced using Microsoft SQL Server. We identified 1,017 company-sponsored alcohol-brand related sites on Facebook™. Our study advances previous literature by providing a systematic overview of the extent of alcohol brand sites on Facebook™.

  7. Site organization and site arrangement

    International Nuclear Information System (INIS)

    Boissonnet, B.; Macqueron, J.F.

    1976-01-01

    The present paper deals with criteria for the choice of a production unit or power plant site, the organization and development of a site in terms of its particular characteristics and takes into account personnel considerations in site organizations as well as the problem of integrating the architecture into the environment. (RW) [de

  8. The Rocky Flats Environmental Technology Site beryllium characterization project

    International Nuclear Information System (INIS)

    Morrell, D.M.; Miller, J.R.; Allen, D.F.

    1999-01-01

    A site beryllium characterization project was completed at the Rocky Flats Environmental Technology Site (RFETS) in 1997. Information from historical reviews, previous sampling surveys, and a new sampling survey were used to establish a more comprehensive understanding of the locations and levels of beryllium contamination in 35 buildings. A feature of the sampling strategy was to test if process knowledge was a good predictor of where beryllium contamination could be found. Results revealed that this technique was effective at identifying where surface contamination levels might exceed the RFETS smear control level but that it was not effective in identifying where low concentrations of beryllium might be found

  9. Discovery of an All-Pervading Previously Unknown Longitudinal Wave

    Science.gov (United States)

    Wagner, Orvin E.

    2002-04-01

    In 1988 a new species of longitudinal sound like wave was identified in this laboratory. These waves travel through (dark matter filled) vacuum as well as through ordinary matter. So far as is known these waves always appear as standing waves. The data suggest that they organize plants, organize structures in manipulated granular materials, organize planetary systems, and other structures of the universe. They are likely the basis for the beginnings of life and are closely associated with quantum waves. The repeating structures that they produce suggest that they are a basis for fractal structures. Their velocities appear to be a function of the medium as well as the timing of their sources since quantized velocities have been found. 12 years of data collected in this laboratory suggest that the waves are all pervading but they still interact with ordinary matter. These waves apparently provide for the stability of the solar system and probably the whole universe. They interact with gravity within plants, for example, to provide a basis for a plant's response to gravity. See the Wagner web site.

  10. Discovery of an Important Previously Unknown Longitudinal Wave.

    Science.gov (United States)

    Wagner, Orvin

    2002-03-01

    In 1988 a new species of longitudinal sound like wave was identified in this laboratory. These waves travel through (dark matter filled) vacuum as well as through ordinary matter. So far as is known these waves always appear as standing waves. The data suggest that they organize plants, organize structures in manipulated granular materials, organize planetary systems, and other structures of the universe. They are likely the basis for the beginnings of life and are closely associated with quantum waves. The repeating structures that they produce suggest that they are a basis for fractal structures. Their velocities appear to be a function of the medium as well as the timing of their sources since quantized velocities have been found. 12 years of data collected in this laboratory suggest that the waves are all pervading but they still interact with ordinary matter. These waves apparently provide for the stability of the solar system and probably the whole universe. They interact with gravity within plants, for example, to provide a basis for a plant's response to gravity. See the Wagner web site.

  11. NIH Researchers Identify OCD Risk Gene

    Science.gov (United States)

    ... News From NIH NIH Researchers Identify OCD Risk Gene Past Issues / Summer 2006 Table of Contents For ... and Alcoholism (NIAAA) have identified a previously unknown gene variant that doubles an individual's risk for obsessive- ...

  12. Repeat immigration: A previously unobserved source of heterogeneity?

    Science.gov (United States)

    Aradhya, Siddartha; Scott, Kirk; Smith, Christopher D

    2017-07-01

    Register data allow for nuanced analyses of heterogeneities between sub-groups which are not observable in other data sources. One heterogeneity for which register data is particularly useful is in identifying unique migration histories of immigrant populations, a group of interest across disciplines. Years since migration is a commonly used measure of integration in studies seeking to understand the outcomes of immigrants. This study constructs detailed migration histories to test whether misclassified migrations may mask important heterogeneities. In doing so, we identify a previously understudied group of migrants called repeat immigrants, and show that they differ systematically from permanent immigrants. In addition, we quantify the degree to which migration information is misreported in the registers. The analysis is carried out in two steps. First, we estimate income trajectories for repeat immigrants and permanent immigrants to understand the degree to which they differ. Second, we test data validity by cross-referencing migration information with changes in income to determine whether there are inconsistencies indicating misreporting. From the first part of the analysis, the results indicate that repeat immigrants systematically differ from permanent immigrants in terms of income trajectories. Furthermore, income trajectories differ based on the way in which years since migration is calculated. The second part of the analysis suggests that misreported migration events, while present, are negligible. Repeat immigrants differ in terms of income trajectories, and may differ in terms of other outcomes as well. Furthermore, this study underlines that Swedish registers provide a reliable data source to analyze groups which are unidentifiable in other data sources.

  13. Identification of sites for the low-level waste disposal development and demonstration program

    International Nuclear Information System (INIS)

    Ketelle, R.H.; Lee, D.W.

    1988-04-01

    This report presents the results of site selection studies for potential low-level radioactive waste disposal sites on the Oak Ridge Reservation (ORR). Summaries of the site selection procedures used and results of previous site selection studies on the ORR are included. This report includes recommendations of sites for demonstration of shallow land burial using engineered trench designs and demonstration of above-grade disposal using design concepts similar to those used in tumulus disposal. The site selection study, like its predecessor (ORNL/TM-9717, Use of DOE Site Selection Criteria for Screening Low-Level Waste Disposal Sites on the Oak Ridge Reservation), involved application of exclusionary site screening criteria to the region of interest to eliminate unacceptable areas from consideration. Also like the previous study, the region of interest for this study was limited to the Oak Ridge Department of Energy Reservation. Reconnaissance-level environmental data were used in the study, and field inspections of candidate sites were made to verify the available reconnaissance data. Five candidate sites, all underlain by Knox dolomite residuum and bedrock, were identified for possible development of shallow land burial facilities. Of the five candidate sites, the West Chestnut site was judged to be best suited for deployment of the shallow land burial technology. Three candidate sites, all underlain by the Conasauga Group in Bear Creek Valley, were identified for possible development of above-grade disposal technologies. Of the three sites identified, the Central Bear Creek Valley site lying between State Route 95 and Gum Hollow Road was ranked most favorable for deployment of the above-grade disposal technology

  14. Site operations

    International Nuclear Information System (INIS)

    House, W.B.; Ebenhack, D.G.

    1989-01-01

    This chapter is a discussion of the management and operations practices used at the Barnwell Waste Management Facility in Barnwell, SC. The following topics are discussed: (1) Waste receiving and inspection, including manifest and certificates of compliance, radiological surveys, disposition of nonconforming items, and decontamination and disposition of secondary waste streams; (2) Waste disposal, including Title 10 CFR 61 requirements, disposal area evaluations, shipment offloading, container emplacement, and radiation protection; (3) Trench closure, including trench backfilling, trench capping, and permanent markers; (4) Site maintenance and stabilization, including trench maintenance, surface water management, and site closure activities; (5) Site monitoring programs, including operational monitoring, and environmental monitoring program; (6) Personnel training and qualifications, including basic training program, safety training program, special skills training, and physical qualifications; (7) Records management, including waste records, personnel training records, personnel dosimetry records, site monitoring records, trench qualification and construction records, and site drawings and stabilization records; (8) Site security; (9) Emergency response plans; and (10) Quality assurance

  15. Sudden unexpected death in children with a previously diagnosed cardiovascular disorder

    NARCIS (Netherlands)

    Polderman, Florens N.; Cohen, Joeri; Blom, Nico A.; Delhaas, Tammo; Helbing, Wim A.; Lam, Jan; Sobotka-Plojhar, Marta A.; Temmerman, Arno M.; Sreeram, Narayanswani

    2004-01-01

    BACKGROUND: It is known that children with previously diagnosed heart defects die suddenly. The causes of death are often unknown. OBJECTIVE: The aim of the study was to identify all infants and children within the Netherlands with previously diagnosed heart disease who had a sudden unexpected death

  16. Sudden unexpected death in children with a previously diagnosed cardiovascular disorder

    NARCIS (Netherlands)

    Polderman, F.N.; Cohen, Joeri; Blom, N.A.; Delhaas, T.; Helbing, W.A.; Lam, J.; Sobotka-Plojhar, M.A.; Temmerman, Arno M.; Sreeram, N.

    2004-01-01

    Background: It is known that children with previously diagnosed heart defects die suddenly. The causes of death are often unknown. Objective: The aim of the study was to identify all infants and children within the Netherlands with previously diagnosed heart disease who had a sudden unexpected death

  17. Impact of previously disadvantaged land-users on sustainable ...

    African Journals Online (AJOL)

    Impact of previously disadvantaged land-users on sustainable agricultural ... about previously disadvantaged land users involved in communal farming systems ... of input, capital, marketing, information and land use planning, with effect on ...

  18. Eight previously unidentified mutations found in the OA1 ocular albinism gene

    Directory of Open Access Journals (Sweden)

    Dufier Jean-Louis

    2006-04-01

    Full Text Available Abstract Background Ocular albinism type 1 (OA1 is an X-linked ocular disorder characterized by a severe reduction in visual acuity, nystagmus, hypopigmentation of the retinal pigmented epithelium, foveal hypoplasia, macromelanosomes in pigmented skin and eye cells, and misrouting of the optical tracts. This disease is primarily caused by mutations in the OA1 gene. Methods The ophthalmologic phenotype of the patients and their family members was characterized. We screened for mutations in the OA1 gene by direct sequencing of the nine PCR-amplified exons, and for genomic deletions by PCR-amplification of large DNA fragments. Results We sequenced the nine exons of the OA1 gene in 72 individuals and found ten different mutations in seven unrelated families and three sporadic cases. The ten mutations include an amino acid substitution and a premature stop codon previously reported by our team, and eight previously unidentified mutations: three amino acid substitutions, a duplication, a deletion, an insertion and two splice-site mutations. The use of a novel Taq polymerase enabled us to amplify large genomic fragments covering the OA1 gene. and to detect very likely six distinct large deletions. Furthermore, we were able to confirm that there was no deletion in twenty one patients where no mutation had been found. Conclusion The identified mutations affect highly conserved amino acids, cause frameshifts or alternative splicing, thus affecting folding of the OA1 G protein coupled receptor, interactions of OA1 with its G protein and/or binding with its ligand.

  19. Mediastinal involvement in lymphangiomatosis: a previously unreported MRI sign

    Energy Technology Data Exchange (ETDEWEB)

    Shah, Vikas; Shah, Sachit; Barnacle, Alex; McHugh, Kieran [Great Ormond Street Hospital for Children, Department of Radiology, London (United Kingdom); Sebire, Neil J. [Great Ormond Street Hospital for Children, Department of Histopathology, London (United Kingdom); Brock, Penelope [Great Ormond Street Hospital for Children, Department of Oncology, London (United Kingdom); Harper, John I. [Great Ormond Street Hospital for Children, Department of Dermatology, London (United Kingdom)

    2011-08-15

    Multifocal lymphangiomatosis is a rare systemic disorder affecting children. Due to its rarity and wide spectrum of clinical, histological and imaging features, establishing the diagnosis of multifocal lymphangiomatosis can be challenging. The purpose of this study was to describe a new imaging sign in this disorder: paraspinal soft tissue and signal abnormality at MRI. We retrospectively reviewed the imaging, clinical and histopathological findings in a cohort of eight children with thoracic involvement from this condition. Evidence of paraspinal chest disease was identified at MRI and CT in all eight of these children. The changes comprise heterogeneous intermediate-to-high signal parallel to the thoracic vertebrae on T2-weighted sequences at MRI, with abnormal paraspinal soft tissue at CT and plain radiography. Multifocal lymphangiomatosis is a rare disorder with a broad range of clinicopathological and imaging features. MRI allows complete evaluation of disease extent without the use of ionising radiation and has allowed us to describe a previously unreported imaging sign in this disorder, namely, heterogeneous hyperintense signal in abnormal paraspinal tissue on T2-weighted images. (orig.)

  20. Molecular characterization of previously elusive badnaviruses associated with symptomatic cacao in the New World.

    Science.gov (United States)

    Chingandu, Nomatter; Zia-Ur-Rehman, Muhammad; Sreenivasan, Thyail N; Surujdeo-Maharaj, Surendra; Umaharan, Pathmanathan; Gutierrez, Osman A; Brown, Judith K

    2017-05-01

    Suspected virus-like symptoms were observed in cacao plants in Trinidad during 1943, and the viruses associated with these symptoms were designated as strains A and B of cacao Trinidad virus (CTV). However, viral etiology has not been demonstrated for either phenotype. Total DNA was isolated from symptomatic cacao leaves exhibiting the CTV A and B phenotypes and subjected to Illumina HiSeq and Sanger DNA sequencing. Based on de novo assembly, two apparently full-length badnavirus genomes of 7,533 and 7,454 nucleotides (nt) were associated with CTV strain A and B, respectively. The Trinidad badnaviral genomes contained four open reading frames, three of which are characteristic of other known badnaviruses, and a fourth that is present in only some badnaviruses. Both badnaviral genomes harbored hallmark caulimovirus-like features, including a tRNA Met priming site, a TATA box, and a polyadenylation-like signal. Pairwise comparisons of the RT-RNase H region indicated that the Trinidad isolates share 57-71% nt sequence identity with other known badnaviruses. Based on the system for badnavirus species demarcation in which viruses with less than 80% nt sequence identity in the RT-RNase gene are considered members of separate species, these isolates represent two previously unidentified badnaviruses, herein named cacao mild mosaic virus and cacao yellow vein banding virus, making them the first cacao-infecting badnaviruses identified thus far in the Western Hemisphere.

  1. 22 CFR 40.91 - Certain aliens previously removed.

    Science.gov (United States)

    2010-04-01

    ... 22 Foreign Relations 1 2010-04-01 2010-04-01 false Certain aliens previously removed. 40.91... IMMIGRANTS UNDER THE IMMIGRATION AND NATIONALITY ACT, AS AMENDED Aliens Previously Removed § 40.91 Certain aliens previously removed. (a) 5-year bar. An alien who has been found inadmissible, whether as a result...

  2. Determining root correspondence between previously and newly detected objects

    Science.gov (United States)

    Paglieroni, David W.; Beer, N Reginald

    2014-06-17

    A system that applies attribute and topology based change detection to networks of objects that were detected on previous scans of a structure, roadway, or area of interest. The attributes capture properties or characteristics of the previously detected objects, such as location, time of detection, size, elongation, orientation, etc. The topology of the network of previously detected objects is maintained in a constellation database that stores attributes of previously detected objects and implicitly captures the geometrical structure of the network. A change detection system detects change by comparing the attributes and topology of new objects detected on the latest scan to the constellation database of previously detected objects.

  3. Accessibility and content of individualized adult reconstructive hip and knee/musculoskeletal oncology fellowship web sites.

    Science.gov (United States)

    Young, Bradley L; Cantrell, Colin K; Patt, Joshua C; Ponce, Brent A

    2018-06-01

    Accessible, adequate online information is important to fellowship applicants. Program web sites can affect which programs applicants apply to, subsequently altering interview costs incurred by both parties and ultimately impacting rank lists. Web site analyses have been performed for all orthopaedic subspecialties other than those involved in the combined adult reconstruction and musculoskeletal (MSK) oncology fellowship match. A complete list of active programs was obtained from the official adult reconstruction and MSK oncology society web sites. Web site accessibility was assessed using a structured Google search. Accessible web sites were evaluated based on 21 previously reported content criteria. Seventy-four adult reconstruction programs and 11 MSK oncology programs were listed on the official society web sites. Web sites were identified and accessible for 58 (78%) adult reconstruction and 9 (82%) MSK oncology fellowship programs. No web site contained all content criteria and more than half of both adult reconstruction and MSK oncology web sites failed to include 12 of the 21 criteria. Several programs participating in the combined Adult Reconstructive Hip and Knee/Musculoskeletal Oncology Fellowship Match did not have accessible web sites. Of the web sites that were accessible, none contained comprehensive information and the majority lacked information that has been previously identified as being important to perspective applicants.

  4. Site directed recombination

    Science.gov (United States)

    Jurka, Jerzy W.

    1997-01-01

    Enhanced homologous recombination is obtained by employing a consensus sequence which has been found to be associated with integration of repeat sequences, such as Alu and ID. The consensus sequence or sequence having a single transition mutation determines one site of a double break which allows for high efficiency of integration at the site. By introducing single or double stranded DNA having the consensus sequence flanking region joined to a sequence of interest, one can reproducibly direct integration of the sequence of interest at one or a limited number of sites. In this way, specific sites can be identified and homologous recombination achieved at the site by employing a second flanking sequence associated with a sequence proximal to the 3'-nick.

  5. Site decommissioning management plan

    International Nuclear Information System (INIS)

    Fauver, D.N.; Austin, J.H.; Johnson, T.C.; Weber, M.F.; Cardile, F.P.; Martin, D.E.; Caniano, R.J.; Kinneman, J.D.

    1993-10-01

    The Nuclear Regulatory Commission (NRC) staff has identified 48 sites contaminated with radioactive material that require special attention to ensure timely decommissioning. While none of these sites represent an immediate threat to public health and safety they have contamination that exceeds existing NRC criteria for unrestricted use. All of these sites require some degree of remediation, and several involve regulatory issues that must be addressed by the Commission before they can be released for unrestricted use and the applicable licenses terminated. This report contains the NRC staff's strategy for addressing the technical, legal, and policy issues affecting the timely decommissioning of the 48 sites and describes the status of decommissioning activities at the sites

  6. Site decommissioning management plan

    Energy Technology Data Exchange (ETDEWEB)

    Fauver, D.N.; Austin, J.H.; Johnson, T.C.; Weber, M.F.; Cardile, F.P.; Martin, D.E.; Caniano, R.J.; Kinneman, J.D.

    1993-10-01

    The Nuclear Regulatory Commission (NRC) staff has identified 48 sites contaminated with radioactive material that require special attention to ensure timely decommissioning. While none of these sites represent an immediate threat to public health and safety they have contamination that exceeds existing NRC criteria for unrestricted use. All of these sites require some degree of remediation, and several involve regulatory issues that must be addressed by the Commission before they can be released for unrestricted use and the applicable licenses terminated. This report contains the NRC staff`s strategy for addressing the technical, legal, and policy issues affecting the timely decommissioning of the 48 sites and describes the status of decommissioning activities at the sites.

  7. Identifying potential surface water sampling sites for emerging ...

    African Journals Online (AJOL)

    Emerging chemical pollutants (ECPs) are defined as new chemicals which do not have a regulatory status, but which may have an adverse effect on human health and the environment. The occurrence and concentrations of ECPs in South African water bodies are largely unknown, so monitoring is required in order to ...

  8. CT Perfusion Characteristics Identify Metastatic Sites in Liver

    Directory of Open Access Journals (Sweden)

    Yuan Wang

    2015-01-01

    Full Text Available Tissue perfusion plays a critical role in oncology because growth and migration of cancerous cells require proliferation of new blood vessels through the process of tumor angiogenesis. Computed tomography (CT perfusion is an emerging functional imaging modality that measures tissue perfusion through dynamic CT scanning following intravenous administration of contrast medium. This noninvasive technique provides a quantitative basis for assessing tumor angiogenesis. CT perfusion has been utilized on a variety of organs including lung, prostate, liver, and brain, with promising results in cancer diagnosis, disease prognostication, prediction, and treatment monitoring. In this paper, we focus on assessing the extent to which CT perfusion characteristics can be used to discriminate liver metastases from neuroendocrine tumors from normal liver tissues. The neuroendocrine liver metastases were analyzed by distributed parameter modeling to yield tissue blood flow (BF, blood volume (BV, mean transit time (MTT, permeability (PS, and hepatic arterial fraction (HAF, for tumor and normal liver. The result reveals the potential of CT perfusion as a tool for constructing biomarkers from features of the hepatic vasculature for guiding cancer detection, prognostication, and treatment selection.

  9. Methods and systems for identifying ligand-protein binding sites

    KAUST Repository

    Gao, Xin; Naveed, Hammad

    2016-01-01

    The invention provides a novel integrated structure and system-based approach for drug target prediction that enables the large-scale discovery of new targets for existing drugs Novel computer-readable storage media and computer systems are also

  10. Superfund Sites

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This layer represents active Superfund Sites published by the Environmental Protection Agency (EPA). These data were extracted from the Superfund Enterprise...

  11. Site development

    International Nuclear Information System (INIS)

    Noack, J.

    1975-01-01

    The subject of this paper is a general view over all necessary considerations to develop the site after it has been chosen and before starting with the construction of a nuclear power plant. (orig./RW) [de

  12. Site selection

    International Nuclear Information System (INIS)

    Olsen, C.W.

    1983-07-01

    The conditions and criteria for selecting a site for a nuclear weapons test at the Nevada Test Site are summarized. Factors considered are: (1) scheduling of drill rigs, (2) scheduling of site preparation (dirt work, auger hole, surface casing, cementing), (3) schedule of event (when are drill hole data needed), (4) depth range of proposed W.P., (5) geologic structure (faults, Pz contact, etc.), (6) stratigraphy (alluvium, location of Grouse Canyon Tuff, etc.), (7) material properties (particularly montmorillonite and CO 2 content), (8) water table depth, (9) potential drilling problems (caving), (10) adjacent collapse craters and chimneys, (11) adjacent expended but uncollapsed sites, (12) adjacent post-shot or other small diameter holes, (13) adjacent stockpile emplacement holes, (14) adjacent planned events (including LANL), (15) projected needs of Test Program for various DOB's and operational separations, and (16) optimal use of NTS real estate

  13. Predictive factors for the development of diabetes in women with previous gestational diabetes mellitus

    DEFF Research Database (Denmark)

    Damm, P.; Kühl, C.; Bertelsen, Aksel

    1992-01-01

    OBJECTIVES: The purpose of this study was to determine the incidence of diabetes in women with previous dietary-treated gestational diabetes mellitus and to identify predictive factors for development of diabetes. STUDY DESIGN: Two to 11 years post partum, glucose tolerance was investigated in 241...... women with previous dietary-treated gestational diabetes mellitus and 57 women without previous gestational diabetes mellitus (control group). RESULTS: Diabetes developed in 42 (17.4%) women with previous gestational diabetes mellitus (3.7% insulin-dependent diabetes mellitus and 13.7% non...... of previous patients with gestational diabetes mellitus in whom plasma insulin was measured during an oral glucose tolerance test in late pregnancy a low insulin response at diagnosis was found to be an independent predictive factor for diabetes development. CONCLUSIONS: Women with previous dietary...

  14. Savannah River Site's Site Specific Plan

    International Nuclear Information System (INIS)

    1991-01-01

    This Site Specific Plan (SSP) has been prepared by the Savannah River Site (SRS) in order to show the Environmental Restoration and Waste Management activities that were identified during the preparation of the Department of Energy-Headquarters (DOE-HQ) Environmental Restoration and Waste Management Five-Year Plan (FYP) for FY 1992--1996. The SSP has been prepared in accordance with guidance received from DOE-HQ. DOE-SR is accountable to DOE-HQ for the implementation of this plan. The purpose of the SSP is to develop a baseline for policy, budget, and schedules for the DOE Environmental Restoration and Waste Management activities. The plan explains accomplishments since the Fiscal Year (FY) 1990 plan, demonstrates how present and future activities are prioritized, identifies currently funded activities and activities that are planned to be funded in the upcoming fiscal year, and describes future activities that SRS is considering

  15. The site selection process

    International Nuclear Information System (INIS)

    Kittel, J.H.

    1989-01-01

    One of the most arduous tasks associated with the management of radioactive wastes is the siting of new disposal facilities. Experience has shown that the performance of the disposal facility during and after disposal operations is critically dependent on the characteristics of the site itself. The site selection process consists of defining needs and objectives, identifying geographic regions of interest, screening and selecting candidate sites, collecting data on the candidate sites, and finally selecting the preferred site. Before the site selection procedures can be implemented, however, a formal legal system must be in place that defines broad objectives and, most importantly, clearly establishes responsibilities and accompanying authorities for the decision-making steps in the procedure. Site selection authorities should make every effort to develop trust and credibility with the public, local officials, and the news media. The responsibilities of supporting agencies must also be spelled out. Finally, a stable funding arrangement must be established so that activities such as data collection can proceed without interruption. Several examples, both international and within the US, are given

  16. 49 CFR 173.23 - Previously authorized packaging.

    Science.gov (United States)

    2010-10-01

    ... 49 Transportation 2 2010-10-01 2010-10-01 false Previously authorized packaging. 173.23 Section... REQUIREMENTS FOR SHIPMENTS AND PACKAGINGS Preparation of Hazardous Materials for Transportation § 173.23 Previously authorized packaging. (a) When the regulations specify a packaging with a specification marking...

  17. 28 CFR 10.5 - Incorporation of papers previously filed.

    Science.gov (United States)

    2010-07-01

    ... 28 Judicial Administration 1 2010-07-01 2010-07-01 false Incorporation of papers previously filed... CARRYING ON ACTIVITIES WITHIN THE UNITED STATES Registration Statement § 10.5 Incorporation of papers previously filed. Papers and documents already filed with the Attorney General pursuant to the said act and...

  18. 75 FR 76056 - FEDERAL REGISTER CITATION OF PREVIOUS ANNOUNCEMENT:

    Science.gov (United States)

    2010-12-07

    ... SECURITIES AND EXCHANGE COMMISSION Sunshine Act Meeting FEDERAL REGISTER CITATION OF PREVIOUS ANNOUNCEMENT: STATUS: Closed meeting. PLACE: 100 F Street, NE., Washington, DC. DATE AND TIME OF PREVIOUSLY ANNOUNCED MEETING: Thursday, December 9, 2010 at 2 p.m. CHANGE IN THE MEETING: Time change. The closed...

  19. No discrimination against previous mates in a sexually cannibalistic spider

    Science.gov (United States)

    Fromhage, Lutz; Schneider, Jutta M.

    2005-09-01

    In several animal species, females discriminate against previous mates in subsequent mating decisions, increasing the potential for multiple paternity. In spiders, female choice may take the form of selective sexual cannibalism, which has been shown to bias paternity in favor of particular males. If cannibalistic attacks function to restrict a male's paternity, females may have little interest to remate with males having survived such an attack. We therefore studied the possibility of female discrimination against previous mates in sexually cannibalistic Argiope bruennichi, where females almost always attack their mate at the onset of copulation. We compared mating latency and copulation duration of males having experienced a previous copulation either with the same or with a different female, but found no evidence for discrimination against previous mates. However, males copulated significantly shorter when inserting into a used, compared to a previously unused, genital pore of the female.

  20. Implant breast reconstruction after salvage mastectomy in previously irradiated patients.

    Science.gov (United States)

    Persichetti, Paolo; Cagli, Barbara; Simone, Pierfranco; Cogliandro, Annalisa; Fortunato, Lucio; Altomare, Vittorio; Trodella, Lucio

    2009-04-01

    The most common surgical approach in case of local tumor recurrence after quadrantectomy and radiotherapy is salvage mastectomy. Breast reconstruction is the subsequent phase of the treatment and the plastic surgeon has to operate on previously irradiated and manipulated tissues. The medical literature highlights that breast reconstruction with tissue expanders is not a pursuable option, considering previous radiotherapy a contraindication. The purpose of this retrospective study is to evaluate the influence of previous radiotherapy on 2-stage breast reconstruction (tissue expander/implant). Only patients with analogous timing of radiation therapy and the same demolitive and reconstructive procedures were recruited. The results of this study prove that, after salvage mastectomy in previously irradiated patients, implant reconstruction is still possible. Further comparative studies are, of course, advisable to draw any conclusion on the possibility to perform implant reconstruction in previously irradiated patients.

  1. Stress thallium-201 myocardial scintigraphy for the detection of individual coronary arterial lesions in patients with and without previous myocardial infarction

    International Nuclear Information System (INIS)

    Rigo, P.; Bailey, I.K.; Griffith, L.S.; Pitt, B.; Wagner, H.N. Jr.; Becker, L.C.

    1981-01-01

    The value of stress thallium-201 scintigraphy for detecting individual coronary arterial stenoses was analyzed in 141 patients with angiographically proved coronary artery disease, 101 with and 40 without a previous myocardial infarction. In patients without infarction, the sensitivity for detecting greater than 50 percent narrowing in the left anterior descending, the right and the left circumflex coronary artery was 66, 53 and 24 percent, respectively. In those with a previous infarction, the sensitivity for demonstrating disease in the artery corresponding to the site of infarction was 100 percent for the left anterior descending, 79 percent for the right and 63 percent for the left circumflex coronary artery. In patients with a prior anterior infarction, concomitant right or left circumflex coronary arterial lesions were detected in only 1 of 12 cases, whereas in those with previous inferior or inferolateral infarction, the sensitivity for left anterior descending coronary artery disease was 69 percent. Because of the reasonably high sensitivity for detecting left anterior descending arterial disease, irrespective of the presence and location of previous infarction, myocardial scintigraphy was useful in identifying multivessel disease in patients with a previous inferior infarction. However, because of its relative insensitivity for right or left circumflex coronary artery disease, scintigraphy proved to be a poor predictor of multivessel disease in patients with a prior anterior infarction and in patients without previous myocardial infarction

  2. Site descriptions for preliminary radiological assessments of low-level waste repositories

    International Nuclear Information System (INIS)

    Burgess, W.E.; Jones, C.H.; Sumerling, T.J.; Ashton, J.

    1988-07-01

    The environmental contexts of four sites, previously under investigation by UK Nirex Ltd. as potential locations for low-level waste disposal facilities, are described. Information on geographical setting, climate, surface hydrology, land use, agriculture, fisheries, geology and hydrogeology is presented. The geological and hydrogeological data are interpreted with the support of deterministic modelling of groundwater conditions. The routes by which radionuclides may migrate from the site are identified and reduced to 1D statistical descriptions suitable for use in probabilistic risk assessments. Additional data required to improve the assessment of the performance of the site are identified. (author)

  3. Drupal 7 Multi Sites Configuration

    CERN Document Server

    Butcher, Matt

    2012-01-01

    Follow the creation of a multi-site instance with Drupal. The practical examples and accompanying screenshots will help you to get multiple Drupal sites set up in no time. This book is for Drupal site builders. It is assumed that readers are familiar with Drupal already, with a basic grasp of its concepts and components. System administration concepts, such as configuring Apache, MySQL, and Vagrant are covered but no previous knowledge of these tools is required.

  4. Aortic pseudoaneurysm detected on external jugular venous distention following a Bentall procedure 10 years previously.

    Science.gov (United States)

    Fukunaga, Naoto; Shomura, Yu; Nasu, Michihiro; Okada, Yukikatsu

    2010-11-01

    An asymptomatic 49-year-old woman was admitted for the purpose of surgery for aortic pseudoaneurysm. She had Marfan syndrome and had undergone an emergent Bentall procedure 10 years previously. About six months previously, she could palpate distended bilateral external jugular veins, which became distended only in a supine position and without any other symptoms. Enhanced computed tomography revealed an aortic pseudoaneurysm originating from a previous distal anastomosis site. During induction of general anesthesia in a supine position, bilateral external jugular venous distention was remarkable. Immediately after a successful operation, distention completely resolved. The present case emphasizes the importance of physical examination leading to a diagnosis of asymptomatic life-threatening diseases in patients with a history of previous aortic surgery.

  5. Site development

    International Nuclear Information System (INIS)

    Gaynor, R.K.

    1989-01-01

    Development of a low-level radioactive waste land disposal facility is little different than any industrial development of similar scope. Consideration must be made for normal business and operations management, security, facility maintenance, traffic control and necessary amenities for personnel. The item specific to the low-level waste site is the handling of radioactive waste materials and the regulatory and environmental protection procedures that must be planned for and accomodated in the site design and development. Each of these elements and the facility as a whole must be designed to be compatible with local land use plans, available transportation and support services, and the social and economic goals of the local community. Plans should also be made for quality control and orderly construction. This chapter deals with those aspects of the facility, its design and construction which are integral parts to the overall performance of the site

  6. Site Practice

    DEFF Research Database (Denmark)

    Wahedi, Haseebullah

    2016-01-01

    different practices in the construction phase. The research is based on an ethnographic study of a case in Denmark. The empirical data were collected through direct observations and semi-structured interviews with site managers, contract managers, foremen and craftsmen. Findings revealed...... that the construction phase comprises several communities and practices, leading to various uses of the drawings. The results indicated that the craftsmen used drawings to position themselves in the correct location, and that the site managers and contract managers used them as management tools and legal documents...

  7. Structures of Pseudomonas aeruginosa β-ketoacyl-(acyl-carrier-protein) synthase II (FabF) and a C164Q mutant provide templates for antibacterial drug discovery and identify a buried potassium ion and a ligand-binding site that is an artefact of the crystal form

    Energy Technology Data Exchange (ETDEWEB)

    Baum, Bernhard [Johannes Gutenberg-Universität, Staudinger Weg 5, 55128 Mainz (Germany); Lecker, Laura S. M.; Zoltner, Martin [University of Dundee, Dundee DD1 4EH, Scotland (United Kingdom); Jaenicke, Elmar [Johannes Gutenberg-Universität, Jakob Welder Weg 26, 55128 Mainz (Germany); Schnell, Robert [Karolinska Institutet, 17 177 Stockholm (Sweden); Hunter, William N., E-mail: w.n.hunter@dundee.ac.uk [University of Dundee, Dundee DD1 4EH, Scotland (United Kingdom); Brenk, Ruth, E-mail: w.n.hunter@dundee.ac.uk [Johannes Gutenberg-Universität, Staudinger Weg 5, 55128 Mainz (Germany)

    2015-07-28

    Three crystal structures of recombinant P. aeruginosa FabF are reported: the apoenzyme, an active-site mutant and a complex with a fragment of a natural product inhibitor. The characterization provides reagents and new information to support antibacterial drug discovery. Bacterial infections remain a serious health concern, in particular causing life-threatening infections of hospitalized and immunocompromised patients. The situation is exacerbated by the rise in antibacterial drug resistance, and new treatments are urgently sought. In this endeavour, accurate structures of molecular targets can support early-stage drug discovery. Here, crystal structures, in three distinct forms, of recombinant Pseudomonas aeruginosa β-ketoacyl-(acyl-carrier-protein) synthase II (FabF) are presented. This enzyme, which is involved in fatty-acid biosynthesis, has been validated by genetic and chemical means as an antibiotic target in Gram-positive bacteria and represents a potential target in Gram-negative bacteria. The structures of apo FabF, of a C164Q mutant in which the binding site is altered to resemble the substrate-bound state and of a complex with 3-(benzoylamino)-2-hydroxybenzoic acid are reported. This compound mimics aspects of a known natural product inhibitor, platensimycin, and surprisingly was observed binding outside the active site, interacting with a symmetry-related molecule. An unusual feature is a completely buried potassium-binding site that was identified in all three structures. Comparisons suggest that this may represent a conserved structural feature of FabF relevant to fold stability. The new structures provide templates for structure-based ligand design and, together with the protocols and reagents, may underpin a target-based drug-discovery project for urgently needed antibacterials.

  8. Structures of Pseudomonas aeruginosa β-ketoacyl-(acyl-carrier-protein) synthase II (FabF) and a C164Q mutant provide templates for antibacterial drug discovery and identify a buried potassium ion and a ligand-binding site that is an artefact of the crystal form

    International Nuclear Information System (INIS)

    Baum, Bernhard; Lecker, Laura S. M.; Zoltner, Martin; Jaenicke, Elmar; Schnell, Robert; Hunter, William N.; Brenk, Ruth

    2015-01-01

    Three crystal structures of recombinant P. aeruginosa FabF are reported: the apoenzyme, an active-site mutant and a complex with a fragment of a natural product inhibitor. The characterization provides reagents and new information to support antibacterial drug discovery. Bacterial infections remain a serious health concern, in particular causing life-threatening infections of hospitalized and immunocompromised patients. The situation is exacerbated by the rise in antibacterial drug resistance, and new treatments are urgently sought. In this endeavour, accurate structures of molecular targets can support early-stage drug discovery. Here, crystal structures, in three distinct forms, of recombinant Pseudomonas aeruginosa β-ketoacyl-(acyl-carrier-protein) synthase II (FabF) are presented. This enzyme, which is involved in fatty-acid biosynthesis, has been validated by genetic and chemical means as an antibiotic target in Gram-positive bacteria and represents a potential target in Gram-negative bacteria. The structures of apo FabF, of a C164Q mutant in which the binding site is altered to resemble the substrate-bound state and of a complex with 3-(benzoylamino)-2-hydroxybenzoic acid are reported. This compound mimics aspects of a known natural product inhibitor, platensimycin, and surprisingly was observed binding outside the active site, interacting with a symmetry-related molecule. An unusual feature is a completely buried potassium-binding site that was identified in all three structures. Comparisons suggest that this may represent a conserved structural feature of FabF relevant to fold stability. The new structures provide templates for structure-based ligand design and, together with the protocols and reagents, may underpin a target-based drug-discovery project for urgently needed antibacterials

  9. Personality disorders in previously detained adolescent females: a prospective study

    NARCIS (Netherlands)

    Krabbendam, A.; Colins, O.F.; Doreleijers, T.A.H.; van der Molen, E.; Beekman, A.T.F.; Vermeiren, R.R.J.M.

    2015-01-01

    This longitudinal study investigated the predictive value of trauma and mental health problems for the development of antisocial personality disorder (ASPD) and borderline personality disorder (BPD) in previously detained women. The participants were 229 detained adolescent females who were assessed

  10. Payload specialist Reinhard Furrer show evidence of previous blood sampling

    Science.gov (United States)

    1985-01-01

    Payload specialist Reinhard Furrer shows evidence of previous blood sampling while Wubbo J. Ockels, Dutch payload specialist (only partially visible), extends his right arm after a sample has been taken. Both men show bruises on their arms.

  11. Choice of contraception after previous operative delivery at a family ...

    African Journals Online (AJOL)

    Choice of contraception after previous operative delivery at a family planning clinic in Northern Nigeria. Amina Mohammed‑Durosinlorun, Joel Adze, Stephen Bature, Caleb Mohammed, Matthew Taingson, Amina Abubakar, Austin Ojabo, Lydia Airede ...

  12. Previous utilization of service does not improve timely booking in ...

    African Journals Online (AJOL)

    Previous utilization of service does not improve timely booking in antenatal care: Cross sectional study ... Journal Home > Vol 24, No 3 (2010) > ... Results: Past experience on antenatal care service utilization did not come out as a predictor for ...

  13. A previous hamstring injury affects kicking mechanics in soccer players.

    Science.gov (United States)

    Navandar, Archit; Veiga, Santiago; Torres, Gonzalo; Chorro, David; Navarro, Enrique

    2018-01-10

    Although the kicking skill is influenced by limb dominance and sex, how a previous hamstring injury affects kicking has not been studied in detail. Thus, the objective of this study was to evaluate the effect of sex and limb dominance on kicking in limbs with and without a previous hamstring injury. 45 professional players (males: n=19, previously injured players=4, age=21.16 ± 2.00 years; females: n=19, previously injured players=10, age=22.15 ± 4.50 years) performed 5 kicks each with their preferred and non-preferred limb at a target 7m away, which were recorded with a three-dimensional motion capture system. Kinematic and kinetic variables were extracted for the backswing, leg cocking, leg acceleration and follow through phases. A shorter backswing (20.20 ± 3.49% vs 25.64 ± 4.57%), and differences in knee flexion angle (58 ± 10o vs 72 ± 14o) and hip flexion velocity (8 ± 0rad/s vs 10 ± 2rad/s) were observed in previously injured, non-preferred limb kicks for females. A lower peak hip linear velocity (3.50 ± 0.84m/s vs 4.10 ± 0.45m/s) was observed in previously injured, preferred limb kicks of females. These differences occurred in the backswing and leg-cocking phases where the hamstring muscles were the most active. A variation in the functioning of the hamstring muscles and that of the gluteus maximus and iliopsoas in the case of a previous injury could account for the differences observed in the kicking pattern. Therefore, the effects of a previous hamstring injury must be considered while designing rehabilitation programs to re-educate kicking movement.

  14. Site selection

    CERN Multimedia

    CERN PhotoLab

    1968-01-01

    To help resolve the problem of site selection for the proposed 300 GeV machine, the Council selected "three wise men" (left to right, J H Bannier of the Netherlands, A Chavanne of Switzerland and L K Boggild of Denmark).

  15. Site Restoration

    Energy Technology Data Exchange (ETDEWEB)

    Noynaert, L.; Bruggeman, A.; Cornelissen, R.; Massaut, V.; Rahier, A

    2001-04-01

    The objectives, the programme, and the achievements of the Site Restoration Department of SCK-CEN in 2000 are summarised. Main activities include the decommissioning of the BR3 PWR-reactor as well as other clean-up activities, projects on waste minimisation and activities related to the management of decommissioning projects. The department provides consultancy and services to external organisations.

  16. Site Restoration

    International Nuclear Information System (INIS)

    Noynaert, L.; Bruggeman, A.; Cornelissen, R.; Massaut, V.; Rahier, A.

    2001-01-01

    The objectives, the programme, and the achievements of the Site Restoration Department of SCK-CEN in 2000 are summarised. Main activities include the decommissioning of the BR3 PWR-reactor as well as other clean-up activities, projects on waste minimisation and activities related to the management of decommissioning projects. The department provides consultancy and services to external organisations

  17. Secondary recurrent miscarriage is associated with previous male birth.

    LENUS (Irish Health Repository)

    Ooi, Poh Veh

    2012-01-31

    Secondary recurrent miscarriage (RM) is defined as three or more consecutive pregnancy losses after delivery of a viable infant. Previous reports suggest that a firstborn male child is associated with less favourable subsequent reproductive potential, possibly due to maternal immunisation against male-specific minor histocompatibility antigens. In a retrospective cohort study of 85 cases of secondary RM we aimed to determine if secondary RM was associated with (i) gender of previous child, maternal age, or duration of miscarriage history, and (ii) increased risk of pregnancy complications. Fifty-three women (62.0%; 53\\/85) gave birth to a male child prior to RM compared to 32 (38.0%; 32\\/85) who gave birth to a female child (p=0.002). The majority (91.7%; 78\\/85) had uncomplicated, term deliveries and normal birth weight neonates, with one quarter of the women previously delivered by Caesarean section. All had routine RM investigations and 19.0% (16\\/85) had an abnormal result. Fifty-seven women conceived again and 33.3% (19\\/57) miscarried, but there was no significant difference in failure rates between those with a previous male or female child (13\\/32 vs. 6\\/25, p=0.2). When patients with abnormal results were excluded, or when women with only one previous child were considered, there was still no difference in these rates. A previous male birth may be associated with an increased risk of secondary RM but numbers preclude concluding whether this increases recurrence risk. The suggested association with previous male birth provides a basis for further investigations at a molecular level.

  18. Secondary recurrent miscarriage is associated with previous male birth.

    LENUS (Irish Health Repository)

    Ooi, Poh Veh

    2011-01-01

    Secondary recurrent miscarriage (RM) is defined as three or more consecutive pregnancy losses after delivery of a viable infant. Previous reports suggest that a firstborn male child is associated with less favourable subsequent reproductive potential, possibly due to maternal immunisation against male-specific minor histocompatibility antigens. In a retrospective cohort study of 85 cases of secondary RM we aimed to determine if secondary RM was associated with (i) gender of previous child, maternal age, or duration of miscarriage history, and (ii) increased risk of pregnancy complications. Fifty-three women (62.0%; 53\\/85) gave birth to a male child prior to RM compared to 32 (38.0%; 32\\/85) who gave birth to a female child (p=0.002). The majority (91.7%; 78\\/85) had uncomplicated, term deliveries and normal birth weight neonates, with one quarter of the women previously delivered by Caesarean section. All had routine RM investigations and 19.0% (16\\/85) had an abnormal result. Fifty-seven women conceived again and 33.3% (19\\/57) miscarried, but there was no significant difference in failure rates between those with a previous male or female child (13\\/32 vs. 6\\/25, p=0.2). When patients with abnormal results were excluded, or when women with only one previous child were considered, there was still no difference in these rates. A previous male birth may be associated with an increased risk of secondary RM but numbers preclude concluding whether this increases recurrence risk. The suggested association with previous male birth provides a basis for further investigations at a molecular level.

  19. DOE site performance assessment activities

    International Nuclear Information System (INIS)

    1990-07-01

    Information on performance assessment capabilities and activities was collected from eight DOE sites. All eight sites either currently dispose of low-level radioactive waste (LLW) or plan to dispose of LLW in the near future. A survey questionnaire was developed and sent to key individuals involved in DOE Order 5820.2A performance assessment activities at each site. The sites surveyed included: Hanford Site (Hanford), Idaho National Engineering Laboratory (INEL), Los Alamos National Laboratory (LANL), Nevada Test Site (NTS), Oak Ridge National Laboratory (ORNL), Paducah Gaseous Diffusion Plant (Paducah), Portsmouth Gaseous Diffusion Plant (Portsmouth), and Savannah River Site (SRS). The questionnaire addressed all aspects of the performance assessment process; from waste source term to dose conversion factors. This report presents the information developed from the site questionnaire and provides a comparison of site-specific performance assessment approaches, data needs, and ongoing and planned activities. All sites are engaged in completing the radioactive waste disposal facility performance assessment required by DOE Order 5820.2A. Each site has achieved various degrees of progress and have identified a set of critical needs. Within several areas, however, the sites identified common needs and questions

  20. Erlotinib-induced rash spares previously irradiated skin

    International Nuclear Information System (INIS)

    Lips, Irene M.; Vonk, Ernest J.A.; Koster, Mariska E.Y.; Houwing, Ronald H.

    2011-01-01

    Erlotinib is an epidermal growth factor receptor inhibitor prescribed to patients with locally advanced or metastasized non-small cell lung carcinoma after failure of at least one earlier chemotherapy treatment. Approximately 75% of the patients treated with erlotinib develop acneiform skin rashes. A patient treated with erlotinib 3 months after finishing concomitant treatment with chemotherapy and radiotherapy for non-small cell lung cancer is presented. Unexpectedly, the part of the skin that had been included in his previously radiotherapy field was completely spared from the erlotinib-induced acneiform skin rash. The exact mechanism of erlotinib-induced rash sparing in previously irradiated skin is unclear. The underlying mechanism of this phenomenon needs to be explored further, because the number of patients being treated with a combination of both therapeutic modalities is increasing. The therapeutic effect of erlotinib in the area of the previously irradiated lesion should be assessed. (orig.)

  1. Reasoning with Previous Decisions: Beyond the Doctrine of Precedent

    DEFF Research Database (Denmark)

    Komárek, Jan

    2013-01-01

    in different jurisdictions use previous judicial decisions in their argument, we need to move beyond the concept of precedent to a wider notion, which would embrace practices and theories in legal systems outside the Common law tradition. This article presents the concept of ‘reasoning with previous decisions...... law method’, but they are no less rational and intellectually sophisticated. The reason for the rather conceited attitude of some comparatists is in the dominance of the common law paradigm of precedent and the accompanying ‘case law method’. If we want to understand how courts and lawyers......’ as such an alternative and develops its basic models. The article first points out several shortcomings inherent in limiting the inquiry into reasoning with previous decisions by the common law paradigm (1). On the basis of numerous examples provided in section (1), I will present two basic models of reasoning...

  2. [Prevalence of previously diagnosed diabetes mellitus in Mexico.

    Science.gov (United States)

    Rojas-Martínez, Rosalba; Basto-Abreu, Ana; Aguilar-Salinas, Carlos A; Zárate-Rojas, Emiliano; Villalpando, Salvador; Barrientos-Gutiérrez, Tonatiuh

    2018-01-01

    To compare the prevalence of previously diagnosed diabetes in 2016 with previous national surveys and to describe treatment and its complications. Mexico's national surveys Ensa 2000, Ensanut 2006, 2012 and 2016 were used. For 2016, logistic regression models and measures of central tendency and dispersion were obtained. The prevalence of previously diagnosed diabetes in 2016 was 9.4%. The increase of 2.2% relative to 2012 was not significant and only observed in patients older than 60 years. While preventive measures have increased, the access to medical treatment and lifestyle has not changed. The treatment has been modified, with an increase in insulin and decrease in hypoglycaemic agents. Population aging, lack of screening actions and the increase in diabetes complications will lead to an increase on the burden of disease. Policy measures targeting primary and secondary prevention of diabetes are crucial.

  3. Cardiovascular magnetic resonance in adults with previous cardiovascular surgery.

    Science.gov (United States)

    von Knobelsdorff-Brenkenhoff, Florian; Trauzeddel, Ralf Felix; Schulz-Menger, Jeanette

    2014-03-01

    Cardiovascular magnetic resonance (CMR) is a versatile non-invasive imaging modality that serves a broad spectrum of indications in clinical cardiology and has proven evidence. Most of the numerous applications are appropriate in patients with previous cardiovascular surgery in the same manner as in non-surgical subjects. However, some specifics have to be considered. This review article is intended to provide information about the application of CMR in adults with previous cardiovascular surgery. In particular, the two main scenarios, i.e. following coronary artery bypass surgery and following heart valve surgery, are highlighted. Furthermore, several pictorial descriptions of other potential indications for CMR after cardiovascular surgery are given.

  4. Western gorilla diet: a synthesis from six sites.

    Science.gov (United States)

    Rogers, M Elizabeth; Abernethy, Kate; Bermejo, Magdalena; Cipolletta, Chloe; Doran, Diane; McFarland, Kelley; Nishihara, Tomoaki; Remis, Melissa; Tutin, Caroline E G

    2004-10-01

    The objective of this paper is to collate information on western gorilla diet from six study sites throughout much of their current range, including preliminary information from two sites (Afi and Lossi), where studies of diet have begun only recently. Food lists were available from each site, derived from indirect signs of gorilla feeding (such as feces), with some observational data. Important staple, seasonal, and fallback foods have been identified, and a number of striking similarities across sites have been revealed based on a much larger data set than was previously available. It was confirmed that the western gorilla diet is always eclectic, including up to 230 items and 180 species. The greatest diversity is found among the fruit species eaten, fruit being included in western gorilla diets from all sites and throughout most or all of the year. Eight plant families provide important foods at five, or all six, sites, suggesting that it may be possible in the future to predict which habitats are the most suitable for gorillas. Gorillas exploit both rare and common forest species. Similarities and differences among sites can be explained superficially on the basis of geography and the past history of the forest. Gorilla density across sites appears to be most affected by the density of monocotyledonous bulk food plants, but its relationship to the density of important tree food species has yet to be tested.

  5. Site 300 SPCC Plan

    Energy Technology Data Exchange (ETDEWEB)

    Griffin, D. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2016-11-23

    This Spill Prevention, Control, and Countermeasure (SPCC) Plan describes the measures that are taken at Lawrence Livermore National Laboratory’s (LLNL) Experimental Test Site (Site 300) near Tracy, California, to prevent, control, and handle potential spills from aboveground containers that can contain 55 gallons or more of oil. This SPCC Plan complies with the Oil Pollution Prevention regulation in Title 40 of the Code of Federal Regulations, Part 112 (40 CFR 112) and with 40 CFR 761.65(b) and (c), which regulates the temporary storage of polychlorinated biphenyls (PCBs). This Plan has also been prepared in accordance with Division 20, Chapter 6.67 of the California Health and Safety Code (HSC 6.67) requirements for oil pollution prevention (referred to as the Aboveground Petroleum Storage Act [APSA]), and the United States Department of Energy (DOE) Order No. 436.1. This SPCC Plan establishes procedures, methods, equipment, and other requirements to prevent the discharge of oil into or upon the navigable waters of the United States or adjoining shorelines for aboveground oil storage and use at Site 300. This SPCC Plan has been prepared for the entire Site 300 facility and replaces the three previous plans prepared for Site 300: LLNL SPCC for Electrical Substations Near Buildings 846 and 865 (LLNL 2015), LLNL SPCC for Building 883 (LLNL 2015), and LLNL SPCC for Building 801 (LLNL 2014).

  6. Squamous cell carcinoma arising in previously burned or irradiated skin

    International Nuclear Information System (INIS)

    Edwards, M.J.; Hirsch, R.M.; Broadwater, J.R.; Netscher, D.T.; Ames, F.C.

    1989-01-01

    Squamous cell carcinoma (SCC) arising in previously burned or irradiated skin was reviewed in 66 patients treated between 1944 and 1986. Healing of the initial injury was complicated in 70% of patients. Mean interval from initial injury to diagnosis of SCC was 37 years. The overwhelming majority of patients presented with a chronic intractable ulcer in previously injured skin. The regional relapse rate after surgical excision was very high, 58% of all patients. Predominant patterns of recurrence were in local skin and regional lymph nodes (93% of recurrences). Survival rates at 5, 10, and 20 years were 52%, 34%, and 23%, respectively. Five-year survival rates in previously burned and irradiated patients were not significantly different (53% and 50%, respectively). This review, one of the largest reported series, better defines SCC arising in previously burned or irradiated skin as a locally aggressive disease that is distinct from SCC arising in sunlight-damaged skin. An increased awareness of the significance of chronic ulceration in scar tissue may allow earlier diagnosis. Regional disease control and survival depend on surgical resection of all known disease and may require radical lymph node dissection or amputation

  7. Outcome Of Pregnancy Following A Previous Lower Segment ...

    African Journals Online (AJOL)

    Background: A previous ceasarean section is an important variable that influences patient management in subsequent pregnancies. A trial of vaginal delivery in such patients is a feasible alternative to a secondary section, thus aiding to reduce the ceasarean section rate and its associated co-morbidities. Objective: To ...

  8. 24 CFR 1710.552 - Previously accepted state filings.

    Science.gov (United States)

    2010-04-01

    ... of Substantially Equivalent State Law § 1710.552 Previously accepted state filings. (a) Materials... and contracts or agreements contain notice of purchaser's revocation rights. In addition see § 1715.15..., unless the developer is obligated to do so in the contract. (b) If any such filing becomes inactive or...

  9. Haemophilus influenzae type f meningitis in a previously healthy boy

    DEFF Research Database (Denmark)

    Ronit, Andreas; Berg, Ronan M G; Bruunsgaard, Helle

    2013-01-01

    Non-serotype b strains of Haemophilus influenzae are extremely rare causes of acute bacterial meningitis in immunocompetent individuals. We report a case of acute bacterial meningitis in a 14-year-old boy, who was previously healthy and had been immunised against H influenzae serotype b (Hib...

  10. Research Note Effects of previous cultivation on regeneration of ...

    African Journals Online (AJOL)

    We investigated the effects of previous cultivation on regeneration potential under miombo woodlands in a resettlement area, a spatial product of Zimbabwe's land reforms. We predicted that cultivation would affect population structure, regeneration, recruitment and potential grazing capacity of rangelands. Plant attributes ...

  11. Cryptococcal meningitis in a previously healthy child | Chimowa ...

    African Journals Online (AJOL)

    An 8-year-old previously healthy female presented with a 3 weeks history of headache, neck stiffness, deafness, fever and vomiting and was diagnosed with cryptococcal meningitis. She had documented hearing loss and was referred to tertiary-level care after treatment with fluconazole did not improve her neurological ...

  12. Investigation of previously derived Hyades, Coma, and M67 reddenings

    International Nuclear Information System (INIS)

    Taylor, B.J.

    1980-01-01

    New Hyades polarimetry and field star photometry have been obtained to check the Hyades reddening, which was found to be nonzero in a previous paper. The new Hyades polarimetry implies essentially zero reddening; this is also true of polarimetry published by Behr (which was incorrectly interpreted in the previous paper). Four photometric techniques which are presumed to be insensitive to blanketing are used to compare the Hyades to nearby field stars; these four techniques also yield essentially zero reddening. When all of these results are combined with others which the author has previously published and a simultaneous solution for the Hyades, Coma, and M67 reddenings is made, the results are E (B-V) =3 +- 2 (sigma) mmag, -1 +- 3 (sigma) mmag, and 46 +- 6 (sigma) mmag, respectively. No support for a nonzero Hyades reddening is offered by the new results. When the newly obtained reddenings for the Hyades, Coma, and M67 are compared with results from techniques given by Crawford and by users of the David Dunlap Observatory photometric system, no differences between the new and other reddenings are found which are larger than about 2 sigma. The author had previously found that the M67 main-sequence stars have about the same blanketing as that of Coma and less blanketing than the Hyades; this conclusion is essentially unchanged by the revised reddenings

  13. 18 CFR 154.302 - Previously submitted material.

    Science.gov (United States)

    2010-04-01

    ... 18 Conservation of Power and Water Resources 1 2010-04-01 2010-04-01 false Previously submitted material. 154.302 Section 154.302 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY... concurrently with the rate change filing. There must be furnished to the Director, Office of Energy Market...

  14. Process cells dismantling of EUREX pant: previous activities

    International Nuclear Information System (INIS)

    Gili, M.

    1998-01-01

    In the '98-'99 period some process cells of the EUREX pant will be dismantled, in order to place there the liquid wastes conditioning plant 'CORA'. This report resumes the previous activities (plant rinsing campaigns and inactive Cell 014 dismantling), run in the past three years and the drawn experience [it

  15. Obstructive pulmonary disease in patients with previous tuberculosis ...

    African Journals Online (AJOL)

    Obstructive pulmonary disease in patients with previous tuberculosis: Pathophysiology of a community-based cohort. B.W. Allwood, R Gillespie, M Galperin-Aizenberg, M Bateman, H Olckers, L Taborda-Barata, G.L. Calligaro, Q Said-Hartley, R van Zyl-Smit, C.B. Cooper, E van Rikxoort, J Goldin, N Beyers, E.D. Bateman ...

  16. Abiraterone in metastatic prostate cancer without previous chemotherapy

    NARCIS (Netherlands)

    Ryan, Charles J.; Smith, Matthew R.; de Bono, Johann S.; Molina, Arturo; Logothetis, Christopher J.; de Souza, Paul; Fizazi, Karim; Mainwaring, Paul; Piulats, Josep M.; Ng, Siobhan; Carles, Joan; Mulders, Peter F. A.; Basch, Ethan; Small, Eric J.; Saad, Fred; Schrijvers, Dirk; van Poppel, Hendrik; Mukherjee, Som D.; Suttmann, Henrik; Gerritsen, Winald R.; Flaig, Thomas W.; George, Daniel J.; Yu, Evan Y.; Efstathiou, Eleni; Pantuck, Allan; Winquist, Eric; Higano, Celestia S.; Taplin, Mary-Ellen; Park, Youn; Kheoh, Thian; Griffin, Thomas; Scher, Howard I.; Rathkopf, Dana E.; Boyce, A.; Costello, A.; Davis, I.; Ganju, V.; Horvath, L.; Lynch, R.; Marx, G.; Parnis, F.; Shapiro, J.; Singhal, N.; Slancar, M.; van Hazel, G.; Wong, S.; Yip, D.; Carpentier, P.; Luyten, D.; de Reijke, T.

    2013-01-01

    Abiraterone acetate, an androgen biosynthesis inhibitor, improves overall survival in patients with metastatic castration-resistant prostate cancer after chemotherapy. We evaluated this agent in patients who had not received previous chemotherapy. In this double-blind study, we randomly assigned

  17. Response to health insurance by previously uninsured rural children.

    Science.gov (United States)

    Tilford, J M; Robbins, J M; Shema, S J; Farmer, F L

    1999-08-01

    To examine the healthcare utilization and costs of previously uninsured rural children. Four years of claims data from a school-based health insurance program located in the Mississippi Delta. All children who were not Medicaid-eligible or were uninsured, were eligible for limited benefits under the program. The 1987 National Medical Expenditure Survey (NMES) was used to compare utilization of services. The study represents a natural experiment in the provision of insurance benefits to a previously uninsured population. Premiums for the claims cost were set with little or no information on expected use of services. Claims from the insurer were used to form a panel data set. Mixed model logistic and linear regressions were estimated to determine the response to insurance for several categories of health services. The use of services increased over time and approached the level of utilization in the NMES. Conditional medical expenditures also increased over time. Actuarial estimates of claims cost greatly exceeded actual claims cost. The provision of a limited medical, dental, and optical benefit package cost approximately $20-$24 per member per month in claims paid. An important uncertainty in providing health insurance to previously uninsured populations is whether a pent-up demand exists for health services. Evidence of a pent-up demand for medical services was not supported in this study of rural school-age children. States considering partnerships with private insurers to implement the State Children's Health Insurance Program could lower premium costs by assembling basic data on previously uninsured children.

  18. Siting factors for the Swedish deep repository for spent fuel

    International Nuclear Information System (INIS)

    Stroem, A.; Ericsson, Lars O.; Svemar, C.; Almen, K.E.; Andersson, Johan

    1998-01-01

    A project entitled Siting factors and criteria for site evaluation was initiated at the SKB in 1997. The project comprises an important part of the work of siting and site selection that is being pursued within SKB. The purpose of the project is to create a logical structure for the continued siting work, and its results should also be able to be used to assist in evaluating sites. The project will thereby also provide a means - in accordance with the Government's decision regarding Research Programme 95 - to obtain more detailed and quantified siting factors and criteria than those previously presented in the supplement to Research Programme 92. The overall goals of the project are to identify and quantify requirements and preferences regarding the properties of the rock and the soil from the perspectives of long-term safety, performance and planning and design of the rock works, and to identify siting factors and criteria. The latter should be able to be used to determine whether requirements and preferences are satisfied, both when screening sites for site investigation and after completed site investigation. Presented requirements, preferences, factors and criteria must be acceptable to national and municipal authorities or others with influence over the siting work. To start with, requirements and preferences regarding the performance of the rock in a deep repository have been clarified. These requirements and preferences are based on many years of experience of safety assessments and construction analyses within SKB. What is new here is the structuring that has been done, where a classification is made into different geoscientific disciplines, and the formalism that has been developed for the concepts requirements, preferences and performance. This is a prerequisite for a consistent and hopefully comprehensive set of requirements from a functional perspective. Work has continued on siting factors with reference to a coming site investigation programme. A

  19. Reoperative sentinel lymph node biopsy after previous mastectomy.

    Science.gov (United States)

    Karam, Amer; Stempel, Michelle; Cody, Hiram S; Port, Elisa R

    2008-10-01

    Sentinel lymph node (SLN) biopsy is the standard of care for axillary staging in breast cancer, but many clinical scenarios questioning the validity of SLN biopsy remain. Here we describe our experience with reoperative-SLN (re-SLN) biopsy after previous mastectomy. Review of the SLN database from September 1996 to December 2007 yielded 20 procedures done in the setting of previous mastectomy. SLN biopsy was performed using radioisotope with or without blue dye injection superior to the mastectomy incision, in the skin flap in all patients. In 17 of 20 patients (85%), re-SLN biopsy was performed for local or regional recurrence after mastectomy. Re-SLN biopsy was successful in 13 of 20 patients (65%) after previous mastectomy. Of the 13 patients, 2 had positive re-SLN, and completion axillary dissection was performed, with 1 having additional positive nodes. In the 11 patients with negative re-SLN, 2 patients underwent completion axillary dissection demonstrating additional negative nodes. One patient with a negative re-SLN experienced chest wall recurrence combined with axillary recurrence 11 months after re-SLN biopsy. All others remained free of local or axillary recurrence. Re-SLN biopsy was unsuccessful in 7 of 20 patients (35%). In three of seven patients, axillary dissection was performed, yielding positive nodes in two of the three. The remaining four of seven patients all had previous modified radical mastectomy, so underwent no additional axillary surgery. In this small series, re-SLN was successful after previous mastectomy, and this procedure may play some role when axillary staging is warranted after mastectomy.

  20. Hormone profile in juvenile systemic lupus erythematosus with previous or current amenorrhea

    NARCIS (Netherlands)

    Silva, Clovis A.; Deen, Maria E. J.; Febronio, Marilia V.; Oliveira, Sheila K.; Terreri, Maria T.; Sacchetti, Silvana B.; Sztajnbok, Flavio R.; Marini, Roberto; Quintero, Maria V.; Bica, Blanca E.; Pereira, Rosa M.; Bonfa, Eloisa; Ferriani, Virginia P.; Robazzi, Teresa C.; Magalhaes, Claudia S.; Hilario, Maria O.

    To identify the underlying mechanism of amenorrhea in juvenile systemic lupus erythematosus (JSLE) patients, thirty-five (11.7%) JSLE patients with current or previous amenorrhea were consecutively selected among the 298 post-menarche patients followed in 12 Brazilian pediatric rheumatology centers.

  1. 75 FR 82329 - Airworthiness Directives; Piper Aircraft, Inc. (Type Certificate Previously Held by The New Piper...

    Science.gov (United States)

    2010-12-30

    ...-1295; Directorate Identifier 2010-CE-060-AD] RIN 2120-AA64 Airworthiness Directives; Piper Aircraft, Inc. (Type Certificate Previously Held by The New Piper Aircraft, Inc.) Models PA-46-310P, PA- 46-350P... applies to certain Piper Aircraft, Inc. Models PA-46-310P and PA-46-350P airplanes that are equipped with...

  2. 76 FR 18033 - Airworthiness Directives; Piper Aircraft, Inc. (Type Certificate Previously Held by The New Piper...

    Science.gov (United States)

    2011-04-01

    ... Airworthiness Directives; Piper Aircraft, Inc. (Type Certificate Previously Held by The New Piper Aircraft, Inc... applies to certain Piper Aircraft, Inc. Models PA-46-310P and PA- 46-350P airplanes that are equipped with... information identified in this AD, contact Piper Aircraft, Inc., 2926 Piper Drive, Vero Beach, Florida 32960...

  3. 77 FR 14316 - Airworthiness Directives; Piper Aircraft, Inc. (Type Certificate Previously Held by The New Piper...

    Science.gov (United States)

    2012-03-09

    ...-0251; Directorate Identifier 2012-CE-002-AD] RIN 2120-AA64 Airworthiness Directives; Piper Aircraft, Inc. (Type Certificate Previously Held by The New Piper Aircraft Inc.) Airplanes AGENCY: Federal... supersede an existing airworthiness directive (AD) that applies to certain Piper Aircraft, Inc. (type...

  4. 78 FR 76050 - Airworthiness Directives; EADS CASA (Type Certificate Previously Held by Construcciones...

    Science.gov (United States)

    2013-12-16

    ... Airworthiness Directives; EADS CASA (Type Certificate Previously Held by Construcciones Aeron[aacute]uticas, S.A... rule. SUMMARY: We are adopting a new airworthiness directive (AD) for certain EADS CASA (Type...., Washington, DC. For EADS-CASA service information identified in this AD, contact EADS-CASA, Military...

  5. 76 FR 41432 - Airworthiness Directives; Gulfstream Aerospace LP (Type Certificate Previously Held by Israel...

    Science.gov (United States)

    2011-07-14

    ... Aerospace LP (Type Certificate Previously Held by Israel Aircraft Industries, Ltd.) Model Galaxy, Gulfstream... proposed AD. Discussion The Civil Aviation Authority (CAA), which is the aviation authority for Israel, has... Held by Israel Aircraft Industries, Ltd.): Docket No. FAA-2011-0716; Directorate Identifier 2011-NM-013...

  6. Thoughts on identifiers

    CERN Multimedia

    CERN. Geneva

    2005-01-01

    As business processes and information transactions have become an inextricably intertwined with the Web, the importance of assignment, registration, discovery, and maintenance of identifiers has increased. In spite of this, integrated frameworks for managing identifiers have been slow to emerge. Instead, identification systems arise (quite naturally) from immediate business needs without consideration for how they fit into larger information architectures. In addition, many legacy identifier systems further complicate the landscape, making it difficult for content managers to select and deploy identifier systems that meet both the business case and long term information management objectives. This presentation will outline a model for evaluating identifier applications and the functional requirements of the systems necessary to support them. The model is based on a layered analysis of the characteristics of identifier systems, including: * Functional characteristics * Technology * Policy * Business * Social T...

  7. Rac1 GTPase activates the WAVE regulatory complex through two distinct binding sites

    Science.gov (United States)

    Brautigam, Chad A; Xing, Wenmin; Yang, Sheng; Henry, Lisa; Doolittle, Lynda K; Walz, Thomas

    2017-01-01

    The Rho GTPase Rac1 activates the WAVE regulatory complex (WRC) to drive Arp2/3 complex-mediated actin polymerization, which underpins diverse cellular processes. Here we report the structure of a WRC-Rac1 complex determined by cryo-electron microscopy. Surprisingly, Rac1 is not located at the binding site on the Sra1 subunit of the WRC previously identified by mutagenesis and biochemical data. Rather, it binds to a distinct, conserved site on the opposite end of Sra1. Biophysical and biochemical data on WRC mutants confirm that Rac1 binds to both sites, with the newly identified site having higher affinity and both sites required for WRC activation. Our data reveal that the WRC is activated by simultaneous engagement of two Rac1 molecules, suggesting a mechanism by which cells may sense the density of active Rac1 at membranes to precisely control actin assembly. PMID:28949297

  8. Identifiability in stochastic models

    CERN Document Server

    1992-01-01

    The problem of identifiability is basic to all statistical methods and data analysis, occurring in such diverse areas as Reliability Theory, Survival Analysis, and Econometrics, where stochastic modeling is widely used. Mathematics dealing with identifiability per se is closely related to the so-called branch of ""characterization problems"" in Probability Theory. This book brings together relevant material on identifiability as it occurs in these diverse fields.

  9. Site identification presentation: Basalt Waste Isolation Project

    International Nuclear Information System (INIS)

    1979-11-01

    The final step in the site identification process for the Basalt Waste Isolation Project is described. The candidate sites are identified. The site identification methodology is presented. The general objectives which must be met in selecting the final site are listed. Considerations used in the screening process are also listed. Summary tables of the guidelines used are included

  10. Antimicrobial Pesticide Use Site Index

    Science.gov (United States)

    This Use Site Index provides guidance to assist applicants for antimicrobial pesticide registration by helping them identify the data requirements necessary to register a pesticide or support their product registrations.

  11. [Fatal amnioinfusion with previous choriocarcinoma in a parturient woman].

    Science.gov (United States)

    Hrgović, Z; Bukovic, D; Mrcela, M; Hrgović, I; Siebzehnrübl, E; Karelovic, D

    2004-04-01

    The case of 36-year-old tercipare is described who developed choriocharcinoma in a previous pregnancy. During the first term labour the patient developed cardiac arrest, so reanimation and sectio cesarea was performed. A male new-born was delivered in good condition, but even after intensive therapy and reanimation occurred death of parturient woman with picture of disseminate intravascular coagulopathia (DIK). On autopsy and on histology there was no sign of malignant disease, so it was not possible to connect previous choricarcinoma with amniotic fluid embolism. Maybe was place of choriocarcinoma "locus minoris resistentiae" which later resulted with failure in placentation what was hard to prove. On autopsy we found embolia of lung with a microthrombosis of terminal circulation with punctiformis bleeding in mucous, what stands for DIK.

  12. Challenging previous conceptions of vegetarianism and eating disorders.

    Science.gov (United States)

    Fisak, B; Peterson, R D; Tantleff-Dunn, S; Molnar, J M

    2006-12-01

    The purpose of this study was to replicate and expand upon previous research that has examined the potential association between vegetarianism and disordered eating. Limitations of previous research studies are addressed, including possible low reliability of measures of eating pathology within vegetarian samples, use of only a few dietary restraint measures, and a paucity of research examining potential differences in body image and food choice motives of vegetarians versus nonvegetarians. Two hundred and fifty-six college students completed a number of measures of eating pathology and body image, and a food choice motives questionnaire. Interestingly, no significant differences were found between vegetarians and nonvegetarians in measures of eating pathology or body image. However, significant differences in food choice motives were found. Implications for both researchers and clinicians are discussed.

  13. Previously unreported abnormalities in Wolfram Syndrome Type 2.

    Science.gov (United States)

    Akturk, Halis Kaan; Yasa, Seda

    2017-01-01

    Wolfram syndrome (WFS) is a rare autosomal recessive disease with non-autoimmune childhood onset insulin dependent diabetes and optic atrophy. WFS type 2 (WFS2) differs from WFS type 1 (WFS1) with upper intestinal ulcers, bleeding tendency and the lack ofdiabetes insipidus. Li-fespan is short due to related comorbidities. Only a few familieshave been reported with this syndrome with the CISD2 mutation. Here we report two siblings with a clinical diagnosis of WFS2, previously misdiagnosed with type 1 diabetes mellitus and diabetic retinopathy-related blindness. We report possible additional clinical and laboratory findings that have not been pre-viously reported, such as asymptomatic hypoparathyroidism, osteomalacia, growth hormone (GH) deficiency and hepatomegaly. Even though not a requirement for the diagnosis of WFS2 currently, our case series confirm hypogonadotropic hypogonadism to be also a feature of this syndrome, as reported before. © Polish Society for Pediatric Endocrinology and Diabetology.

  14. Previous climatic alterations are caused by the sun

    International Nuclear Information System (INIS)

    Groenaas, Sigbjoern

    2003-01-01

    The article surveys the scientific results of previous research into the contribution of the sun to climatic alterations. The author concludes that there is evidence of eight cold periods after the last ice age and that the alterations largely were due to climate effects from the sun. However, these effects are only causing a fraction of the registered global warming. It is assumed that the human activities are contributing to the rest of the greenhouse effect

  15. Influence of previous knowledge in Torrance tests of creative thinking

    OpenAIRE

    Aranguren, María; Consejo Nacional de Investigaciones Científicas y Técnicas CONICET

    2015-01-01

    The aim of this work is to analyze the influence of study field, expertise and recreational activities participation in Torrance Tests of Creative Thinking (TTCT, 1974) performance. Several hypotheses were postulated to explore the possible effects of previous knowledge in TTCT verbal and TTCT figural university students’ outcomes. Participants in this study included 418 students from five study fields: Psychology;Philosophy and Literature, Music; Engineering; and Journalism and Advertisin...

  16. Measuring site occupancy

    DEFF Research Database (Denmark)

    Rogowska-Wrzesinska, Adelina; Wojdyla, Katarzyna; Williamson, James

    2014-01-01

    occupancy of the modification site. We show that, on one hand, heavily modified cysteines are not necessarily involved in the response to oxidative stress. On the other hand residues with low modification level can be dramatically affected by mild oxidative imbalance. We make use of high resolution mass...... peptides corresponding to 90 proteins. Only 6 modified peptides changed significantly under mild oxidative stress. Quantitative information allowed us to determine relative modification site occupancy of each identified modified residue and pin point heavily modified ones. The method proved to be precise...... and sensitive enough to detect and quantify endogenous levels of oxidative stress on proteome-wide scale and brings a new perspective on the role of the modification site occupancy in cellular redox response....

  17. Analysis of previous screening examinations for patients with breast cancer

    International Nuclear Information System (INIS)

    Lee, Eun Hye; Cha, Joo Hee; Han, Dae Hee; Choi, Young Ho; Hwang, Ki Tae; Ryu, Dae Sik; Kwak, Jin Ho; Moon, Woo Kyung

    2007-01-01

    We wanted to improve the quality of subsequent screening by reviewing the previous screening of breast cancer patients. Twenty-four breast cancer patients who underwent previous screening were enrolled. All 24 took mammograms and 15 patients also took sonograms. We reviewed the screening retrospectively according to the BI-RADS criteria and we categorized the results into false negative, true negative, true positive and occult cancers. We also categorized the causes of false negative cancers into misperception, misinterpretation and technical factors and then we analyzed the attributing factors. Review of the previous screening revealed 66.7% (16/24) false negative, 25.0% (6/24) true negative, and 8.3% (2/24) true positive cancers. False negative cancers were caused by the mammogram in 56.3% (9/16) and by the sonogram in 43.7% (7/16). For the false negative cases, all of misperception were related with mammograms and this was attributed to dense breast, a lesion located at the edge of glandular tissue or the image, and findings seen on one view only. Almost all misinterpretations were related with sonograms and attributed to loose application of the final assessment. To improve the quality of breast screening, it is essential to overcome the main causes of false negative examinations, including misperception and misinterpretation. We need systematic education and strict application of final assessment categories of BI-RADS. For effective communication among physicians, it is also necessary to properly educate them about BI-RADS

  18. Shaft siting decision

    International Nuclear Information System (INIS)

    1987-08-01

    This study identifies and establishes relative guidelines to be used for siting of repository shafts. Weights were determined for the significant factors that impact the selection of shaft locations for a nuclear waste repository in salt. The study identified a total of 45 factors. A panel of experienced mining people utilized the Kepner-Tregoe (K-T) Decision Analysis Process to perform a structured evaluation of each significant shaft siting factor. The evaluation determined that 22 of the factors were absolute constraints and that the other 23 factors were desirable characteristics. The group established the relative weights for each of the 23 desirable characteristics by using a paired comparison method. 8 refs., 2 figs., 5 tabs

  19. Site Restoration

    Energy Technology Data Exchange (ETDEWEB)

    Noynaert, L.; Bruggeman, A.; Cornelissen, R.; Massaut, V.; Rahier, A

    2002-04-01

    The objectives, the programme, and the achievements of SCK-CEN's Site Restoration Department for 2001 are described. Main activities include the decommissioning of the BR3 PWR-reactor as well as other clean-up activities, projects on waste minimisation and the management of spent fuel and the flow of dismantled materials and the recycling of materials from decommissioning activities based on the smelting of metallic materials in specialised foundries. The department provides consultancy and services to external organisations and performs R and D on new techniques including processes for the treatment of various waste components including the reprocessing of spent fuel, the treatment of tritium, the treatment of liquid alkali metals into cabonates through oxidation, the treatment of radioactive organic waste and the reconditioning of bituminised waste products.

  20. Mochovce site

    International Nuclear Information System (INIS)

    1997-01-01

    In Mochovce site the construction of four units of WWER 440 NPP with V-213 type of reactor is being carried out. The financing of Mochovce units completion was resolved in April 1996. The completion work commenced at the construction site under leadership of SKODA Prague, the general supplier. The completion work on building part and tests of constructional electric distributions and lightning constructors started. The revisions in technological part were finished, and final protocols from revisions are the basis for starting of completion work. The assembly of transport container anchorage,ventilation system in hermetic areas and hermetic coverage of pools for stored spent nuclear fuel is being carried out. The pre-completion tests of instrumentation and control of ventilation systems, individual dosimetric control in medical station, and tests of nuclear programme according to commissioning and assembling work schedule at the equipment for physical protection of the NPP area started. Inspection activities at Mochovce were performed in accordance with inspection plan for 1996. Evaluation of routine inspections was performed by means of quarterly protocols. Main findings from the inspections performed in Mochovce were in the following areas: (a) deficiencies in the knowledge of the respective regulation and conditions from the Resolution of the state regulatory body, concerning selected employees; (b) training of the selected employees; (c) aim of the measures imposes by inspectors is to eliminate deficiencies in preparation of programmes for pre-completion and completion testing. NRA SR assessment activities at Mochovce NPP were focused mainly on approving and inspecting of design modification to approving programmes for pre-completion and completion testing of system s and equipment and on approving quality assurance programmes. The suggestions of international missions, which reviewed Mochovce safety in the years, were taken into consideration in the programme

  1. Milky Way Past Was More Turbulent Than Previously Known

    Science.gov (United States)

    2004-04-01

    Results of 1001 observing nights shed new light on our Galaxy [1] Summary A team of astronomers from Denmark, Switzerland and Sweden [2] has achieved a major breakthrough in our understanding of the Milky Way, the galaxy in which we live. After more than 1,000 nights of observations spread over 15 years, they have determined the spatial motions of more than 14,000 solar-like stars residing in the neighbourhood of the Sun. For the first time, the changing dynamics of the Milky Way since its birth can now be studied in detail and with a stellar sample sufficiently large to allow a sound analysis. The astronomers find that our home galaxy has led a much more turbulent and chaotic life than previously assumed. PR Photo 10a/04: Distribution on the sky of the observed stars. PR Photo 10b/04: Stars in the solar neigbourhood and the Milky Way galaxy (artist's view). PR Video Clip 04/04: The motions of the observed stars during the past 250 million years. Unknown history Home is the place we know best. But not so in the Milky Way - the galaxy in which we live. Our knowledge of our nearest stellar neighbours has long been seriously incomplete and - worse - skewed by prejudice concerning their behaviour. Stars were generally selected for observation because they were thought to be "interesting" in some sense, not because they were typical. This has resulted in a biased view of the evolution of our Galaxy. The Milky Way started out just after the Big Bang as one or more diffuse blobs of gas of almost pure hydrogen and helium. With time, it assembled into the flattened spiral galaxy which we inhabit today. Meanwhile, generation after generation of stars were formed, including our Sun some 4,700 million years ago. But how did all this really happen? Was it a rapid process? Was it violent or calm? When were all the heavier elements formed? How did the Milky Way change its composition and shape with time? Answers to these and many other questions are 'hot' topics for the

  2. 2016 Inspection and Annual Site Status Report for the Site A/Plot M, Illinois, Decommissioned Reactor Site July 2016

    Energy Technology Data Exchange (ETDEWEB)

    Murl, Jeffrey [USDOE Office of Legacy Management, Washington, DC (United States); Miller, Michele [Navarro Research and Engineering, Oak Ridge, TN (United States)

    2016-07-01

    The Site A/Plot M, Illinois, Decommissioned Reactor Site was inspected on May 17, 2016. The site, located within Cook County forest preserve that is open to the public, was found to be in good condition with one exception. Erosion on top of the grass-covered mound at Plot M continues to be a concern as presented in previous inspections. Ruts form in the soil on top of Plot M as a result of bike traffic using the open field as a pass thru between established bike trails within the forest preserve. Argonne National Laboratory (ANL) who is contracted directly from U.S. Department of Energy (DOE) has filled in the ruts with top soil and reseeding remains an ongoing process. Reseeded areas from 2015 are progressing nicely. No cause for a follow-up inspection was identified. In 2015, ANL plugged and abandoned 8 of 25 monitoring wells (BH41, BH51, BH52, BH54, DH9, DH10, DH13, and DH17). The 17 groundwater monitoring wells remaining at the site were inspected to confirm that they were locked and in good condition. Preliminary environmental monitoring results for 2015 are provided in a draft report titled Surveillance of Site A and Plot M, Report for 2015, prepared by ANL. The report also contains results of an independent analysis conducted by the Illinois Emergency Management Agency on some of the samples collected by ANL in 2015. The draft report states that the results of the surveillance program continue to indicate that the impact of radioactivity at Site A/Plot M is very low and does not endanger the health of those living in the area or visiting the site. The ANL monitoring report will be made available to the public on the DOE Office of Legacy Management public website when it is issued as final. A new county forest preserve campsite opened in 2015 at Bull Frog Lake, which is east of Plot M. Hiking trails connect Bull Frog Lake with Site A/Plot M. The site might receive more traffic from forest preserve visitors now that this new campsite is opened.

  3. SITE-94. Mineralogy of the Aespoe site

    International Nuclear Information System (INIS)

    Andersson, Karin

    1996-12-01

    The water composition has several impacts on the repository. It will influence the behaviour of the engineered materials (e.g. corrosion). It may also determine the possible solubility and speciation of released radionuclides. It also acts as a transport medium for the released elements. The groundwater composition and the potential development of the composition due to the presence of the repository as well as due to external variations is thus an important issue in a safety analysis. The development of the groundwater composition is strongly dependent on reactions with the minerals present in water bearing fractures. Here equilibrium chemistry may be of importance, but also reaction kinetics is important to the long-term behaviour. Within the SITE-94 project, a safety analysis is performed for the conditions at the Aespoe site. The mineralogy of the area has been evaluated from drill cores at various places at the site. In this report a recommendation for selection of mineralogy to be used in geochemical modelling of the repository is given. Calcite and iron containing minerals dominate the fracture filling mineralogy at the Aespoe site. Some typical fracture filling mineralogies may be identified in the fractures: epidote, chlorite, calcite, hematite, some illite/smectite + quartz, fluorite, pyrite and goethite. In addition to these a number of minor minerals are found in the fractures. Uncertainties in the fracture filling data may be due to problems when taking out the drill cores. Drilling water may remove important clay minerals and sealed fractures may be reopened mechanically and treated as water conducting fractures. The problem of determining the variability of the mineralogy along the flow paths also remains. This problem will never be solved when the investigation is performed by drilling investigation holes

  4. Moyamoya disease in a child with previous acute necrotizing encephalopathy

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Taik-Kun; Cha, Sang Hoon; Chung, Kyoo Byung; Kim, Jung Hyuck; Kim, Baek Hyun; Chung, Hwan Hoon [Department of Diagnostic Radiology, Korea University College of Medicine, Ansan Hospital, 516 Kojan-Dong, Ansan City, Kyungki-Do 425-020 (Korea); Eun, Baik-Lin [Department of Pediatrics, Korea University College of Medicine, Seoul (Korea)

    2003-09-01

    A previously healthy 24-day-old boy presented with a 2-day history of fever and had a convulsion on the day of admission. MRI showed abnormal signal in the thalami, caudate nuclei and central white matter. Acute necrotising encephalopathy was diagnosed, other causes having been excluded after biochemical and haematological analysis of blood, urine and CSF. He recovered, but with spastic quadriparesis. At the age of 28 months, he suffered sudden deterioration of consciousness and motor weakness of his right limbs. MRI was consistent with an acute cerebrovascular accident. Angiography showed bilateral middle cerebral artery stenosis or frank occlusion with numerous lenticulostriate collateral vessels consistent with moyamoya disease. (orig.)

  5. MCNP HPGe detector benchmark with previously validated Cyltran model.

    Science.gov (United States)

    Hau, I D; Russ, W R; Bronson, F

    2009-05-01

    An exact copy of the detector model generated for Cyltran was reproduced as an MCNP input file and the detection efficiency was calculated similarly with the methodology used in previous experimental measurements and simulation of a 280 cm(3) HPGe detector. Below 1000 keV the MCNP data correlated to the Cyltran results within 0.5% while above this energy the difference between MCNP and Cyltran increased to about 6% at 4800 keV, depending on the electron cut-off energy.

  6. HEART TRANSPLANTATION IN PATIENTS WITH PREVIOUS OPEN HEART SURGERY

    Directory of Open Access Journals (Sweden)

    R. Sh. Saitgareev

    2016-01-01

    Full Text Available Heart Transplantation (HTx to date remains the most effective and radical method of treatment of patients with end-stage heart failure. The defi cit of donor hearts is forcing to resort increasingly to the use of different longterm mechanical circulatory support systems, including as a «bridge» to the follow-up HTx. According to the ISHLT Registry the number of recipients underwent cardiopulmonary bypass surgery increased from 40% in the period from 2004 to 2008 to 49.6% for the period from 2009 to 2015. HTx performed in repeated patients, on the one hand, involves considerable technical diffi culties and high risks; on the other hand, there is often no alternative medical intervention to HTx, and if not dictated by absolute contradictions the denial of the surgery is equivalent to 100% mortality. This review summarizes the results of a number of published studies aimed at understanding the immediate and late results of HTx in patients, previously underwent open heart surgery. The effect of resternotomy during HTx and that of the specifi c features associated with its implementation in recipients previously operated on open heart, and its effects on the immediate and long-term survival were considered in this review. Results of studies analyzing the risk factors for perioperative complications in repeated recipients were also demonstrated. Separately, HTx risks after implantation of prolonged mechanical circulatory support systems were examined. The literature does not allow to clearly defi ning the impact factor of earlier performed open heart surgery on the course of perioperative period and on the prognosis of survival in recipients who underwent HTx. On the other hand, subject to the regular fl ow of HTx and the perioperative period the risks in this clinical situation are justifi ed as a long-term prognosis of recipients previously conducted open heart surgery and are comparable to those of patients who underwent primary HTx. Studies

  7. Umatilla Satellite and Release Sites Project : Final Siting Report.

    Energy Technology Data Exchange (ETDEWEB)

    Montgomery, James M.

    1992-04-01

    This report presents the results of site analysis for the Umatilla Satellite and Release Sites Project. The purpose of this project is to provide engineering services for the siting and conceptual design of satellite and release facilities for the Umatilla Basin hatchery program. The Umatilla Basin hatchery program consists of artificial production facilities for salmon and steelhead to enhance production in the Umatilla River as defined in the Umatilla master plan approved in 1989 by the Northwest Power Planning Council. Facilities identified in the master plan include adult salmon broodstock holding and spawning facilities, facilities for recovery, acclimation, and/or extended rearing of salmon juveniles, and development of river sites for release of hatchery salmon and steelhead. The historic and current distribution of fall chinook, summer chinook, and coho salmon and steelhead trout was summarized for the Umatilla River basin. Current and future production and release objectives were reviewed. Twenty seven sites were evaluated for the potential and development of facilities. Engineering and environmental attributes of the sites were evaluated and compared to facility requirements for water and space. Site screening was conducted to identify the sites with the most potential for facility development. Alternative sites were selected for conceptual design of each facility type. A proposed program for adult holding facilities, final rearing/acclimation, and direct release facilities was developed.

  8. Identifying Strategic Scientific Opportunities

    Science.gov (United States)

    As NCI's central scientific strategy office, CRS collaborates with the institute's divisions, offices, and centers to identify research opportunities to advance NCI's vision for the future of cancer research.

  9. Identifying Breast Cancer Oncogenes

    Science.gov (United States)

    2011-10-01

    cells we observed that it promoted transformation of HMLE cells, suggesting a tumor suppressive role of Merlin in breast cancer (Figure 4B). A...08-1-0767 TITLE: Identifying Breast Cancer Oncogenes PRINCIPAL INVESTIGATOR: Yashaswi Shrestha...Standard Form 298 (Rev. 8-98) Prescribed by ANSI Std. Z39.18 W81XWH-08-1-0767 Identifying Breast Cancer Oncogenes Yashaswi Shrestha Dana-Farber

  10. The Relationship of Lumbar Multifidus Muscle Morphology to Previous, Current, and Future Low Back Pain

    DEFF Research Database (Denmark)

    Hebert, Jeffrey J; Kjær, Per; Fritz, Julie M

    2014-01-01

    of LBP after five and nine years.Summary of Background Data. Although low back pain (LBP) is a major source of disease burden, the biologic determinants of LBP are poorly understood.Methods. Participants were 40-year-old adults randomly sampled from a Danish population and followed-up at ages 45 and 49....... At each time point, participants underwent magnetic resonance imaging and reported ever having had LBP, LBP in the previous year, non-trivial LBP in the previous year, or a history of pain radiating into the legs. Pixel intensity and frequencies from T1-weighted magnetic resonance images identified...

  11. Emergency Preparedness Hazards Assessment for solid waste management facilities in E-area not previously evaluated

    International Nuclear Information System (INIS)

    Hadlock, D.J.

    1999-01-01

    This report documents the facility Emergency Preparedness Hazards Assessment (EPHA) for the Solid Waste Management Department (SWMD) activities located on the Department of Energy (DOE) Savannah River Site (SRS) within E Area that are not described in the EPHAs for Mixed Hazardous Waste storage, the TRU Waste Storage Pads or the E-Area Vaults. The hazards assessment is intended to identify and analyze those hazards that are significant enough to warrant consideration in the SWMD operational emergency management program

  12. Relationship of deer and moose populations to previous winters' snow

    Science.gov (United States)

    Mech, L.D.; McRoberts, R.E.; Peterson, R.O.; Page, R.E.

    1987-01-01

    (1) Linear regression was used to relate snow accumulation during single and consecutive winters with white-tailed deer (Odocoileus virginianus) fawn:doe ratios, mosse (Alces alces) twinning rates and calf:cow ratios, and annual changes in deer and moose populations. Significant relationships were found between snow accumulation during individual winters and these dependent variables during the following year. However, the strongest relationships were between the dependent variables and the sums of the snow accumulations over the previous three winters. The percentage of the variability explained was 36 to 51. (2) Significant relationships were also found between winter vulnerability of moose calves and the sum of the snow accumulations in the current, and up to seven previous, winters, with about 49% of the variability explained. (3) No relationship was found between wolf numbers and the above dependent variables. (4) These relationships imply that winter influences on maternal nutrition can accumulate for several years and that this cumulative effect strongly determines fecundity and/or calf and fawn survivability. Although wolf (Canis lupus L.) predation is the main direct mortality agent on fawns and calves, wolf density itself appears to be secondary to winter weather in influencing the deer and moose populations.

  13. Do emotional intelligence and previous caring experience influence student nurse performance? A comparative analysis.

    Science.gov (United States)

    Stenhouse, Rosie; Snowden, Austyn; Young, Jenny; Carver, Fiona; Carver, Hannah; Brown, Norrie

    2016-08-01

    Reports of poor nursing care have focused attention on values based selection of candidates onto nursing programmes. Values based selection lacks clarity and valid measures. Previous caring experience might lead to better care. Emotional intelligence (EI) might be associated with performance, is conceptualised and measurable. To examine the impact of 1) previous caring experience, 2) emotional intelligence 3) social connection scores on performance and retention in a cohort of first year nursing and midwifery students in Scotland. A longitudinal, quasi experimental design. Adult and mental health nursing, and midwifery programmes in a Scottish University. Adult, mental health and midwifery students (n=598) completed the Trait Emotional Intelligence Questionnaire-short form and Schutte's Emotional Intelligence Scale on entry to their programmes at a Scottish University, alongside demographic and previous caring experience data. Social connection was calculated from a subset of questions identified within the TEIQue-SF in a prior factor and Rasch analysis. Student performance was calculated as the mean mark across the year. Withdrawal data were gathered. 598 students completed baseline measures. 315 students declared previous caring experience, 277 not. An independent-samples t-test identified that those without previous caring experience scored higher on performance (57.33±11.38) than those with previous caring experience (54.87±11.19), a statistically significant difference of 2.47 (95% CI, 0.54 to 4.38), t(533)=2.52, p=.012. Emotional intelligence scores were not associated with performance. Social connection scores for those withdrawing (mean rank=249) and those remaining (mean rank=304.75) were statistically significantly different, U=15,300, z=-2.61, p$_amp_$lt;0.009. Previous caring experience led to worse performance in this cohort. Emotional intelligence was not a useful indicator of performance. Lower scores on the social connection factor were associated

  14. [ANTITHROMBOTIC MEDICATION IN PREGNANT WOMEN WITH PREVIOUS INTRAUTERINE GROWTH RESTRICTION].

    Science.gov (United States)

    Neykova, K; Dimitrova, V; Dimitrov, R; Vakrilova, L

    2016-01-01

    To analyze pregnancy outcome in patients who were on antithrombotic medication (AM) because of previous pregnancy with fetal intrauterine growth restriction (IUGR). The studied group (SG) included 21 pregnancies in 15 women with history of previous IUGR. The patients were on low dose aspirin (LDA) and/or low molecular weight heparin (LMWH). Pregnancy outcome was compared to the one in two more groups: 1) primary group (PG) including the previous 15 pregnancies with IUGR of the same women; 2) control group (CG) including 45 pregnancies of women matched for parity with the ones in the SG, with no history of IUGR and without medication. The SG, PG and CG were compared for the following: mean gestational age (g.a.) at birth, mean birth weight (BW), proportion of cases with early preeclampsia (PE), IUGR (total, moderate, and severe), intrauterine fetal death (IUFD), neonatal death (NND), admission to NICU, cesarean section (CS) because of chronic or acute fetal distress (FD) related to IUGR, PE or placental abruption. Student's t-test was applied to assess differences between the groups. P values < 0.05 were considered statistically significant. The differences between the SG and the PG regarding mean g. a. at delivery (33.7 and 29.8 w.g. respectively) and the proportion of babies admitted to NICU (66.7% vs. 71.4%) were not statistically significant. The mean BW in the SG (2114,7 g.) was significantly higher than in the PG (1090.8 g.). In the SG compared with the PG there were significantly less cases of IUFD (14.3% and 53.3% respectively), early PE (9.5% vs. 46.7%) moderate and severe IUGR (10.5% and 36.8% vs. 41.7% and 58.3%). Neonatal mortality in the SG (5.6%) was significantly lower than in the PG (57.1%), The proportion of CS for FD was not significantly different--53.3% in the SG and 57.1% in the PG. On the other hand, comparison between the SG and the CG demonstrated significantly lower g.a. at delivery in the SG (33.7 vs. 38 w.g.) an lower BW (2114 vs. 3094 g

  15. The genomic HDV ribozyme utilizes a previously unnoticed U-turn motif to accomplish fast site-specific catalysis

    Czech Academy of Sciences Publication Activity Database

    Šefčíková, J.; Krasovská, Maryna V.; Šponer, Jiří; Walter, N.G.

    2007-01-01

    Roč. 35, č. 6 (2007), s. 1933-1946 ISSN 0305-1048 R&D Projects: GA ČR(CZ) GA203/05/0388; GA ČR(CZ) GA203/05/0009; GA AV ČR(CZ) 1QS500040581; GA AV ČR(CZ) IAA400550701; GA MŠk(CZ) LC512 Institutional research plan: CEZ:AV0Z50040702; CEZ:AV0Z40550506 Keywords : hepatitis delta virus * molecular dynamics * self-cleavage Subject RIV: BO - Biophysics Impact factor: 6.954, year: 2007

  16. An effective automatic procedure for testing parameter identifiability of HIV/AIDS models.

    Science.gov (United States)

    Saccomani, Maria Pia

    2011-08-01

    Realistic HIV models tend to be rather complex and many recent models proposed in the literature could not yet be analyzed by traditional identifiability testing techniques. In this paper, we check a priori global identifiability of some of these nonlinear HIV models taken from the recent literature, by using a differential algebra algorithm based on previous work of the author. The algorithm is implemented in a software tool, called DAISY (Differential Algebra for Identifiability of SYstems), which has been recently released (DAISY is freely available on the web site http://www.dei.unipd.it/~pia/ ). The software can be used to automatically check global identifiability of (linear and) nonlinear models described by polynomial or rational differential equations, thus providing a general and reliable tool to test global identifiability of several HIV models proposed in the literature. It can be used by researchers with a minimum of mathematical background.

  17. Deepwater Gulf of Mexico more profitable than previously thought

    International Nuclear Information System (INIS)

    Craig, M.J.K.; Hyde, S.T.

    1997-01-01

    Economic evaluations and recent experience show that the deepwater Gulf of Mexico (GOM) is much more profitable than previously thought. Four factors contributing to the changed viewpoint are: First, deepwater reservoirs have proved to have excellent productive capacity, distribution, and continuity when compared to correlative-age shelf deltaic sands. Second, improved technologies and lower perceived risks have lowered the cost of floating production systems (FPSs). Third, projects now get on-line quicker. Fourth, a collection of other important factors are: Reduced geologic risk and associated high success rates for deepwater GOM wells due primarily to improved seismic imaging and processing tools (3D, AVO, etc.); absence of any political risk in the deepwater GOM (common overseas, and very significant in some international areas); and positive impact of deepwater federal royalty relief. This article uses hypothetical reserve distributions and price forecasts to illustrate indicative economics of deepwater prospects. Economics of Shell Oil Co.'s three deepwater projects are also discussed

  18. Interference from previous distraction disrupts older adults' memory.

    Science.gov (United States)

    Biss, Renée K; Campbell, Karen L; Hasher, Lynn

    2013-07-01

    Previously relevant information can disrupt the ability of older adults to remember new information. Here, the researchers examined whether prior irrelevant information, or distraction, can also interfere with older adults' memory for new information. Younger and older adults first completed a 1-back task on pictures that were superimposed with distracting words. After a delay, participants learned picture-word paired associates and memory was tested using picture-cued recall. In 1 condition (high interference), some pairs included pictures from the 1-back task now paired with new words. In a low-interference condition, the transfer list used all new items. Older adults had substantially lower cued-recall performance in the high- compared with the low-interference condition. In contrast, younger adults' performance did not vary across conditions. These findings suggest that even never-relevant information from the past can disrupt older adults' memory for new associations.

  19. The long-term consequences of previous hyperthyroidism

    DEFF Research Database (Denmark)

    Hjelm Brandt Kristensen, Frans

    2015-01-01

    Thyroid hormones affect every cell in the human body, and the cardiovascular changes associated with increased levels of thyroid hormones are especially well described. As an example, short-term hyperthyroidism has positive chronotropic and inotropic effects on the heart, leading to a hyperdynamic...... with CVD, LD and DM both before and after the diagnosis of hyperthyroidism. Although the design used does not allow a stringent distinction between cause and effect, the findings indicate a possible direct association between hyperthyroidism and these morbidities, or vice versa....... vascular state. While it is biologically plausible that these changes may induce long-term consequences, the insight into morbidity as well as mortality in patients with previous hyperthyroidism is limited. The reasons for this are a combination of inadequately powered studies, varying definitions...

  20. Using Soluble Reactive Phosphorus and Ammonia to Identify Point Source Discharge from Large Livestock Facilities

    Science.gov (United States)

    Borrello, M. C.; Scribner, M.; Chessin, K.

    2013-12-01

    A growing body of research draws attention to the negative environmental impacts on surface water from large livestock facilities. These impacts are mostly in the form of excessive nutrient loading resulting in significantly decreased oxygen levels. Over-application of animal waste on fields as well as direct discharge into surface water from facilities themselves has been identified as the main contributor to the development of hypoxic zones in Lake Erie, Chesapeake Bay and the Gulf of Mexico. Some regulators claim enforcement of water quality laws is problematic because of the nature and pervasiveness of non-point source impacts. Any direct discharge by a facility is a violation of permits governed by the Clean Water Act, unless the facility has special dispensation for discharge. Previous research by the principal author and others has shown runoff and underdrain transport are the main mechanisms by which nutrients enter surface water. This study utilized previous work to determine if the effects of non-point source discharge can be distinguished from direct (point-source) discharge using simple nutrient analysis and dissolved oxygen (DO) parameters. Nutrient and DO parameters were measured from three sites: 1. A stream adjacent to a field receiving manure, upstream of a large livestock facility with a history of direct discharge, 2. The same stream downstream of the facility and 3. A stream in an area relatively unimpacted by large-scale agriculture (control site). Results show that calculating a simple Pearson correlation coefficient (r) of soluble reactive phosphorus (SRP) and ammonia over time as well as temperature and DO, distinguishes non-point source from point source discharge into surface water. The r value for SRP and ammonia for the upstream site was 0.01 while the r value for the downstream site was 0.92. The control site had an r value of 0.20. Likewise, r values were calculated on temperature and DO for each site. High negative correlations

  1. Identifying Knowledge and Communication

    Directory of Open Access Journals (Sweden)

    Eduardo Coutinho Lourenço de Lima

    2006-12-01

    Full Text Available In this paper, I discuss how the principle of identifying knowledge which Strawson advances in ‘Singular Terms and Predication’ (1961, and in ‘Identifying Reference and Truth-Values’ (1964 turns out to constrain communication. The principle states that a speaker’s use of a referring expression should invoke identifying knowledge on the part of the hearer, if the hearer is to understand what the speaker is saying, and also that, in so referring, speakers are attentive to hearers’ epistemic states. In contrasting it with Russell’s Principle (Evans 1982, as well as with the principle of identifying descriptions (Donnellan 1970, I try to show that the principle of identifying knowledge, ultimately a condition for understanding, makes sense only in a situation of conversation. This allows me to conclude that the cooperative feature of communication (Grice 1975 and reference (Clark andWilkes-Gibbs 1986 holds also at the understanding level. Finally, I discuss where Strawson’s views seem to be unsatisfactory, and suggest how they might be improved.

  2. Is Previous Respiratory Disease a Risk Factor for Lung Cancer?

    Science.gov (United States)

    Denholm, Rachel; Schüz, Joachim; Straif, Kurt; Stücker, Isabelle; Jöckel, Karl-Heinz; Brenner, Darren R.; De Matteis, Sara; Boffetta, Paolo; Guida, Florence; Brüske, Irene; Wichmann, Heinz-Erich; Landi, Maria Teresa; Caporaso, Neil; Siemiatycki, Jack; Ahrens, Wolfgang; Pohlabeln, Hermann; Zaridze, David; Field, John K.; McLaughlin, John; Demers, Paul; Szeszenia-Dabrowska, Neonila; Lissowska, Jolanta; Rudnai, Peter; Fabianova, Eleonora; Dumitru, Rodica Stanescu; Bencko, Vladimir; Foretova, Lenka; Janout, Vladimir; Kendzia, Benjamin; Peters, Susan; Behrens, Thomas; Vermeulen, Roel; Brüning, Thomas; Kromhout, Hans

    2014-01-01

    Rationale: Previous respiratory diseases have been associated with increased risk of lung cancer. Respiratory conditions often co-occur and few studies have investigated multiple conditions simultaneously. Objectives: Investigate lung cancer risk associated with chronic bronchitis, emphysema, tuberculosis, pneumonia, and asthma. Methods: The SYNERGY project pooled information on previous respiratory diseases from 12,739 case subjects and 14,945 control subjects from 7 case–control studies conducted in Europe and Canada. Multivariate logistic regression models were used to investigate the relationship between individual diseases adjusting for co-occurring conditions, and patterns of respiratory disease diagnoses and lung cancer. Analyses were stratified by sex, and adjusted for age, center, ever-employed in a high-risk occupation, education, smoking status, cigarette pack-years, and time since quitting smoking. Measurements and Main Results: Chronic bronchitis and emphysema were positively associated with lung cancer, after accounting for other respiratory diseases and smoking (e.g., in men: odds ratio [OR], 1.33; 95% confidence interval [CI], 1.20–1.48 and OR, 1.50; 95% CI, 1.21–1.87, respectively). A positive relationship was observed between lung cancer and pneumonia diagnosed 2 years or less before lung cancer (OR, 3.31; 95% CI, 2.33–4.70 for men), but not longer. Co-occurrence of chronic bronchitis and emphysema and/or pneumonia had a stronger positive association with lung cancer than chronic bronchitis “only.” Asthma had an inverse association with lung cancer, the association being stronger with an asthma diagnosis 5 years or more before lung cancer compared with shorter. Conclusions: Findings from this large international case–control consortium indicate that after accounting for co-occurring respiratory diseases, chronic bronchitis and emphysema continue to have a positive association with lung cancer. PMID:25054566

  3. Urethrotomy has a much lower success rate than previously reported.

    Science.gov (United States)

    Santucci, Richard; Eisenberg, Lauren

    2010-05-01

    We evaluated the success rate of direct vision internal urethrotomy as a treatment for simple male urethral strictures. A retrospective chart review was performed on 136 patients who underwent urethrotomy from January 1994 through March 2009. The Kaplan-Meier method was used to analyze stricture-free probability after the first, second, third, fourth and fifth urethrotomy. Patients with complex strictures (36) were excluded from the study for reasons including previous urethroplasty, neophallus or previous radiation, and 24 patients were lost to followup. Data were available for 76 patients. The stricture-free rate after the first urethrotomy was 8% with a median time to recurrence of 7 months. For the second urethrotomy stricture-free rate was 6% with a median time to recurrence of 9 months. For the third urethrotomy stricture-free rate was 9% with a median time to recurrence of 3 months. For procedures 4 and 5 stricture-free rate was 0% with a median time to recurrence of 20 and 8 months, respectively. Urethrotomy is a popular treatment for male urethral strictures. However, the performance characteristics are poor. Success rates were no higher than 9% in this series for first or subsequent urethrotomy during the observation period. Most of the patients in this series will be expected to experience failure with longer followup and the expected long-term success rate from any (1 through 5) urethrotomy approach is 0%. Urethrotomy should be considered a temporizing measure until definitive curative reconstruction can be planned. 2010 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

  4. Typing DNA profiles from previously enhanced fingerprints using direct PCR.

    Science.gov (United States)

    Templeton, Jennifer E L; Taylor, Duncan; Handt, Oliva; Linacre, Adrian

    2017-07-01

    Fingermarks are a source of human identification both through the ridge patterns and DNA profiling. Typing nuclear STR DNA markers from previously enhanced fingermarks provides an alternative method of utilising the limited fingermark deposit that can be left behind during a criminal act. Dusting with fingerprint powders is a standard method used in classical fingermark enhancement and can affect DNA data. The ability to generate informative DNA profiles from powdered fingerprints using direct PCR swabs was investigated. Direct PCR was used as the opportunity to generate usable DNA profiles after performing any of the standard DNA extraction processes is minimal. Omitting the extraction step will, for many samples, be the key to success if there is limited sample DNA. DNA profiles were generated by direct PCR from 160 fingermarks after treatment with one of the following dactyloscopic fingerprint powders: white hadonite; silver aluminium; HiFi Volcano silk black; or black magnetic fingerprint powder. This was achieved by a combination of an optimised double-swabbing technique and swab media, omission of the extraction step to minimise loss of critical low-template DNA, and additional AmpliTaq Gold ® DNA polymerase to boost the PCR. Ninety eight out of 160 samples (61%) were considered 'up-loadable' to the Australian National Criminal Investigation DNA Database (NCIDD). The method described required a minimum of working steps, equipment and reagents, and was completed within 4h. Direct PCR allows the generation of DNA profiles from enhanced prints without the need to increase PCR cycle numbers beyond manufacturer's recommendations. Particular emphasis was placed on preventing contamination by applying strict protocols and avoiding the use of previously used fingerprint brushes. Based on this extensive survey, the data provided indicate minimal effects of any of these four powders on the chance of obtaining DNA profiles from enhanced fingermarks. Copyright © 2017

  5. Ecthyma gangrenosum in the periorbital region in a previously healthy immunocompetent woman without bacteremia

    Directory of Open Access Journals (Sweden)

    Somenath Sarkar

    2016-01-01

    Full Text Available Ecthyma gangrenosum (EG is a cutaneous lesion classically associated with potentially fatal Pseudomonas septicemia in immunocompromised patients. Other bacterial and fungal pathogens have also been implicated. Although EG typically occurs in immunocompromised or neutropenic patients, it may occasionally affect a previously healthy person. The cutaneous findings are characteristic with small indurated papulovesicles progressing rapidly to necrotic ulcers with surrounding erythema and a central black Eschar. While lesions can occur at any site, most are commonly found over the buttocks, perineum, limbs, and axillae. We describe a case of EG in periorbital region in a previously healthy woman who responded to appropriate antibiotic treatment for Pseudomonas. It is very important to establish the diagnosis early so that appropriate systemic antibiotic therapy can be initiated to reduce morbidity and potential mortality.

  6. Streamlined approach for environmental restoration closure report for Corrective Action Unit 452: Historical underground storage tank release sites, Nevada Test Site, Nevada

    International Nuclear Information System (INIS)

    1998-04-01

    This report addresses the site characterization of three historical underground storage tank (UST) petroleum hydrocarbon release sites identified as 25-3101-1, 25-3102-3, and 25-3152-1. The sites are located within the Nevada Test Site in Area 25 at Buildings 3101, 3102, and 3152. The characterization was completed to support administrative closure of the sites. Characterization was completed using drilling equipment to delineate the extent of hydrocarbon impact. Clean closure had been previously attempted at each of these sites using backhoe equipment without success due to adjacent structures, buried utilities, or depth restrictions associated with each site. Although the depth and extent of hydrocarbon impact was determined to be too extensive for clean closure, it was verified through drilling that the sites should be closed through an administrative closure. The Nevada Administrative Code ''A Through K'' evaluation completed for each site supports that there is no significant risk to human health or the environment from the impacted soils remaining at each site

  7. Siting the superconducting super collider

    International Nuclear Information System (INIS)

    Price, R.; Rooney, R.C.

    1988-01-01

    At the request of the Department of Energy, the National Academy of Sciences and the National Academy of Engineering established the Super Collider Site Evaluation Committee to evaluate the suitability of proposed sites for the Superconducting Super Collider. Thirty-six proposals were examined by the committee. Using the set of criteria announced by DOE in its Invitation for Site Proposals, the committee identified eight sites that merited inclusion on a ''best qualified list.'' The list represents the best collective judgment of 21 individuals, carefully chosen for their expertise and impartiality, after a detailed assessment of the proposals using 19 technical subcriteria and DOE's life cycle cost estimates. The sites, in alphabetical order, are: Arizona/Maricopa; Colorado; Illinois; Michigan/Stockbridge; New York/Rochester; North Carolina; Tennessee; and Texas/Dallas-Fort Worth. The evaluation of these sites and the Superconducting Super Collider are discussed in this book

  8. FRS (Facility Registration System) Sites, Geographic NAD83, EPA (2007) [facility_registration_system_sites_LA_EPA_2007

    Data.gov (United States)

    Louisiana Geographic Information Center — This dataset contains locations of Facility Registry System (FRS) sites which were pulled from a centrally managed database that identifies facilities, sites or...

  9. Pactamycin binding site on archaebacterial and eukaryotic ribosomes

    International Nuclear Information System (INIS)

    Tejedor, F.; Amils, R.; Ballesta, J.P.G.

    1987-01-01

    The presence of a photoreactive acetophenone group in the protein synthesis inhibitor pactamycin and the possibility of obtaining active iodinated derivatives that retain full biological activity allow the antibiotic binding site on Saccharomyces cerevisiae and archaebacterium Sulfolobus solfataricus ribosomes to be photoaffinity labeled. Four major labeled proteins have been identified in the yeast ribosomes, i.e., YS10, YS18, YS21/24, and YS30, while proteins AL1a, AS10/L8, AS18/20, and AS21/22 appeared as radioactive spots in S. solfataricus. There seems to be a correlation between some of the proteins labeled in yeast and those previously reported in Escherichia coli indicating that the pactamycin binding sites of both species, which are in the small subunit close to the initiation factors and mRNA binding sites, must have similar characteristics

  10. Splice Site Mutations in the ATP7A Gene

    DEFF Research Database (Denmark)

    Skjørringe, Tina; Tümer, Zeynep; Møller, Lisbeth Birk

    2011-01-01

    Menkes disease (MD) is caused by mutations in the ATP7A gene. We describe 33 novel splice site mutations detected in patients with MD or the milder phenotypic form, Occipital Horn Syndrome. We review these 33 mutations together with 28 previously published splice site mutations. We investigate 12...... mutations for their effect on the mRNA transcript in vivo. Transcriptional data from another 16 mutations were collected from the literature. The theoretical consequences of splice site mutations, predicted with the bioinformatics tool Human Splice Finder, were investigated and evaluated in relation...... to in vivo results. Ninety-six percent of the mutations identified in 45 patients with classical MD were predicted to have a significant effect on splicing, which concurs with the absence of any detectable wild-type transcript in all 19 patients investigated in vivo. Sixty-seven percent of the mutations...

  11. The pathogenicity of genetic variants previously associated with left ventricular non-compaction

    DEFF Research Database (Denmark)

    Abbasi, Yeganeh; Jabbari, Javad; Jabbari, Reza

    2016-01-01

    BACKGROUND: Left ventricular non-compaction (LVNC) is a rare cardiomyopathy. Many genetic variants have been associated with LVNC. However, the number of the previous LVNC-associated variants that are common in the background population remains unknown. The aim of this study was to provide...... an updated list of previously reported LVNC-associated variants with biologic description and investigate the prevalence of LVNC variants in healthy general population to find false-positive LVNC-associated variants. METHODS AND RESULTS: The Human Gene Mutation Database and PubMed were systematically...... searched to identify all previously reported LVNC-associated variants. Thereafter, the Exome Sequencing Project (ESP) and the Exome Aggregation Consortium (ExAC), that both represent the background population, was searched for all variants. Four in silico prediction tools were assessed to determine...

  12. Identifying and Managing Risk.

    Science.gov (United States)

    Abraham, Janice M.

    1999-01-01

    The role of the college or university chief financial officer in institutional risk management is (1) to identify risk (physical, casualty, fiscal, business, reputational, workplace safety, legal liability, employment practices, general liability), (2) to develop a campus plan to reduce and control risk, (3) to transfer risk, and (4) to track and…

  13. Parental anxiety associated with Kawasaki disease in previously healthy children.

    Science.gov (United States)

    Chahal, Nita; Clarizia, Nadia A; McCrindle, Brian W; Boydell, Katherine M; Obadia, Maya; Manlhiot, Cedric; Dillenburg, Rejane; Yeung, Rae S M

    2010-01-01

    The objective of this study was to explore the lived experience of parents of children diagnosed with Kawasaki disease (KD) and to identify factors associated with increased levels of parental anxiety. Three focus groups were conducted including 25 parents of 17 patients with KD, seven (41%) of whom had coronary artery complications. A conceptual model was developed to depict parental experiences and illustrate the key issues related to heightened anxiety. Themes identified included anxiety related to the child's sudden illness and delay in obtaining a correct diagnosis because of the lack of health care providers' awareness and knowledge regarding KD. Parents were frustrated by the lack of information available in lay language and the limited scientific knowledge regarding the long-term consequences of the disease. Parents also reported positive transformations and different perspective toward challenges in life. However, the parents of children with coronary artery complications expressed persistent anxiety even years after the acute phase of the illness due to the uncertainty of the long-term prognosis. There remains a critical need for richly textured research data on the perspective and experience of families of children with KD. Copyright 2010 National Association of Pediatric Nurse Practitioners. Published by Mosby, Inc. All rights reserved.

  14. Central diabetes insipidus: a previously unreported side effect of temozolomide.

    Science.gov (United States)

    Faje, Alexander T; Nachtigall, Lisa; Wexler, Deborah; Miller, Karen K; Klibanski, Anne; Makimura, Hideo

    2013-10-01

    Temozolomide (TMZ) is an alkylating agent primarily used to treat tumors of the central nervous system. We describe 2 patients with apparent TMZ-induced central diabetes insipidus. Using our institution's Research Patient Database Registry, we identified 3 additional potential cases of TMZ-induced diabetes insipidus among a group of 1545 patients treated with TMZ. A 53-year-old male with an oligoastrocytoma and a 38-year-old male with an oligodendroglioma each developed symptoms of polydipsia and polyuria approximately 2 months after the initiation of TMZ. Laboratory analyses demonstrated hypernatremia and urinary concentrating defects, consistent with the presence of diabetes insipidus, and the patients were successfully treated with desmopressin acetate. Desmopressin acetate was withdrawn after the discontinuation of TMZ, and diabetes insipidus did not recur. Magnetic resonance imaging of the pituitary and hypothalamus was unremarkable apart from the absence of a posterior pituitary bright spot in both of the cases. Anterior pituitary function tests were normal in both cases. Using the Research Patient Database Registry database, we identified the 2 index cases and 3 additional potential cases of diabetes insipidus for an estimated prevalence of 0.3% (5 cases of diabetes insipidus per 1545 patients prescribed TMZ). Central diabetes insipidus is a rare but reversible side effect of treatment with TMZ.

  15. Do attitudes of families concerned influence features of children who claim to remember previous lives?

    Science.gov (United States)

    Pasricha, Satwant K

    2011-01-01

    Reported cases of nearly 2600 children (subjects) who claim to remember previous lives have been investigated in cultures with and without belief in reincarnation. The authenticity in most cases has been established. To study the influence of attitudes of parents of the subjects, families of the deceased person with whom they are identified and attention paid by others on the features of the cases. The study is based on field investigations. Data is derived from analysis of a larger series of an ongoing project. Information on initial and subsequent attitudes of subjects' mothers was available for 292 and 136 cases, respectively; attitudes of 227 families of deceased person (previous personality) with whom he is identified, and the extent of attention received from outsiders for 252 cases. Observations and interviews with multiple firsthand informants on both sides of the case as well as some neutral informants supplemented by examination of objective data were the chief methods of investigation. The initial attitude of mothers varied from encouragement (21%) to neutral or tolerance (51%) to discouragement (28%). However, it changed significantly from neutrality to taking measures to induce amnesia in their children for previous life memories due to various psychosocial pressures and prevalent beliefs. Families of the previous personalities, once convinced, showed complete acceptance in a majority of cases. Outside attention was received in 58% cases. The positive attitude of parents might facilitate expression of memories but subsequently attitudes of persons concerned do not seem to alter features of the cases.

  16. Site specific plan

    International Nuclear Information System (INIS)

    Hutchison, J.; Jernigan, G.

    1989-12-01

    The Environmental Restoration and Waste Management Five-Year Plan (FYP) covers the period for FY 1989 through FY 1995. The plan establishes a Department of Energy -- Headquarters (DOE-HQ) agenda for cleanup and compliance against which overall progress can be measured. The FYP covers three areas: Corrective Activities, Environmental Restoration, and Waste Management Operations. Corrective Activities are those activities necessary to bring active or standby facilities into compliance with local, state, and federal environmental regulations. Environmental restoration activities include the assessment and cleanup of surplus facilities and inactive waste sites. Waste management operations includes the treatment, storage, and disposal of wastes which are generated as a result of ongoing operations. This Site Specific Plan (SSP) has been prepared by the Savannah River Site (SRS) in order to show how environmental restoration and waste management activities that were identified during the preparation of the FYP will be implemented, tracked, and reported. The SSP describes DOE Savannah River (DOE-SR) and operating contractor, Westinghouse Savannah River Company (WSRC), organizations that are responsible, for undertaking the activities identified in this plan. The SSP has been prepared in accordance with guidance received from DOE-HQ. DOE-SR is accountable to DOE-HQ for the implementation of this plan. 8 refs., 46 figs., 23 tabs

  17. In vitro site selection of a consensus binding site for the Drosophila melanogaster Tbx20 homolog midline.

    Directory of Open Access Journals (Sweden)

    Nima Najand

    Full Text Available We employed in vitro site selection to identify a consensus binding sequence for the Drosophila melanogaster Tbx20 T-box transcription factor homolog Midline. We purified a bacterially expressed T-box DNA binding domain of Midline, and used it in four rounds of precipitation and polymerase-chain-reaction based amplification. We cloned and sequenced 54 random oligonucleotides selected by Midline. Electromobility shift-assays confirmed that 27 of these could bind the Midline T-box. Sequence alignment of these 27 clones suggests that Midline binds as a monomer to a consensus sequence that contains an AGGTGT core. Thus, the Midline consensus binding site we define in this study is similar to that defined for vertebrate Tbx20, but differs from a previously reported Midline binding sequence derived through site selection.

  18. Radon anomalies prior to earthquakes (1). Review of previous studies

    International Nuclear Information System (INIS)

    Ishikawa, Tetsuo; Tokonami, Shinji; Yasuoka, Yumi; Shinogi, Masaki; Nagahama, Hiroyuki; Omori, Yasutaka; Kawada, Yusuke

    2008-01-01

    The relationship between radon anomalies and earthquakes has been studied for more than 30 years. However, most of the studies dealt with radon in soil gas or in groundwater. Before the 1995 Hyogoken-Nanbu earthquake, an anomalous increase of atmospheric radon was observed at Kobe Pharmaceutical University. The increase was well fitted with a mathematical model related to earthquake fault dynamics. This paper reports the significance of this observation, reviewing previous studies on radon anomaly before earthquakes. Groundwater/soil radon measurements for earthquake prediction began in 1970's in Japan as well as foreign countries. One of the most famous studies in Japan is groundwater radon anomaly before the 1978 Izu-Oshima-kinkai earthquake. We have recognized the significance of radon in earthquake prediction research, but recently its limitation was also pointed out. Some researchers are looking for a better indicator for precursors; simultaneous measurements of radon and other gases are new trials in recent studies. Contrary to soil/groundwater radon, we have not paid much attention to atmospheric radon before earthquakes. However, it might be possible to detect precursors in atmospheric radon before a large earthquake. In the next issues, we will discuss the details of the anomalous atmospheric radon data observed before the Hyogoken-Nanbu earthquake. (author)

  19. Cerebral Metastasis from a Previously Undiagnosed Appendiceal Adenocarcinoma

    Directory of Open Access Journals (Sweden)

    Antonio Biroli

    2012-01-01

    Full Text Available Brain metastases arise in 10%–40% of all cancer patients. Up to one third of the patients do not have previous cancer history. We report a case of a 67-years-old male patient who presented with confusion, tremor, and apraxia. A brain MRI revealed an isolated right temporal lobe lesion. A thorax-abdomen-pelvis CT scan showed no primary lesion. The patient underwent a craniotomy with gross-total resection. Histopathology revealed an intestinal-type adenocarcinoma. A colonoscopy found no primary lesion, but a PET-CT scan showed elevated FDG uptake in the appendiceal nodule. A right hemicolectomy was performed, and the specimen showed a moderately differentiated mucinous appendiceal adenocarcinoma. Whole brain radiotherapy was administrated. A subsequent thorax-abdomen CT scan revealed multiple lung and hepatic metastasis. Seven months later, the patient died of disease progression. In cases of undiagnosed primary lesions, patients present in better general condition, but overall survival does not change. Eventual identification of the primary tumor does not affect survival. PET/CT might be a helpful tool in detecting lesions of the appendiceal region. To the best of our knowledge, such a case was never reported in the literature, and an appendiceal malignancy should be suspected in patients with brain metastasis from an undiagnosed primary tumor.

  20. Coronary collateral vessels in patients with previous myocardial infarction

    International Nuclear Information System (INIS)

    Nakatsuka, M.; Matsuda, Y.; Ozaki, M.

    1987-01-01

    To assess the degree of collateral vessels after myocardial infarction, coronary angiograms, left ventriculograms, and exercise thallium-201 myocardial scintigrams of 36 patients with previous myocardial infarction were reviewed. All 36 patients had total occlusion of infarct-related coronary artery and no more than 70% stenosis in other coronary arteries. In 19 of 36 patients with transient reduction of thallium-201 uptake in the infarcted area during exercise (Group A), good collaterals were observed in 10 patients, intermediate collaterals in 7 patients, and poor collaterals in 2 patients. In 17 of 36 patients without transient reduction of thallium-201 uptake in the infarcted area during exercise (Group B), good collaterals were seen in 2 patients, intermediate collaterals in 7 patients, and poor collaterals in 8 patients (p less than 0.025). Left ventricular contractions in the infarcted area were normal or hypokinetic in 10 patients and akinetic or dyskinetic in 9 patients in Group A. In Group B, 1 patient had hypokinetic contraction and 16 patients had akinetic or dyskinetic contraction (p less than 0.005). Thus, patients with transient reduction of thallium-201 uptake in the infarcted area during exercise had well developed collaterals and preserved left ventricular contraction, compared to those in patients without transient reduction of thallium-201 uptake in the infarcted area during exercise. These results suggest that the presence of viable myocardium in the infarcted area might be related to the degree of collateral vessels

  1. Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins.

    Directory of Open Access Journals (Sweden)

    Pingzhao Hu

    2009-04-01

    Full Text Available One-third of the 4,225 protein-coding genes of Escherichia coli K-12 remain functionally unannotated (orphans. Many map to distant clades such as Archaea, suggesting involvement in basic prokaryotic traits, whereas others appear restricted to E. coli, including pathogenic strains. To elucidate the orphans' biological roles, we performed an extensive proteomic survey using affinity-tagged E. coli strains and generated comprehensive genomic context inferences to derive a high-confidence compendium for virtually the entire proteome consisting of 5,993 putative physical interactions and 74,776 putative functional associations, most of which are novel. Clustering of the respective probabilistic networks revealed putative orphan membership in discrete multiprotein complexes and functional modules together with annotated gene products, whereas a machine-learning strategy based on network integration implicated the orphans in specific biological processes. We provide additional experimental evidence supporting orphan participation in protein synthesis, amino acid metabolism, biofilm formation, motility, and assembly of the bacterial cell envelope. This resource provides a "systems-wide" functional blueprint of a model microbe, with insights into the biological and evolutionary significance of previously uncharacterized proteins.

  2. Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins.

    Science.gov (United States)

    Hu, Pingzhao; Janga, Sarath Chandra; Babu, Mohan; Díaz-Mejía, J Javier; Butland, Gareth; Yang, Wenhong; Pogoutse, Oxana; Guo, Xinghua; Phanse, Sadhna; Wong, Peter; Chandran, Shamanta; Christopoulos, Constantine; Nazarians-Armavil, Anaies; Nasseri, Negin Karimi; Musso, Gabriel; Ali, Mehrab; Nazemof, Nazila; Eroukova, Veronika; Golshani, Ashkan; Paccanaro, Alberto; Greenblatt, Jack F; Moreno-Hagelsieb, Gabriel; Emili, Andrew

    2009-04-28

    One-third of the 4,225 protein-coding genes of Escherichia coli K-12 remain functionally unannotated (orphans). Many map to distant clades such as Archaea, suggesting involvement in basic prokaryotic traits, whereas others appear restricted to E. coli, including pathogenic strains. To elucidate the orphans' biological roles, we performed an extensive proteomic survey using affinity-tagged E. coli strains and generated comprehensive genomic context inferences to derive a high-confidence compendium for virtually the entire proteome consisting of 5,993 putative physical interactions and 74,776 putative functional associations, most of which are novel. Clustering of the respective probabilistic networks revealed putative orphan membership in discrete multiprotein complexes and functional modules together with annotated gene products, whereas a machine-learning strategy based on network integration implicated the orphans in specific biological processes. We provide additional experimental evidence supporting orphan participation in protein synthesis, amino acid metabolism, biofilm formation, motility, and assembly of the bacterial cell envelope. This resource provides a "systems-wide" functional blueprint of a model microbe, with insights into the biological and evolutionary significance of previously uncharacterized proteins.

  3. Influence of Previous Knowledge in Torrance Tests of Creative Thinking

    Directory of Open Access Journals (Sweden)

    María Aranguren

    2015-07-01

    Full Text Available The aim of this work is to analyze the influence of study field, expertise and recreational activities participation in Torrance Tests of Creative Thinking (TTCT, 1974 performance. Several hypotheses were postulated to explore the possible effects of previous knowledge in TTCT verbal and TTCT figural university students’ outcomes. Participants in this study included 418 students from five study fields: Psychology;Philosophy and Literature, Music; Engineering; and Journalism and Advertising (Communication Sciences. Results found in this research seem to indicate that there in none influence of the study field, expertise and recreational activities participation in neither of the TTCT tests. Instead, the findings seem to suggest some kind of interaction between certain skills needed to succeed in specific studies fields and performance on creativity tests, such as the TTCT. These results imply that TTCT is a useful and valid instrument to measure creativity and that some cognitive process involved in innovative thinking can be promoted using different intervention programs in schools and universities regardless the students study field.

  4. Gastrointestinal tolerability with ibandronate after previous weekly bisphosphonate treatment.

    Science.gov (United States)

    Derman, Richard; Kohles, Joseph D; Babbitt, Ann

    2009-01-01

    Data from two open-label trials (PRIOR and CURRENT) of women with postmenopausal osteoporosis or osteopenia were evaluated to assess whether monthly oral and quarterly intravenous (IV) ibandronate dosing improved self-reported gastrointestinal (GI) tolerability for patients who had previously experienced GI irritation with bisphosphonate (BP) use. In PRIOR, women who had discontinued daily or weekly BP treatment due to GI intolerance received monthly oral or quarterly IV ibandronate for 12 months. The CURRENT subanalysis included women receiving weekly BP treatment who switched to monthly oral ibandronate for six months. GI symptom severity and frequency were assessed using the Osteoporosis Patient Satisfaction Questionnaire. In PRIOR, mean GI tolerability scores increased significantly at month 1 from screening for both treatment groups (oral: 79.3 versus 54.1; IV: 84.4 versus 51.0; p 90% at Month 10). In the CURRENT subanalysis >60% of patients reported improvements in heartburn or acid reflux and >70% indicated improvement in other stomach upset at month 6. Postmenopausal women with GI irritability with daily or weekly BPs experienced improvement in symptoms with extended dosing monthly or quarterly ibandronate compared with baseline.

  5. Pertussis-associated persistent cough in previously vaccinated children.

    Science.gov (United States)

    Principi, Nicola; Litt, David; Terranova, Leonardo; Picca, Marina; Malvaso, Concetta; Vitale, Cettina; Fry, Norman K; Esposito, Susanna

    2017-11-01

    To evaluate the role of Bordetella pertussis infection, 96 otherwise healthy 7- to 17-year-old subjects who were suffering from a cough lasting from 2 to 8 weeks were prospectively recruited. At enrolment, a nasopharyngeal swab and an oral fluid sample were obtained to search for pertussis infection by the detection of B. pertussis DNA and/or an elevated titre of anti-pertussis toxin IgG. Evidence of pertussis infection was found in 18 (18.7 %; 95 % confidence interval, 11.5-28.0) cases. In 15 cases, the disease occurred despite booster administration. In two cases, pertussis was diagnosed less than 2 years after the booster injection, whereas in the other cases it was diagnosed between 2 and 9 years after the booster dose. This study used non-invasive testing to show that pertussis is one of the most important causes of long-lasting cough in school-age subjects. Moreover, the protection offered by acellular pertussis vaccines currently wanes more rapidly than previously thought.

  6. Multispecies Coevolution Particle Swarm Optimization Based on Previous Search History

    Directory of Open Access Journals (Sweden)

    Danping Wang

    2017-01-01

    Full Text Available A hybrid coevolution particle swarm optimization algorithm with dynamic multispecies strategy based on K-means clustering and nonrevisit strategy based on Binary Space Partitioning fitness tree (called MCPSO-PSH is proposed. Previous search history memorized into the Binary Space Partitioning fitness tree can effectively restrain the individuals’ revisit phenomenon. The whole population is partitioned into several subspecies and cooperative coevolution is realized by an information communication mechanism between subspecies, which can enhance the global search ability of particles and avoid premature convergence to local optimum. To demonstrate the power of the method, comparisons between the proposed algorithm and state-of-the-art algorithms are grouped into two categories: 10 basic benchmark functions (10-dimensional and 30-dimensional, 10 CEC2005 benchmark functions (30-dimensional, and a real-world problem (multilevel image segmentation problems. Experimental results show that MCPSO-PSH displays a competitive performance compared to the other swarm-based or evolutionary algorithms in terms of solution accuracy and statistical tests.

  7. Waste site characterization through digital analysis of historical aerial photographs at Los Alamos National Laboratory and Eglin Air Force Base

    International Nuclear Information System (INIS)

    Van Eeckhout, E.; Pope, P.; Wells, B.; Rofer, C.; Martin, B.

    1995-01-01

    Historical aerial photographs are used to provide a physical history and preliminary mapping information for characterizing hazardous waste sites at Los Alamos National Laboratory and Eglin Air Force Base. The examples cited show how imagery was used to accurately locate and identify previous activities at a site, monitor changes that occurred over time, and document the observable of such activities today. The methodology demonstrates how historical imagery (along with any other pertinent data) can be used in the characterization of past environmental damage

  8. Allogeneic cell transplant expands bone marrow distribution by colonizing previously abandoned areas: an FDG PET/CT analysis.

    Science.gov (United States)

    Fiz, Francesco; Marini, Cecilia; Campi, Cristina; Massone, Anna Maria; Podestà, Marina; Bottoni, Gianluca; Piva, Roberta; Bongioanni, Francesca; Bacigalupo, Andrea; Piana, Michele; Sambuceti, Gianmario; Frassoni, Francesco

    2015-06-25

    Mechanisms of hematopoietic reconstitution after bone marrow (BM) transplantation remain largely unknown. We applied a computational quantification software application to hybrid 18F-fluorodeoxyglucose positron emission tomography (PET)/computed tomography (CT) images to assess activity and distribution of the hematopoietic system throughout the whole skeleton of recently transplanted patients. Thirty-four patients underwent PET/CT 30 days after either adult stem cell transplantation (allogeneic cell transplantation [ACT]; n = 18) or cord blood transplantation (CBT; n = 16). Our software automatically recognized compact bone volume and trabecular bone volume (IBV) in CT slices. Within IBV, coregistered PET data were extracted to identify the active BM (ABM) from the inactive tissue. Patients were compared with 34 matched controls chosen among a published normalcy database. Whole body ABM increased in ACT and CBT when compared with controls (12.4 ± 3 and 12.8 ± 6.8 vs 8.1 ± 2.6 mL/kg of ideal body weight [IBW], P bones, ABM increased three- and sixfold in CBT and ACT, respectively, compared with controls (0.9 ± 0.9 and 1.7 ± 2.5 vs 0.3 ± 0.3 mL/kg IBW, P transplanted BM into previously abandoned BM sites. © 2015 by The American Society of Hematology.

  9. TWRS Privatization Phase 1 Master Site Plan

    International Nuclear Information System (INIS)

    PARAZIN, R.J.

    1999-01-01

    The U.S. Department of Energy (DOE) has chosen to accomplish the Tank Waste Remediation System disposal mission via privatization. The disposal mission has been divided into two privatization phases. Phase I, a 'proof of concept' phase, will establish and demonstrate the technical, commercial, and procurement capabilities necessary far privatization to proceed. Once established, privatization will be expanded in the form of a second phase (Phase II) to dispose of the remainder of the tank waste. In conjunction with preparation of the Tank Waste Remediation System (TWRS) Privatization Request for Proposals (RFP)(RL, 1996), a location was selected for the Phase I demonstration facilities (Shord, 1996). The location selected was the area previously developed and characterized for the Grout Disposal Site, adjoining the 200 East Area. The site is of sufficient size for a Private Contractor (PC) to carry out pretreatment, immobilization, and vitrification operations and possesses the required characteristics (e.g., close to feed tanks) to best facilitate the Phase I operations. This overall long-range Master Site Plan (MSP) has been developed to establish a ''baseline'' for the (TWRS) Privatization Phase I (TPPI) PC Site. The MSP depicts the planned layout for the PC Site along with various interfaces between the site and other Hanford utilities and functions. The complete integration of TPPl MSP with overall Hanford Site planning process will assist in establishing the PC site and the necessary priorities to meet the Hanford cleanup mission. The MSP has been developed systematically into a comprehensive, safe, flexible, logical and cost-effective plan. The general philosophy behind the preparation of a MSP for the TPPl program is that it will serve as a single source documentation of the planning for the development of the TPPl complex. The effort will plan temporary and permanent land use, utilities, and traffic flow for the overall program. It will identify needs

  10. Association between previous splenectomy and gastric dilatation-volvulus in dogs: 453 cases (2004-2009).

    Science.gov (United States)

    Sartor, Angela J; Bentley, Adrienne M; Brown, Dorothy C

    2013-05-15

    To evaluate the association between previous splenectomy and gastric dilatation-volvulus (GDV) in dogs. Multi-institutional retrospective case-control study. Animals-151 dogs treated surgically for GDV and 302 control dogs with no history of GDV. Computerized records of dogs evaluated via exploratory laparotomy or abdominal ultrasonography were searched, and dogs with GDV and dogs without GDV (control dogs) were identified. Two control dogs were matched with respect to age, body weight, sex, neuter status, and breed to each dog with GDV. Data were collected on the presence or absence of the spleen for both dogs with GDV and control dogs. Conditional logistic regression analysis was used to investigate the association of previous splenectomy with GDV. 6 (4%) dogs in the GDV group and 3 (1%) dogs in the control group had a history of previous splenectomy. The odds of GDV in dogs with a history of previous splenectomy in this population of dogs were 5.3 times those of dogs without a history of previous splenectomy (95% confidence interval, 1.1 to 26.8). For the patients in the present study, there was an increased odds of GDV in dogs with a history of splenectomy. Prophylactic gastropexy may be considered in dogs undergoing a splenectomy, particularly if other risk factors for GDV are present.

  11. Identifying Breast Cancer Oncogenes

    Science.gov (United States)

    2010-10-01

    tyrosine kinases with an SH3, SH2 and catalytic domain, it lacks a native myristylation signal shared by most members of this class [14], [38]. The...therapeutics and consequently, improve clinical outcomes. We aim to identify novel drivers of breast oncogenesis. We hypothesize that a kinase gain-of...human mammary epithelial cells. A pBabe-Puro-Myr-Flag kinase open reading frame (ORF) library was screened in immortalized human mammary epithelial

  12. Rock disposal problems identified

    Energy Technology Data Exchange (ETDEWEB)

    Knox, R

    1978-06-01

    Mathematical models are the only way of examining the return of radioactivity from nuclear waste to the environment over long periods of time. Work in Britain has helped identify areas where more basic data is required, but initial results look very promising for final disposal of high level waste in hard rock repositories. A report by the National Radiological Protection Board of a recent study, is examined.

  13. Sacrococcygeal pilonidal disease: analysis of previously proposed risk factors

    Directory of Open Access Journals (Sweden)

    Ali Harlak

    2010-01-01

    Full Text Available PURPOSE: Sacrococcygeal pilonidal disease is a source of one of the most common surgical problems among young adults. While male gender, obesity, occupations requiring sitting, deep natal clefts, excessive body hair, poor body hygiene and excessive sweating are described as the main risk factors for this disease, most of these need to be verified with a clinical trial. The present study aimed to evaluate the value and effect of these factors on pilonidal disease. METHOD: Previously proposed main risk factors were evaluated in a prospective case control study that included 587 patients with pilonidal disease and 2,780 healthy control patients. RESULTS: Stiffness of body hair, number of baths and time spent seated per day were the three most predictive risk factors. Adjusted odds ratios were 9.23, 6.33 and 4.03, respectively (p<0.001. With an adjusted odds ratio of 1.3 (p<.001, body mass index was another risk factor. Family history was not statistically different between the groups and there was no specific occupation associated with the disease. CONCLUSIONS: Hairy people who sit down for more than six hours a day and those who take a bath two or less times per week are at a 219-fold increased risk for sacrococcygeal pilonidal disease than those without these risk factors. For people with a great deal of hair, there is a greater need for them to clean their intergluteal sulcus. People who engage in work that requires sitting in a seat for long periods of time should choose more comfortable seats and should also try to stand whenever possible.

  14. Impact of Students’ Class Attendance on Recalling Previously Acquired Information

    Directory of Open Access Journals (Sweden)

    Camellia Hemyari

    2018-03-01

    Full Text Available Background: In recent years, availability of class material including typed lectures, the professor’s Power Point slides, sound recordings, and even videos made a group of students feel that it is unnecessary to attend the classes. These students usually read and memorize typed lectures within two or three days prior to the exams and usually pass the tests even with low attendance rate. Thus, the question is how effective is this learning system and how long the one-night memorized lessons may last.Methods: A group of medical students (62 out of 106 students, with their class attendance and educational achievements in the Medical Mycology and Parasitology course being recorded since two years ago, was selected and their knowledge about this course was tested by multiple choice questions (MCQ designed based on the previous lectures.Results: Although the mean re-exam score of the students at the end of the externship was lower than the corresponding final score, a significant association was found between the scores of the students in these two exams (r=0.48, P=0.01. Moreover, a significant negative association was predicted between the number of absences and re-exam scores (r=-0.26, P=0.037.Conclusion: As our findings show, the phenomenon of recalling the acquired lessons is preserved for a long period of time and it is associated with the students’ attendance. Many factors including generation effect (by taking notes and cued-recall (via slide picture might play a significant role in the better recalling of the learned information in students with good class attendance.Keywords: STUDENT, MEMORY, LONG-TERM, RECALL, ABSENTEEISM, LEARNING

  15. Gastrointestinal tolerability with ibandronate after previous weekly bisphosphonate treatment

    Directory of Open Access Journals (Sweden)

    Richard Derman

    2009-09-01

    Full Text Available Richard Derman1, Joseph D Kohles2, Ann Babbitt31Department of Obstetrics and Gynecology, Christiana Hospital, Newark, DE, USA; 2Roche, Nutley, NJ, USA; 3Greater Portland Bone and Joint Specialists, Portland, ME, USAAbstract: Data from two open-label trials (PRIOR and CURRENT of women with postmenopausal osteoporosis or osteopenia were evaluated to assess whether monthly oral and quarterly intravenous (IV ibandronate dosing improved self-reported gastrointestinal (GI tolerability for patients who had previously experienced GI irritation with bisphosphonate (BP use. In PRIOR, women who had discontinued daily or weekly BP treatment due to GI intolerance received monthly oral or quarterly IV ibandronate for 12 months. The CURRENT subanalysis included women receiving weekly BP treatment who switched to monthly oral ibandronate for six months. GI symptom severity and frequency were assessed using the Osteoporosis Patient Satisfaction Questionnaire™. In PRIOR, mean GI tolerability scores increased significantly at month 1 from screening for both treatment groups (oral: 79.3 versus 54.1; IV: 84.4 versus 51.0; p < 0.001 for both. Most patients reported improvement in GI symptom severity and frequency from baseline at all post-screening assessments (>90% at Month 10. In the CURRENT subanalysis >60% of patients reported improvements in heartburn or acid reflux and >70% indicated improvement in other stomach upset at month 6. Postmenopausal women with GI irritability with daily or weekly BPs experienced improvement in symptoms with extended dosing monthly or quarterly ibandronate compared with baseline.Keywords: ibandronate, osteoporosis, bisphosphonate, gastrointestinal

  16. Remedial investigation/feasibility study for the David Witherspoon, Inc., 901 Site, Knoxville, Tennessee: Volume 1

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-10-01

    This remedial investigation (RI)/feasibility study (FS) supports the selection of remedial actions for the David Witherspoon, Inc. 901 Maryville Pike Site in Knoxville, Tennessee. Operations at the site, used as a recycling center, have resulted in past, present, and potential future releases of hazardous substances in to the environment. This Site is a Tennessee Superfund site. A phased approach was planned to (1) gather existing data from previous investigations managed by the Tenn. Dept. of Environment and Conservation; (2) perform a preliminary RI, including risk assessments, and an FS with existing data to identify areas where remedial action may be necessary; (3) gather additional field data to adequately define the nature and extent of risk-based contaminants that present identifiable threats to human and/or ecological receptors; and (4) develop remedial action alternatives to reduce risks to acceptable levels.

  17. Remedial investigation/feasibility study for the David Witherspoon, Inc., 901 Site, Knoxville, Tennessee: Volume 1

    International Nuclear Information System (INIS)

    1996-10-01

    This remedial investigation (RI)/feasibility study (FS) supports the selection of remedial actions for the David Witherspoon, Inc. 901 Maryville Pike Site in Knoxville, Tennessee. Operations at the site, used as a recycling center, have resulted in past, present, and potential future releases of hazardous substances in to the environment. This Site is a Tennessee Superfund site. A phased approach was planned to (1) gather existing data from previous investigations managed by the Tenn. Dept. of Environment and Conservation; (2) perform a preliminary RI, including risk assessments, and an FS with existing data to identify areas where remedial action may be necessary; (3) gather additional field data to adequately define the nature and extent of risk-based contaminants that present identifiable threats to human and/or ecological receptors; and (4) develop remedial action alternatives to reduce risks to acceptable levels

  18. Identification of sites within the Palo Duro Basin. Volume 3. Responses to comments

    International Nuclear Information System (INIS)

    1984-11-01

    This document responds to comments received by the US Department of Energy (DOE) on the draft report entitled Identification of Sites Within the Palo Duro Basin: Volume I - Palo Duro Location A (in Deaf Smith County) and Volume II - Palo Duro Location B (in Swisher County), BMI/ONWI-531, February 1984. The purpose of the report was to review existing geologic, environmental, and socioeconomic data for previously identified potentially acceptable sites consisting of approximately 200 square miles in Swisher County and 400 square miles in Deaf Smith County in the Texas Panhandle and to narrow them to preferred smaller sites for possible further study for a nuclear waste repository. The smaller sites thus identified within the two counties would then be more comparable in size to those in salt deposits in Louisiana, Mississippi, and Utah

  19. Environmental assessment: Davis Canyon site, Utah

    Energy Technology Data Exchange (ETDEWEB)

    none,

    1986-05-01

    In February 1983, the US Department of Energy (DOE) identified the Davis Canyon site in Utah as one of the nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high- level radioactive waste. To determine their suitability, the Davis Canyon site and the eight other potentially acceptable sites have been evaluated in accordance with the DOE's General Guidelines for the Recommendation of Sites for the Nuclear Waste Repositories. These evaluations were reported in draft environmental assessments (EAs), which were issued for public review and comment. After considering the comments received on the draft EAs, the DOE prepared the final EA. The Davis Canyon site is in the Paradox Basin, which is one of five distinct geohydrologic settings considered for the first repository. This setting contains one other potentially acceptable site -- the Lavender Canyon site. Although the Lavender Canyon site is suitable for site characterization, the DOE has concluded that the Davis Canyon site is the preferred site in the Paradox Basin. On the basis of the evaluations reported in this EA, the DOE has found that the Davis Canyon site is not disqualified under the guidelines. Furthermore, the DOE has found that the site is suitable for site characterization because the evidence does not support a conclusion that the site will not be able to meet each of the qualifying conditions specified in the guidelines. On the basis of these findings, the DOE is nominating the Davis Canyon site as one of the five sites suitable for characterization.

  20. Environmental assessment: Davis Canyon site, Utah

    Energy Technology Data Exchange (ETDEWEB)

    none,

    1986-05-01

    In February 1983, the US Department of Energy (DOE) identified the Davis Canyon site in Utah as one of the nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high-level radioactive waste. To determine their suitability, the Davis Canyon site and the eight other potentially acceptable sites have been evaluated in accordance with the DOE's General Guidelines for the Recommendation of Sites for the Nuclear Waste Repositories. These evaluations were reported in draft environmental assessments (EAs), which were issued for public review and comment. After considering the comments received on the draft EAs, the DOE prepared the final EA. The Davis Canyon site is in the Paradox Basin, which is one of five distinct geohydrologic settings considering for the first repository. This setting contains one other potentially acceptable site -- the Lavender Canyon site. Although the Lavender Canyon site is suitable for site characterization, the DOE has concluded that the Davis Canyon site is the preferred site in the Paradox Basin. On the basis of the evaluations reported in this EA, the DOE has found that the Davis Canyon site is not disqualified under the guidelines. Furthermore, the DOE has found that the site is suitable for site characterization because the evidence does not support a conclusion that the site will not be able to meet each of the qualifying conditions specified in the guidelines. On the basis of these findings, the DOE is nominating the Davis Canyon site as one of five sites suitable for characterization.

  1. Environmental assessment: Davis Canyon site, Utah

    International Nuclear Information System (INIS)

    1986-05-01

    In February 1983, the US Department of Energy (DOE) identified the Davis Canyon site in Utah as one of the nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high-level radioactive waste. To determine their suitability, the Davis Canyon site and the eight other potentially acceptable sites have been evaluated in accordance with the DOE's General Guidelines for the Recommendation of Sites for the Nuclear Waste Repositories. These evaluations were reported in draft environmental assessments (EAs), which were issued for public review and comment. After considering the comments received on the draft EAs, the DOE prepared the final EA. The Davis Canyon site is in the Paradox Basin, which is one of five distinct geohydrologic settings considering for the first repository. This setting contains one other potentially acceptable site -- the Lavender Canyon site. Although the Lavender Canyon site is suitable for site characterization, the DOE has concluded that the Davis Canyon site is the preferred site in the Paradox Basin. On the basis of the evaluations reported in this EA, the DOE has found that the Davis Canyon site is not disqualified under the guidelines. Furthermore, the DOE has found that the site is suitable for site characterization because the evidence does not support a conclusion that the site will not be able to meet each of the qualifying conditions specified in the guidelines. On the basis of these findings, the DOE is nominating the Davis Canyon site as one of five sites suitable for characterization

  2. Environmental assessment: Davis Canyon site, Utah

    International Nuclear Information System (INIS)

    1986-05-01

    In February 1983, the US Department of Energy (DOE) identified the Davis Canyon site in Utah as one of the nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high- level radioactive waste. To determine their suitability, the Davis Canyon site and the eight other potentially acceptable sites have been evaluated in accordance with the DOE's General Guidelines for the Recommendation of Sites for the Nuclear Waste Repositories. These evaluations were reported in draft environmental assessments (EAs), which were issued for public review and comment. After considering the comments received on the draft EAs, the DOE prepared the final EA. The Davis Canyon site is in the Paradox Basin, which is one of five distinct geohydrologic settings considered for the first repository. This setting contains one other potentially acceptable site -- the Lavender Canyon site. Although the Lavender Canyon site is suitable for site characterization, the DOE has concluded that the Davis Canyon site is the preferred site in the Paradox Basin. On the basis of the evaluations reported in this EA, the DOE has found that the Davis Canyon site is not disqualified under the guidelines. Furthermore, the DOE has found that the site is suitable for site characterization because the evidence does not support a conclusion that the site will not be able to meet each of the qualifying conditions specified in the guidelines. On the basis of these findings, the DOE is nominating the Davis Canyon site as one of the five sites suitable for characterization

  3. Source term development for tritium at the Sheffield disposal site

    International Nuclear Information System (INIS)

    MacKenzie, D.R.; Barletta, R.E.; Smalley, J.F.; Kempf, C.R.; Davis, R.E.

    1984-01-01

    The Sheffield low-level radioactive waste disposal site, which ceased operation in 1978, has been the focus of modeling efforts by the NRC for the purpose of predicting long-term site behavior. To provide the NRC with the information required for its modeling effort, a study to define the source term for tritium in eight trenches at the Sheffield site has been undertaken. Tritium is of special interest since significant concentrations of the isotope have been found in groundwater samples taken at the site and at locations outside the site boundary. Previous estimates of tritium site inventory at Sheffield are in wide disagreement. In this study, the tritium inventory in the eight trenches was estimated by reviewing the radioactive shipping records (RSRs) for waste buried in these trenches. It has been found that the tritium shipped for burial at the site was probably higher than previously estimated. In the eight trenches surveyed, which amount to roughly one half the total volume and activity buried at Sheffield, approximately 2350 Ci of tritium from non-fuel cycle sources were identified. The review of RSRs also formed the basis for obtaining waste package descriptions and for contacting large waste generators to obtain more detailed information regarding these waste packages. As a result of this review and the selected generator contacts, the non-fuel cycle tritium waste was categorized. The tritium releases from each of these waste categories were modeled. The results of this modeling effort are presented for each of the eight trenches selected. 3 references, 2 figures

  4. Structuring a cost-effective site characterization

    International Nuclear Information System (INIS)

    Berven, B.A.; Little, C.A.; Swaja, R.E.

    1990-01-01

    Successful chemical and radiological site characterizations are complex activities which require meticulously detailed planning. Each layer of investigation is based upon previously generated information about the site. Baseline historical, physical, geological, and regulatory information is prerequisite for preliminary studies at a site. Preliminary studies then provide samples and measurements which define the identity of potential contaminants and define boundaries around the area to be investigated. The goal of a full site characterization is to accurately determine the extent and magnitude of contaminants and carefully define the site conditions such that the future movements of site contaminants can be assessed for potential exposure to human occupants and/or environmental impacts. Critical to this process is the selection of appropriate measurement and sampling methodology, selection and use of appropriate instrumentation and management/interpretation of site information. Site investigations require optimization between the need of information to maximize the understanding of site conditions and the cost of acquiring that information. 5 refs., 1 tab

  5. Identify, Organize, and Retrieve Items Using Zotero

    Science.gov (United States)

    Clark, Brian; Stierman, John

    2009-01-01

    Librarians build collections. To do this they use tools that help them identify, organize, and retrieve items for the collection. Zotero (zoh-TAIR-oh) is such a tool that helps the user build a library of useful books, articles, web sites, blogs, etc., discovered while surfing online. A visit to Zotero's homepage, www.zotero.org, shows a number of…

  6. Identifying particular places through experimental walking

    Directory of Open Access Journals (Sweden)

    Henrik Schultz

    2016-11-01

    Full Text Available Experimental walking can be used to identify particular places, design strategies and spatial visions for urban landscapes. Walking designers can explore sites and, in particular, their temporal dynamics and atmospheric particularities – both essential elements in making particular places. This article illustrates the benefits of this method, using the changing German city of Freiburg as an example.

  7. Characterization of previously unidentified lunar pyroclastic deposits using Lunar Reconnaissance Orbiter Camera (LROC) data

    Science.gov (United States)

    Gustafson, J. Olaf; Bell, James F.; Gaddis, Lisa R.R.; Hawke, B. Ray Ray; Giguere, Thomas A.

    2012-01-01

    We used a Lunar Reconnaissance Orbiter Camera (LROC) global monochrome Wide-angle Camera (WAC) mosaic to conduct a survey of the Moon to search for previously unidentified pyroclastic deposits. Promising locations were examined in detail using LROC multispectral WAC mosaics, high-resolution LROC Narrow Angle Camera (NAC) images, and Clementine multispectral (ultraviolet-visible or UVVIS) data. Out of 47 potential deposits chosen for closer examination, 12 were selected as probable newly identified pyroclastic deposits. Potential pyroclastic deposits were generally found in settings similar to previously identified deposits, including areas within or near mare deposits adjacent to highlands, within floor-fractured craters, and along fissures in mare deposits. However, a significant new finding is the discovery of localized pyroclastic deposits within floor-fractured craters Anderson E and F on the lunar farside, isolated from other known similar deposits. Our search confirms that most major regional and localized low-albedo pyroclastic deposits have been identified on the Moon down to ~100 m/pix resolution, and that additional newly identified deposits are likely to be either isolated small deposits or additional portions of discontinuous, patchy deposits.

  8. 78 FR 22553 - Generic Drug Facilities, Sites, and Organizations

    Science.gov (United States)

    2013-04-16

    ...] Generic Drug Facilities, Sites, and Organizations AGENCY: Food and Drug Administration, HHS. ACTION.... Generic drug facilities, certain sites, and organizations identified in a generic drug submission are... active pharmaceutical ingredients and certain other sites and organizations that support the manufacture...

  9. Novel protein phosphorylation site identification in spinach stroma membranes by titanium dioxide microcolumns and tandem mass spectrometry

    DEFF Research Database (Denmark)

    Rinalducci, Sara; Larsen, Martin Røssel; Mohammed, Shabaz

    2006-01-01

    In this work, spinach stroma membrane, instead of thylakoid, has been investigated for the presence of phosphorylated proteins. We identified seven previously unknown phosphorylation sites by taking advantage of TiO(2) phosphopeptides enrichment coupled to mass spectrometric analysis. Upon...

  10. Identifying phenomenal consciousness.

    Science.gov (United States)

    Schier, Elizabeth

    2009-03-01

    This paper examines the possibility of finding evidence that phenomenal consciousness is independent of access. The suggestion reviewed is that we should look for isomorphisms between phenomenal and neural activation spaces. It is argued that the fact that phenomenal spaces are mapped via verbal report is no problem for this methodology. The fact that activation and phenomenal space are mapped via different means does not mean that they cannot be identified. The paper finishes by examining how data addressing this theoretical question could be obtained.

  11. Site safety progress review of spent fuel central interim storage facility. Final report

    International Nuclear Information System (INIS)

    Gurpinar, A.; Serva, L.; Giuliani

    1995-01-01

    Following the request of the Czech Power Board (CEZ) and within the scope of the Technical Cooperation Project CZR/9/003, a progress review of the site safety of the Spent Fuel Central Interim Storage Facility (SFCISF) was performed. The review involved the first two stages of the works comprising the regional survey and identification of candidate sites for the underground and surface storage options. Five sites have been identified as a result of the previous works. The following two stages will involved the identification of the preferred candidate sites for the two options and the final site qualification. The present review had the purpose of assessing the work already performed and making recommendations for the next two stages of works

  12. Surveillance for previously unmonitored organic contaminants in the San Francisco Estuary.

    Science.gov (United States)

    Oros, Daniel R; Jarman, Walter M; Lowe, Theresa; David, Nicole; Lowe, Sarah; Davis, Jay A

    2003-09-01

    The San Francisco Estuary Regional Monitoring Program initiated surveillance monitoring to identify previously unmonitored synthetic organic contaminants in the San Francisco Estuary. Organic extracts of water samples were analyzed using gas chromatography-mass spectrometry in full scan mode. The major contaminant classes identified in the samples were fire retardants, pesticides, personal care product ingredients, and plasticizers. Evidence from the literature suggests that some of these contaminants can persist in the environment, induce toxicity, and accumulate in marine biota and in higher food chain consumers. The major sources of these contaminants into the marine environment are the discharge of municipal and industrial wastewater effluents, urban stormwater, and agricultural runoff. As a proactive effort, it is suggested that surveillance studies be used routinely in monitoring programs to identify and prevent potential problem contaminants from harming the marine environment.

  13. Contaminated Sites in Iowa

    Data.gov (United States)

    Iowa State University GIS Support and Research Facility — Sites contaminated by hazardous materials or wastes. These sites are those administered by the Contaminated Sites Section of Iowa DNR. Many are sites which are...

  14. Trends in port-site metastasis after laparoscopic resection of incidental gallbladder cancer: A systematic review.

    Science.gov (United States)

    Berger-Richardson, David; Chesney, Tyler R; Englesakis, Marina; Govindarajan, Anand; Cleary, Sean P; Swallow, Carol J

    2017-03-01

    The risk of port-site metastasis after laparoscopic removal of incidental gallbladder cancer was previously estimated to be 14-30%. The present study was designed to determine the incidence of port-site metastasis in incidental gallbladder cancer in the modern era (2000-2014) versus the historic era (1991-1999). We also investigated the site of port-site metastasis. Using PRISMA, a systematic review was conducted to identify papers that addressed the development of port-site metastasis after laparoscopic resection of incidental gallbladder cancer. Studies that described cancer-specific outcomes in ≥5 patients were included. A validated quality appraisal tool was used, and a weighted estimate of the incidence of port-site metastasis was calculated. Based on data extracted from 27 papers that met inclusion criteria, the incidence of port-site metastasis in incidental gallbladder cancer has decreased from 18.6% prior to 2000 (95% confidence interval 15.3-21.9%, n = 7) to 10.3% since then (95% confidence interval 7.9-12.7%, n = 20) (P extraction site is at significantly higher risk than nonextraction sites. The incidence of port-site metastasis in incidental gallbladder cancer has decreased but remains high relative to other primary tumors. Any preoperative finding that raises the suspicion of gallbladder cancer should prompt further investigation and referral to a hepato-pancreato-biliary specialist. Copyright © 2016 Elsevier Inc. All rights reserved.

  15. Sprucing up the site - update

    CERN Multimedia

    2009-01-01

    As mentioned in a previous article the Bulletin will be publishing regular short updates following the consolidation work going on around the CERN sites: All internal lighting is being replaced in the office buildings on the Prevessin site. Work has started in building 866 and will move to 864 and 865 later. New energy-efficient lights are being installed, which will reduce electricity consumption by 30 -50%, and in the common areas like corridors the lighting will be switched on by motion sensors. Also in the Prevessin site, the lines in the car parks are being repainted. This will continue in the Meyrin site later. Work has started in Building 30 to completely refurbish the AT Auditorium.

  16. Retroviral insertions in the VISION database identify molecular pathways in mouse lymphoid leukemia and lymphoma.

    Science.gov (United States)

    Weiser, Keith C; Liu, Bin; Hansen, Gwenn M; Skapura, Darlene; Hentges, Kathryn E; Yarlagadda, Sujatha; Morse Iii, Herbert C; Justice, Monica J

    2007-10-01

    AKXD recombinant inbred (RI) strains develop a variety of leukemias and lymphomas due to somatically acquired insertions of retroviral DNA into the genome of hematopoetic cells that can mutate cellular proto-oncogenes and tumor suppressor genes. We generated a new set of tumors from nine AKXD RI strains selected for their propensity to develop B-cell tumors, the most common type of human hematopoietic cancers. We employed a PCR technique called viral insertion site amplification (VISA) to rapidly isolate genomic sequence at the site of provirus insertion. Here we describe 550 VISA sequence tags (VSTs) that identify 74 common insertion sites (CISs), of which 21 have not been identified previously. Several suspected proto-oncogenes and tumor suppressor genes lie near CISs, providing supportive evidence for their roles in cancer. Furthermore, numerous previously uncharacterized genes lie near CISs, providing a pool of candidate disease genes for future research. Pathway analysis of candidate genes identified several signaling pathways as common and powerful routes to blood cancer, including Notch, E-protein, NFkappaB, and Ras signaling. Misregulation of several Notch signaling genes was confirmed by quantitative RT-PCR. Our data suggest that analyses of insertional mutagenesis on a single genetic background are biased toward the identification of cooperating mutations. This tumor collection represents the most comprehensive study of the genetics of B-cell leukemia and lymphoma development in mice. We have deposited the VST sequences, CISs in a genome viewer, histopathology, and molecular tumor typing data in a public web database called VISION (Viral Insertion Sites Identifying Oncogenes), which is located at http://www.mouse-genome.bcm.tmc.edu/vision .

  17. Identified EM Earthquake Precursors

    Science.gov (United States)

    Jones, Kenneth, II; Saxton, Patrick

    2014-05-01

    recurrence, duration, and frequency response. At the Southern California field sites, one loop antenna was positioned for omni-directional reception and also detected a strong First Schumann Resonance; however, additional Schumann Resonances were absent. At the Timpson, TX field sites, loop antennae were positioned for directional reception, due to earthquake-induced, hydraulic fracturing activity currently conducted by the oil and gas industry. Two strong signals, one moderately strong signal, and approximately 6-8 weaker signals were detected in the immediate vicinity. The three stronger signals were mapped by a biangulation technique, followed by a triangulation technique for confirmation. This was the first antenna mapping technique ever performed for determining possible earthquake epicenters. Six and a half months later, Timpson experienced two M4 (M4.1 and M4.3) earthquakes on September 2, 2013 followed by a M2.4 earthquake three days later, all occurring at a depth of five kilometers. The Timpson earthquake activity now has a cyclical rate and a forecast was given to the proper authorities. As a result, the Southern California and Timpson, TX field results led to an improved design and construction of a third prototype antenna. With a loop antenna array, a viable communication system, and continuous monitoring, a full fracture cycle can be established and observed in real-time. In addition, field data could be reviewed quickly for assessment and lead to a much more improved earthquake forecasting capability. The EM precursors determined by this method appear to surpass all prior precursor claims, and the general public will finally receive long overdue forecasting.

  18. Methanotrophic bacteria in warm geothermal spring sediments identified using stable-isotope probing.

    Science.gov (United States)

    Sharp, Christine E; Martínez-Lorenzo, Azucena; Brady, Allyson L; Grasby, Stephen E; Dunfield, Peter F

    2014-10-01

    We investigated methanotrophic bacteria in sediments of several warm geothermal springs ranging in temperature from 22 to 45 °C. Methane oxidation was measured at potential rates up to 141 μmol CH4 d(-1) g(-1) sediment. Active methanotrophs were identified using (13) CH4 stable-isotope probing (SIP) incubations performed at close to in situ temperatures for each site. Quantitative (q) PCR of pmoA genes identified the position of the heavy ((13) C-labelled) DNA fractions in density gradients, and 16S rRNA gene pyrotag sequencing of the heavy fractions was performed to identify the active methanotrophs. Methanotroph communities identified in heavy fractions of all samples were predominated by species similar (≥ 95% 16S rRNA gene identities) to previously characterized Gammaproteobacteria and Alphaproteobacteria methanotrophs. Among the five hottest samples (45 °C), members of the Gammaproteobacteria genus Methylocaldum dominated in two cases, while three others were dominated by an OTU closely related (96.8% similarity) to the Alphaproteobacteria genus Methylocapsa. These results suggest that diverse methanotroph groups are adapted to warm environments, including the Methylocapsa-Methylocella-Methyloferula group, which has previously only been detected in cooler sites. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  19. Near-Site Transportation Infrastructure Project

    International Nuclear Information System (INIS)

    Viebrock, J.M.; Mote, N.

    1992-02-01

    There are 122 commercial nuclear facilities from which spent nuclear fuel will be accepted by the Federal Waste Management System (FWMS). Since some facilities share common sites and some facilities are on adjacent sites, 76 sites were identified for the Near-Site Transportation Infrastructure (NSTI) project. The objective of the NSTI project was to identify the options available for transportation of spent-fuel casks from each of these commercial nuclear facility sites to the main transportation routes -- interstate highways, commercial rail lines and navigable waterways available for commercial use. The near-site transportation infrastructure from each site was assessed, based on observation of technical features identified during a survey of the routes and facilities plus data collected from referenced information sources. The potential for refurbishment of transportation facilities which are not currently operational was also assessed, as was the potential for establishing new transportation facilities

  20. Dietary self-efficacy predicts AHEI diet quality in women with previous gestational diabetes.

    Science.gov (United States)

    Ferranti, Erin Poe; Narayan, K M Venkat; Reilly, Carolyn M; Foster, Jennifer; McCullough, Marjorie; Ziegler, Thomas R; Guo, Ying; Dunbar, Sandra B

    2014-01-01

    The purpose of this study was to examine the association of intrapersonal influences of diet quality as defined by the Health Belief Model constructs in women with recent histories of gestational diabetes. A descriptive, correlational, cross-sectional design was used to analyze relationships between diet quality and intrapersonal variables, including perceptions of threat of type 2 diabetes mellitus development, benefits and barriers of healthy eating, and dietary self-efficacy, in a convenience sample of 75 community-dwelling women (55% minority; mean age, 35.5 years; SD, 5.5 years) with previous gestational diabetes mellitus. Diet quality was defined by the Alternative Healthy Eating Index (AHEI). Multiple regression was used to identify predictors of AHEI diet quality. Women had moderate AHEI diet quality (mean score, 47.6; SD, 14.3). Only higher levels of education and self-efficacy significantly predicted better AHEI diet quality, controlling for other contributing variables. There is a significant opportunity to improve diet quality in women with previous gestational diabetes mellitus. Improving self-efficacy may be an important component to include in nutrition interventions. In addition to identifying other important individual components, future studies of diet quality in women with previous gestational diabetes mellitus are needed to investigate the scope of influence beyond the individual to potential family, social, and environmental factors. © 2014 The Author(s).

  1. List identifies threatened ecosystems

    Science.gov (United States)

    Showstack, Randy

    2012-09-01

    The International Union for Conservation of Nature (IUCN) announced on 9 September that it will develop a new Red List of Ecosystems that will identify which ecosystems are vulnerable or endangered. The list, which is modeled on the group's Red List of Threatened Species™, could help to guide conservation activities and influence policy processes such as the Convention on Biological Diversity, according to the group. “We will assess the status of marine, terrestrial, freshwater, and subterranean ecosystems at local, regional, and global levels,” stated Jon Paul Rodriguez, leader of IUCN's Ecosystems Red List Thematic Group. “The assessment can then form the basis for concerted implementation action so that we can manage them sustainably if their risk of collapse is low or restore them if they are threatened and then monitor their recovery.”

  2. Global Microbial Identifier

    DEFF Research Database (Denmark)

    Wielinga, Peter; Hendriksen, Rene S.; Aarestrup, Frank Møller

    2017-01-01

    ) will likely also enable a much better understanding of the pathogenesis of the infection and the molecular basis of the host response to infection. But the full potential of these advances will only transpire if the data in this area become transferable and thereby comparable, preferably in open-source...... of microorganisms, for the identification of relevant genes and for the comparison of genomes to detect outbreaks and emerging pathogens. To harness the full potential of WGS, a shared global database of genomes linked to relevant metadata and the necessary software tools needs to be generated, hence the global...... microbial identifier (GMI) initiative. This tool will ideally be used in amongst others in the diagnosis of infectious diseases in humans and animals, in the identification of microorganisms in food and environment, and to track and trace microbial agents in all arenas globally. This will require...

  3. Site locality identification study: Hanford Site. Volume II. Data cataloging

    International Nuclear Information System (INIS)

    1980-07-01

    Data compilation and cataloging for the candidate site locality identification study were conducted in order to provide a retrievable data cataloging system for the present siting study and future site evaluation and licensng processes. This task occurred concurrently with and also independently of other tasks of the candidate site locality identification study. Work in this task provided the data utilized primarily in the development and application of screening and ranking processes to identify candidate site localities on the Hanford Site. The overall approach included two steps: (1) data acquisition and screening; and (2) data compilation and cataloging. Data acquisition and screening formed the basis for preliminary review of data sources with respect to their probable utilization in the candidate site locality identification study and review with respect to the level of completeness and detail of the data. The important working assumption was that the data to be used in the study be based on existing and available published and unpublished literature. The data compilation and cataloging provided the basic product of the Task; a retrievable data cataloging system in the form of an annotated reference list and key word index and an index of compiled data. The annotated reference list and key word index are cross referenced and can be used to trace and retrieve the data sources utilized in the candidate site locality identification study

  4. Assessment of candidate sites for disposal of treated effluents at the Hanford Site, Washington

    International Nuclear Information System (INIS)

    Davis, J.D.

    1992-01-01

    A rigidly defined evaluation process was used to recommend a preferred location to dispose of treated effluents from facilities in the 200 Areas of the US Department of Energy's Hanford Site in Washington State. First, siting constraints were defined based on functional design considerations and siting guidelines. Then, criteria for selecting a preferred site from among several candidates were identified and their relative importance defined. Finally, the weighted criteria were applied and a site was selected for detailed characterization by subsurface investigations

  5. Site Observational Work Plan for the UMTRA Project Site at Shiprock, New Mexico. Revision

    International Nuclear Information System (INIS)

    1995-07-01

    The site observational work plan (SOWP) for the Shiprock, New Mexico, Uranium Mill Tailings Remedial Action (UMTRA) Project Site is one of the first documents for developing an approach for achieving ground water compliance at the site. This SOWP applies Shiprock site information to a regulatory compliance framework, which identifies strategies for meeting ground water compliance at the site. The compliance framework was developed in the UMTRA ground water programmatic environmental impact statement

  6. Parameter identifiability and redundancy: theoretical considerations.

    Directory of Open Access Journals (Sweden)

    Mark P Little

    Full Text Available BACKGROUND: Models for complex biological systems may involve a large number of parameters. It may well be that some of these parameters cannot be derived from observed data via regression techniques. Such parameters are said to be unidentifiable, the remaining parameters being identifiable. Closely related to this idea is that of redundancy, that a set of parameters can be expressed in terms of some smaller set. Before data is analysed it is critical to determine which model parameters are identifiable or redundant to avoid ill-defined and poorly convergent regression. METHODOLOGY/PRINCIPAL FINDINGS: In this paper we outline general considerations on parameter identifiability, and introduce the notion of weak local identifiability and gradient weak local identifiability. These are based on local properties of the likelihood, in particular the rank of the Hessian matrix. We relate these to the notions of parameter identifiability and redundancy previously introduced by Rothenberg (Econometrica 39 (1971 577-591 and Catchpole and Morgan (Biometrika 84 (1997 187-196. Within the widely used exponential family, parameter irredundancy, local identifiability, gradient weak local identifiability and weak local identifiability are shown to be largely equivalent. We consider applications to a recently developed class of cancer models of Little and Wright (Math Biosciences 183 (2003 111-134 and Little et al. (J Theoret Biol 254 (2008 229-238 that generalize a large number of other recently used quasi-biological cancer models. CONCLUSIONS/SIGNIFICANCE: We have shown that the previously developed concepts of parameter local identifiability and redundancy are closely related to the apparently weaker properties of weak local identifiability and gradient weak local identifiability--within the widely used exponential family these concepts largely coincide.

  7. Females use self-referent cues to avoid mating with previous mates.

    Science.gov (United States)

    Ivy, Tracie M; Weddle, Carie B; Sakaluk, Scott K

    2005-12-07

    Females of many species mate repeatedly throughout their lives, often with many different males (polyandry). Females can secure genetic benefits by maximizing their diversity of mating partners, and might be expected, therefore, to forego matings with previous partners in favour of novel males. Indeed, a female preference for novel mating partners has been shown in several taxa, but the mechanism by which females distinguish between novel males and previous mates remains unknown. We show that female crickets (Gryllodes sigillatus) mark males with their own unique chemical signatures during mating, enabling females to recognize prior mates in subsequent encounters and to avoid remating with them. Because self-referent chemosensory cues provide females with a simple, but reliable mechanism of identifying individuals with whom they have mated without requiring any special cognitive ability, they may be a widespread means by which females across a broad range of animal mating systems maximize the genetic benefits of polyandry.

  8. Survival after early-stage breast cancer of women previously treated for depression

    DEFF Research Database (Denmark)

    Suppli, Nis Frederik Palm; Johansen, Christoffer; Kessing, Lars Vedel

    2017-01-01

    treatment of depression and risk of receiving nonguideline treatment of breast cancer were assessed in multivariable logistic regression analyses. We compared the overall survival, breast cancer-specific survival, and risk of death by suicide of women who were and were not treated for depression before......Purpose The aim of this nationwide, register-based cohort study was to determine whether women treated for depression before primary early-stage breast cancer are at increased risk for receiving treatment that is not in accordance with national guidelines and for poorer survival. Material...... and Methods We identified 45,325 women with early breast cancer diagnosed in Denmark from 1998 to 2011. Of these, 744 women (2%) had had a previous hospital contact (as an inpatient or outpatient) for depression and another 6,068 (13%) had been treated with antidepressants. Associations between previous...

  9. Hazardous waste sites and housing appreciation rates

    OpenAIRE

    McCluskey, Jill Jennifer; Rausser, Gordon C

    2000-01-01

    The dynamic effect of a hazardous waste site is analyzed by investigating the causal relationship between housing appreciation rates and house location in relation to a hazardous waste site using resale data from individual sales transactions in Dallas County, Texas. The results indicate that in the period in which the hazardous waste site was identified and cleanup occurred, residential property owners in close proximity to the hazardous waste site experienced lower housing appreciation rate...

  10. Radiograph identifying means

    International Nuclear Information System (INIS)

    Sheldon, A.D.

    1983-01-01

    A flexible character-indentable plastics embossing tape is backed by and bonded to a lead strip, not more than 0.025 inches thick, to form a tape suitable for identifying radiographs. The lead strip is itself backed by a relatively thin and flimsy plastics or fabric strip which, when removed, allows the lead plastic tape to be pressure-bonded to the surface to be radiographed. A conventional tape-embossing gun is used to indent the desired characters in succession into the lead-backed tape, without necessarily severing the lead; and then the backing strip is peeled away to expose the layer of adhesive which pressure-bonds the indented tape to the object to be radiographed. X-rays incident on the embossed tape will cause the raised characters to show up dark on the subsequently-developed film, whilst the raised side areas will show up white. Each character will thus stand out on the developed film. (author)

  11. Analysis of ILRS Site Ties

    Science.gov (United States)

    Husson, V. S.; Long, J. L.; Pearlman, M.

    2001-12-01

    By the end of 2000, 94% of ILRS stations had completed station and site information forms (i.e. site logs). These forms contain six types of information. These six categories include site identifiers, contact information, approximate coordinates, system configuration history, system ranging capabilities, and local survey ties. The ILRS Central Bureau, in conjunction with the ILRS Networks and Engineering Working Group, has developed procedures to quality control site log contents. Part of this verification entails data integrity checks of local site ties and is the primary focus of this paper. Local survey ties are critical to the combination of space geodetic network coordinate solutions (i.e. GPS, SLR, VLBI, DORIS) of the International Terrestrial Reference Frame (ITRF). Approximately 90% of active SLR sites are collocated with at least one other space geodetic technique. The process used to verify these SLR ties, at collocated sites, is identical to the approach used in ITRF2000. Local vectors (X, Y, Z) from each ILRS site log are differenced from its corresponding ITRF2000 position vectors (i.e. no transformations). These X, Y, and Z deltas are converted into North, East, and Up. Any deltas, in any component, larger than 5 millimeter is flagged for investigation. In the absence of ITRF2000 SLR positions, CSR positions were used. To further enhance this comparison and to fill gaps in information, local ties contained in site logs from the other space geodetic services (i.e. IGS, IVS, IDS) were used in addition to ITRF2000 ties. Case studies of two collocated sites (McDonald/Ft. Davis and Hartebeeshtoek) will be explored in-depth. Recommendations on how local site surveys should be conducted and how this information should be managed will also be presented.

  12. In situ hybridization of bat chromosomes with human (TTAGGGn probe, after previous digestion with Alu I

    Directory of Open Access Journals (Sweden)

    Karina de Cassia Faria

    2002-01-01

    Full Text Available The purpose of this work was to verify the ability of the enzyme Alu I to cleave and/or remove satellite DNA sequences from heterochromatic regions in chromosomes of bats, by identifying the occurrence of modifications in the pattern of fluorescence in situ hybridization with telomeric DNA. The localization and fluorescence intensity of the telomeric DNA sites of the Alu-digested and undigested chromosomes of species Eumops glaucinus, Carollia perspicillata, and Platyrrhinus lineatus were analyzed. Telomeric sequences were detected at the termini of chromosomes of all three species, although, in C. perspicillata, the signals were very faint or absent in most chromosomes. This finding was interpreted as being due to a reduced number of copies of the telomeric repeat, resulting from extensive telomeric association and/or rearrangements undergone by the chromosomes of Carollia. Fluorescent signals were also observed in centromeric and pericentromeric regions in several two-arm chromosomes of E. glaucinus and C. perspicillata. In E. glaucinus and P. lineatus, some interstitial and terminal telomeric sites were observed to be in association with regions of constitutive heterochromatin and ribosomal DNA (NORs. After digestion, these telomeric sites showed a significant decrease in signal intensity, indicating that enzyme Alu I cleaves and/or removes part of the satellite DNA present in these regions. These results suggest that the telomeric sequence is a component of the heterochromatin, and that the C-band- positive regions of bat chromosomes have a different DNA composition.

  13. Evaluation of an interdisciplinary re-isolation policy for patients with previous Clostridium difficile diarrhea.

    Science.gov (United States)

    Boone, N; Eagan, J A; Gillern, P; Armstrong, D; Sepkowitz, K A

    1998-12-01

    Diarrhea caused by Clostridium difficile is increasingly recognized as a nosocomial problem. The effectiveness and cost of a new program to decrease nosocomial spread by identifying patients scheduled for readmission who were previously positive for toxin was evaluated. The Memorial Sloan-Kettering Cancer Center is a 410-bed comprehensive cancer center in New York City. Many patients are readmitted during their course of cancer therapy. In 1995 as a result of concern about the nosocomial spread of C difficile, we implemented a policy that all patients who were positive for C difficile toxin in the previous 6 months with no subsequent toxin-negative stool as an outpatient would be placed into contact isolation on readmission pending evaluation of stool specimens. Patients who were previously positive for C difficile toxin were identified to infection control and admitting office databases via computer. Admitting personnel contacted infection control with all readmissions to determine whether a private room was required. Between July 1, 1995, and June 30, 1996, 47 patients who were previously positive for C difficile toxin were readmitted. Before their first scheduled readmission, the specimens for 15 (32%) of these patients were negative for C difficile toxin. They were subsequently cleared as outpatients and were readmitted without isolation. Workup of the remaining 32 patients revealed that the specimens for 7 patients were positive for C difficile toxin and 86 isolation days were used. An additional 25 patients used 107 isolation days and were either cleared after a negative specimen was obtained in-house or discharged without having an appropriate specimen sent. Four patients (9%) had reoccurring C difficile after having toxin-negative stools. We estimate (because outpatient specimens were not collected) the cost incurred at $48,500 annually, including the incremental cost of hospital isolation and equipment. Our policy to control the spread of nosocomial C

  14. High prevalence of genetic variants previously associated with LQT syndrome in new exome data

    DEFF Research Database (Denmark)

    Refsgaard, Lena; Holst, Anders G; Sadjadieh, Golnaz

    2012-01-01

    To date, hundreds of variants in 13 genes have been associated with long QT syndrome (LQTS). The prevalence of LQTS is estimated to be between 1:2000 and 1:5000. The knowledge of genetic variation in the general population has until recently been limited, but newly published data from NHLBI GO...... variants KCNH2 P347S; SCN5A: S216L, V1951L; and CAV3 T78M in the control population (n=704) revealed prevalences comparable to those of ESP. Thus, we identified a much higher prevalence of previously LQTS-associated variants than expected in exome data from population studies. Great caution regarding...

  15. Urinary tract infections in hospital pediatrics: many previous antibiotherapy and antibiotics resistance, including fluoroquinolones.

    Science.gov (United States)

    Garraffo, A; Marguet, C; Checoury, A; Boyer, S; Gardrat, A; Houivet, E; Caron, F

    2014-02-01

    We studied antibiotic resistance in pediatric UTIs and we evaluated the impact of antibiotic exposure in the previous 12 months, very little French data being available for this population. We conducted a multicenter prospective study including children consulting for, or admitted in 2 hospitals. Prior antibiotic exposure was documented from their health record. One hundred and ten patients (73 girls), 11 days to 12 years of age, were included in 10 months. Ninety-six percent presented with pyelonephritis, associated to uropathy for 25%. Escherichia coli was predominant (78%), followed by Proteus spp. and Enterococcus spp. The antibiotic resistance rate of E. coli was high and close to that reported for adults with complicated UTIs: amoxicillin 60%, amoxicillin-clavulanate 35%, cefotaxim 5%, trimethoprim-sulfametoxazole 26%, nalidixic acid 9%, ciprofloxacin 7%, gentamycin 1%, nitrofurantoin and fosfomycin 0%. The antibiotic exposure in the previous 12 months involved 62 children (56%) most frequently with β-lactams (89%) for a respiratory tract infection (56%). A clear relationship between exposure and resistance was observed for amoxicillin (71% vs. 46%), first generation (65% vs. 46%) and third generation (9% vs. 3%) cephalosporins, or trimethoprim-sulfamethoxazole (36% vs. 15%). However, antibiotic exposure could not account alone for the results, as suggested by the 7% of ciprofloxacin resistance, observed without any identified previous treatment. Bacterial species and antibiotic resistance level in children are similar to those reported for adults. Antibiotic exposure in the previous 12 months increases the risk of resistance but other factors are involved (previous antibiotic therapies and fecal-oral or mother-to-child transmission). Copyright © 2013 Elsevier Masson SAS. All rights reserved.

  16. Rhabdomyosarcoma Arising in a Previously Irradiated Field: An Analysis of 43 Patients

    Energy Technology Data Exchange (ETDEWEB)

    Dang, Nguyen D. [Department of Radiation Oncology, Baylor College of Medicine, Houston, Texas (United States); Teh, Bin S. [Department of Radiation Oncology, The Methodist Hospital and Methodist Hospital Research Institute, Houston, Texas (United States); Paulino, Arnold C., E-mail: apaulino@tmhs.org [Department of Radiation Oncology, The Methodist Hospital and Methodist Hospital Research Institute, Houston, Texas (United States)

    2013-03-01

    Patients with soft tissue sarcomas that arise from previously irradiated fields have traditionally been reported to have a poor prognosis. In this report, we examined the characteristics and outcomes of patients who developed a rhabdomyosarcoma in a previously irradiated field (RMS-RIF); we hypothesize that these patients should have a better outcome compared to other postradiation soft tissue sarcomas as these tumors are chemosensitive and radiosensitive. A PubMed search of the literature from 1961-2010 yielded 33 studies with data for patients with RMS-RIF. The study included 43 patients with a median age of 6.5 years at the time of radiation therapy (RT) for the initial tumor. The median RT dose was 48 Gy. The median latency period, the time from RT to development of RMS-RIF, was 8 years. The 3-year overall survival for RMS-RIF was 42%. The 3-year overall survival was 66% for patients receiving chemotherapy and local treatment (surgery and/or RT) compared to 29% for those who had systemic treatment only or local treatment only (P=.049). Other factors associated with increased 3-year overall survival included retinoblastoma initial diagnosis (P<.001), age ≤18 years at diagnosis of RMS-RIF (P=.003), favorable site (P=.008), and stage 1 disease (P=.002). Age at time of RMS-RIF, retinoblastoma initial tumor, favorable site, stage 1 disease, and use of both systemic and local treatment were found to be favorable prognostic factors for 3-year overall survival.

  17. Environmental assessment overview, Davis Canyon site, Utah

    International Nuclear Information System (INIS)

    1986-05-01

    In February 1983, the US Department of Energy (DOE) identified the Davis Canyon site in Utah as one of the nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high-level radioactive waste. To determine their suitability, the Davis Canyon site and the eight other potentially acceptable sites have been evaluated in accordance with the DOE's General Guidelines for the Recommendation of Sites for the Nuclear Waste Repositories. The Davis Canyon site is in the Paradox Basin, which is one of five distinct geohydrologic settings considered for the first repository. On the basis of the evaluations reported in this EA, the DOE has found that the Davis Canyon site is not disqualified under the guidelines. On the basis of these findings, the DOE is nominating the Davis Canyon site as one of five sites suitable for characterization. 3 figs

  18. Environmental assessment overview: Richton Dome site, Mississippi

    International Nuclear Information System (INIS)

    1986-05-01

    In February 1983, the US Department of Energy (DOE) identified the Richton Dome site in Mississippi as one of the nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high-level radioactive waste. To determine their suitability, the Richton Dome site and the eight other potentially acceptable sites have been evaluated in accordance with the DOE's General Guidelines for the Recommendation of Sites for the Nuclear Waste Repositories. The site is in the Gulf interior region, which is one of five distinct geohydrologic settings considered for the first repository. On the basis of the evaluations reported in this EA, the DOE has found that the Richton Dome site is not disqualified under the guidelines. On the basis of these findings, the DOE is nominating the Richton Dome site as one of five sites suitable for characterization. 3 figs

  19. Integrative Analysis of CRISPR/Cas9 Target Sites in the Human HBB Gene

    Directory of Open Access Journals (Sweden)

    Yumei Luo

    2015-01-01

    Full Text Available Recently, the clustered regularly interspaced short palindromic repeats (CRISPR system has emerged as a powerful customizable artificial nuclease to facilitate precise genetic correction for tissue regeneration and isogenic disease modeling. However, previous studies reported substantial off-target activities of CRISPR system in human cells, and the enormous putative off-target sites are labor-intensive to be validated experimentally, thus motivating bioinformatics methods for rational design of CRISPR system and prediction of its potential off-target effects. Here, we describe an integrative analytical process to identify specific CRISPR target sites in the human β-globin gene (HBB and predict their off-target effects. Our method includes off-target analysis in both coding and noncoding regions, which was neglected by previous studies. It was found that the CRISPR target sites in the introns have fewer off-target sites in the coding regions than those in the exons. Remarkably, target sites containing certain transcriptional factor motif have enriched binding sites of relevant transcriptional factor in their off-target sets. We also found that the intron sites have fewer SNPs, which leads to less variation of CRISPR efficiency in different individuals during clinical applications. Our studies provide a standard analytical procedure to select specific CRISPR targets for genetic correction.

  20. Binding-site assessment by virtual fragment screening.

    Directory of Open Access Journals (Sweden)

    Niu Huang

    2010-04-01

    Full Text Available The accurate prediction of protein druggability (propensity to bind high-affinity drug-like small molecules would greatly benefit the fields of chemical genomics and drug discovery. We have developed a novel approach to quantitatively assess protein druggability by computationally screening a fragment-like compound library. In analogy to NMR-based fragment screening, we dock approximately 11,000 fragments against a given binding site and compute a computational hit rate based on the fraction of molecules that exceed an empirically chosen score cutoff. We perform a large-scale evaluation of the approach on four datasets, totaling 152 binding sites. We demonstrate that computed hit rates correlate with hit rates measured experimentally in a previously published NMR-based screening method. Secondly, we show that the in silico fragment screening method can be used to distinguish known druggable and non-druggable targets, including both enzymes and protein-protein interaction sites. Finally, we explore the sensitivity of the results to different receptor conformations, including flexible protein-protein interaction sites. Besides its original aim to assess druggability of different protein targets, this method could be used to identifying druggable conformations of flexible binding site for lead discovery, and suggesting strategies for growing or joining initial fragment hits to obtain more potent inhibitors.

  1. The Importance of Business Model Factors for Cloud Computing Adoption: Role of Previous Experiences

    Directory of Open Access Journals (Sweden)

    Bogataj Habjan Kristina

    2017-08-01

    Full Text Available Background and Purpose: Bringing several opportunities for more effective and efficient IT governance and service exploitation, cloud computing is expected to impact the European and global economies significantly. Market data show that despite many advantages and promised benefits the adoption of cloud computing is not as fast and widespread as foreseen. This situation shows the need for further exploration of the potentials of cloud computing and its implementation on the market. The purpose of this research was to identify individual business model factors with the highest impact on cloud computing adoption. In addition, the aim was to identify the differences in opinion regarding the importance of business model factors on cloud computing adoption according to companies’ previous experiences with cloud computing services.

  2. Nuclear installations sites safety

    International Nuclear Information System (INIS)

    Barber, P.; Candes, P.; Duclos, P.; Doumenc, A.; Faure, J.; Hugon, J.; Mohammadioun, B.

    1988-11-01

    This report is divided into ten parts bearing: 1 Safety analysis procedures for Basis Nuclear Installations sites (BNI) in France 2 Site safety for BNI in France 3 Industrial and transport activities risks for BNI in France 4 Demographic characteristics near BNI sites in France 5 Meteorologic characteristics of BNI sites in France 6 Geological aspects near the BNI sites in France 7 Seismic studies for BNI sites in France 8 Hydrogeological aspects near BNI sites in France 9 Hydrological aspects near BNI sites in France 10 Ecological and radioecological studies of BNI sites in France [fr

  3. Social Media Sites

    Science.gov (United States)

    Media Sites Site Registration Contact Us Search AF.mil: Home > AF Sites > Social Media Sites Social Media Welcome to the Air Force social media directory! The directory is a one-stop shop of official Air Force social media pages across various social media sites. Social media is all about

  4. Low-dose computed tomography image restoration using previous normal-dose scan

    International Nuclear Information System (INIS)

    Ma, Jianhua; Huang, Jing; Feng, Qianjin; Zhang, Hua; Lu, Hongbing; Liang, Zhengrong; Chen, Wufan

    2011-01-01

    of the previous normal-dose scan via the presented ndiNLM algorithm is noticeable as compared to a similar approach without using the previous normal-dose scan. Conclusions: For low-dose CT image restoration, the presented ndiNLM method is robust in preserving the spatial resolution and identifying the low-contrast structure. The authors can draw the conclusion that the presented ndiNLM algorithm may be useful for some clinical applications such as in perfusion imaging, radiotherapy, tumor surveillance, etc.

  5. India: From SITE to INSAT.

    Science.gov (United States)

    Chaudhri, M. M.

    1986-01-01

    Identifies core of India's illiteracy problem and describes use of educational technology to educate rural children. Highlights include descriptions of the Satellite Instructional Television Experiment (SITE) project; motivation behind low-cost educational aids development in rural areas; an educational radio pilot project; and development and…

  6. 75 FR 39143 - Airworthiness Directives; Arrow Falcon Exporters, Inc. (previously Utah State University); AST...

    Science.gov (United States)

    2010-07-08

    ... (previously Precision Helicopters, LLC); Robinson Air Crane, Inc.; San Joaquin Helicopters (previously Hawkins... (Previously Hawkins & Powers Aviation); S.M. &T. Aircraft (Previously Us Helicopter Inc., UNC Helicopters, Inc...

  7. 75 FR 66009 - Airworthiness Directives; Cessna Aircraft Company (Type Certificate Previously Held by Columbia...

    Science.gov (United States)

    2010-10-27

    ... Company (Type Certificate Previously Held by Columbia Aircraft Manufacturing (Previously the Lancair... Company (Type Certificate Previously Held by Columbia Aircraft Manufacturing (Previously The Lancair...-15895. Applicability (c) This AD applies to the following Cessna Aircraft Company (type certificate...

  8. Fire Risk Scoping Study: Investigation of nuclear power plant fire risk, including previously unaddressed issues

    International Nuclear Information System (INIS)

    Lambright, J.A.; Nowlen, S.P.; Nicolette, V.F.; Bohn, M.P.

    1989-01-01

    An investigation of nuclear power plant fire risk issues raised as a result of the USNRC sponsored Fire Protection Research Program at Sandia National Laboratories has been performed. The specific objectives of this study were (1) to review and requantify fire risk scenarios from four fire probabilistic risk assessments (PRAs) in light of updated data bases made available as a result of USNRC sponsored Fire Protection Research Program and updated computer fire modeling capabilities, (2) to identify potentially significant fire risk issues that have not been previously addressed in a fire risk context and to quantify the potential impact of those identified fire risk issues where possible, and (3) to review current fire regulations and plant implementation practices for relevance to the identified unaddressed fire risk issues. In performance of the fire risk scenario requantifications several important insights were gained. It was found that utilization of a more extensive operational experience base resulted in both fire occurrence frequencies and fire duration times (i.e., time required for fire suppression) increasing significantly over those assumed in the original works. Additionally, some thermal damage threshold limits assumed in the original works were identified as being nonconservative based on more recent experimental data. Finally, application of the COMPBRN III fire growth model resulted in calculation of considerably longer fire damage times than those calculated in the original works using COMPBRN I. 14 refs., 2 figs., 16 tabs

  9. Prediction of successful trial of labour in patients with a previous caesarean section

    International Nuclear Information System (INIS)

    Shaheen, N.; Khalil, S.; Iftikhar, P.

    2014-01-01

    Objective: To determine the prediction rate of success in trial of labour after one previous caesarean section. Methods: The cross-sectional study was conducted at the Department of Obstetrics and Gynaecology, Cantonment General Hospital, Rawalpindi, from January 1, 2012 to January 31, 2013, and comprised women with one previous Caesarean section and with single alive foetus at 37-41 weeks of gestation. Women with more than one Caesarean section, unknown site of uterine scar, bony pelvic deformity, placenta previa, intra-uterine growth restriction, deep transverse arrest in previous labour and non-reassuring foetal status at the time of admission were excluded. Intrapartum risk assessment included Bishop score at admission, rate of cervical dilatation and scar tenderness. SPSS 21 was used for statistical analysis. Results: Out of a total of 95 women, the trial was successful in 68 (71.6%). Estimated foetal weight and number of prior vaginal deliveries had a high predictive value for successful trial of labour after Caesarean section. Estimated foetal weight had an odds ratio of 0.46 (p<0.001), while number of prior vaginal deliveries had an odds ratio of 0.85 with (p=0.010). Other factors found to be predictive of successful trial included Bishop score at the time of admission (p<0.037) and rate of cervical dilatation in the first stage of labour (p<0.021). Conclusion: History of prior vaginal deliveries, higher Bishop score at the time of admission, rapid rate of cervical dilatation and lower estimated foetal weight were predictive of a successful trial of labour after Caesarean section. (author)

  10. Emergency diagnosis of cancer and previous general practice consultations: insights from linked patient survey data.

    Science.gov (United States)

    Abel, Gary A; Mendonca, Silvia C; McPhail, Sean; Zhou, Yin; Elliss-Brookes, Lucy; Lyratzopoulos, Georgios

    2017-06-01

    Emergency diagnosis of cancer is common and aetiologically complex. The proportion of emergency presenters who have consulted previously with relevant symptoms is uncertain. To examine how many patients with cancer, who were diagnosed as emergencies, have had previous primary care consultations with relevant symptoms; and among those, to examine how many had multiple consultations. Secondary analysis of patient survey data from the 2010 English Cancer Patient Experience Survey (CPES), previously linked to population-based data on diagnostic route. For emergency presenters with 18 different cancers, associations were examined for two outcomes (prior GP consultation status; and 'three or more consultations' among prior consultees) using logistic regression. Among 4647 emergency presenters, 1349 (29%) reported no prior consultations, being more common in males (32% versus 25% in females, P <0.001), older (44% in ≥85 versus 30% in 65-74-year-olds, P <0.001), and the most deprived (35% versus 25% least deprived, P = 0.001) patients; and highest/lowest for patients with brain cancer (46%) and mesothelioma (13%), respectively ( P <0.001 for overall variation by cancer site). Among 3298 emergency presenters with prior consultations, 1356 (41%) had three or more consultations, which were more likely in females ( P <0.001), younger ( P <0.001), and non-white patients ( P = 0.017) and those with multiple myeloma, and least likely for patients with leukaemia ( P <0.001). Contrary to suggestions that emergency presentations represent missed diagnoses, about one-third of emergency presenters (particularly those in older and more deprived groups) have no prior GP consultations. Furthermore, only about one-third report multiple (three or more) consultations, which are more likely in 'harder-to-suspect' groups. © British Journal of General Practice 2017.

  11. Age, training, and previous experience predict race performance in long-distance inline skaters, not anthropometry.

    Science.gov (United States)

    Knechtle, Beat; Knechtle, Patrizia; Rüst, Christoph Alexander; Rosemann, Thomas; Lepers, Romuald

    2012-02-01

    The association of characteristics of anthropometry, training, and previous experience with race time in 84 recreational, long-distance, inline skaters at the longest inline marathon in Europe (111 km), the Inline One-eleven in Switzerland, was investigated to identify predictor variables for performance. Age, duration per training unit, and personal best time were the only three variables related to race time in a multiple regression, while none of the 16 anthropometric variables were related. Anthropometric characteristics seem to be of no importance for a fast race time in a long-distance inline skating race in contrast to training volume and previous experience, when controlled with covariates. Improving performance in a long-distance inline skating race might be related to a high training volume and previous race experience. Also, doing such a race requires a parallel psychological effort, mental stamina, focus, and persistence. This may be reflected in the preparation and training for the event. Future studies should investigate what motivates these athletes to train and compete.

  12. The Current and Historical Distribution of Special Status Amphibians at the Livermore Site and Site 300

    Energy Technology Data Exchange (ETDEWEB)

    Hattem, M V; Paterson, L; Woollett, J

    2008-08-20

    65 surveys were completed in 2002 to assess the current distribution of special status amphibians at the Lawrence Livermore National Laboratory's (LLNL) Livermore Site and Site 300. Combined with historical information from previous years, the information presented herein illustrates the dynamic and probable risk that amphibian populations face at both sites. The Livermore Site is developed and in stark contrast to the mostly undeveloped Site 300. Yet both sites have significant issues threatening the long-term sustainability of their respective amphibian populations. Livermore Site amphibians are presented with a suite of challenges inherent of urban interfaces, most predictably the bullfrog (Rana catesbeiana), while Site 300's erosion issues and periodic feral pig (Sus scrofa) infestations reduce and threaten populations. The long-term sustainability of LLNL's special status amphibians will require active management and resource commitment to maintain and restore amphibian habitat at both sites.

  13. Particle Physics Education Sites

    Science.gov (United States)

    back to home page Particle Physics Education Sites quick reference Education and Information - National Laboratory Education Programs - Women and Minorities in Physics - Other Physics Sites - Physics Alliance - Accelerators at National Laboratories icon Particle Physics Education and Information sites: top

  14. Novel mutations in the homogentisate 1,2 dioxygenase gene identified in Jordanian patients with alkaptonuria.

    Science.gov (United States)

    Al-sbou, Mohammed

    2012-06-01

    This study was conducted to identify mutations in the homogentisate 1,2 dioxygenase gene (HGD) in alkaptonuria patients among Jordanian population. Blood samples were collected from four alkaptonuria patients, four carriers, and two healthy volunteers. DNA was isolated from peripheral blood. All 14 exons of the HGD gene were amplified using the polymerase chain reaction (PCR) technique. The PCR products were then purified and analyzed by sequencing. Five mutations were identified in our samples. Four of them were novel C1273A, T1046G, 551-552insG, T533G and had not been previously reported, and one mutation T847C has been described before. The types of mutations identified were two missense mutations, one splice site mutation, one frameshift mutation, and one polymorphism. We present the first molecular study of the HGD gene in Jordanian alkaptonuria patients. This study provides valuable information about the molecular basis of alkaptonuria in Jordanian population.

  15. Site characterization plan for groundwater in Waste Area Grouping 1 at Oak Ridge National Laboratory, Oak Ridge, Tennessee

    Energy Technology Data Exchange (ETDEWEB)

    Lee, R.R.; Curtis, A.H.; Houlberg, L.M.; Purucker, S.T.; Singer, M.L.; Tardiff, M.F.; Wolf, D.A.

    1994-07-01

    The Waste Area Grouping (WAG) 1 Groundwater Operable Unit (OU) at Oak Ridge National Laboratory (ORNL) in Oak Ridge, Tennessee, is undergoing a site characterization to identify environmental contamination that may be present. This document, Site Characterization Report for Groundwater in Waste Area Grouping I at Oak Ridge National Laboratory, Oak Ridge, Tennessee, identifies areas of concern with respect to WAG 1 groundwater and presents the rationale, justification, and objectives for conducting this continuing site characterization. This report summarizes the operations that have taken place at each of the areas of concern in WAG 1, summarizes previous characterization studies that have been performed, presents interpretations of previously collected data and information, identifies contaminants of concern, and presents an action plan for further site investigations and early actions that will lead to identification of contaminant sources, their major groundwater pathways, and reduced off-site migration of contaminated groundwater to surface water. Site characterization Activities performed to date at WAG I have indicated that groundwater contamination, principally radiological contamination, is widespread. An extensive network of underground pipelines and utilities have contributed to the dispersal of contaminants to an unknown extent. The general absence of radiological contamination in surface water at the perimeter of WAG 1 is attributed to the presence of pipelines and underground waste storage tank sumps and dry wells distributed throughout WAG 1 which remove more than about 40 million gal of contaminated groundwater per year.

  16. Site characterization plan for groundwater in Waste Area Grouping 1 at Oak Ridge National Laboratory, Oak Ridge, Tennessee

    International Nuclear Information System (INIS)

    Lee, R.R.; Curtis, A.H.; Houlberg, L.M.; Purucker, S.T.; Singer, M.L.; Tardiff, M.F.; Wolf, D.A.

    1994-07-01

    The Waste Area Grouping (WAG) 1 Groundwater Operable Unit (OU) at Oak Ridge National Laboratory (ORNL) in Oak Ridge, Tennessee, is undergoing a site characterization to identify environmental contamination that may be present. This document, Site Characterization Report for Groundwater in Waste Area Grouping I at Oak Ridge National Laboratory, Oak Ridge, Tennessee, identifies areas of concern with respect to WAG 1 groundwater and presents the rationale, justification, and objectives for conducting this continuing site characterization. This report summarizes the operations that have taken place at each of the areas of concern in WAG 1, summarizes previous characterization studies that have been performed, presents interpretations of previously collected data and information, identifies contaminants of concern, and presents an action plan for further site investigations and early actions that will lead to identification of contaminant sources, their major groundwater pathways, and reduced off-site migration of contaminated groundwater to surface water. Site characterization Activities performed to date at WAG I have indicated that groundwater contamination, principally radiological contamination, is widespread. An extensive network of underground pipelines and utilities have contributed to the dispersal of contaminants to an unknown extent. The general absence of radiological contamination in surface water at the perimeter of WAG 1 is attributed to the presence of pipelines and underground waste storage tank sumps and dry wells distributed throughout WAG 1 which remove more than about 40 million gal of contaminated groundwater per year

  17. Sitewide risk perspectives for the Rocky Flats Environmental Technology Site

    International Nuclear Information System (INIS)

    Olinger, S.J.

    1998-05-01

    The US Department of Energy (DOE) has recently finalized a closure plan (originally called the Ten Year Plan) for closure and environmental cleanup of previous nuclear weapons facilities. The DOE Rocky Flats Field Office has established priorities for risk reduction work to Support closure activities, as well as addressing those hazards associated with storage and management of radioactive materials and hazardous chemicals. To provide information for future National Environmental Policy Act (NEPA) or other regulatory assessments of specific risk reduction projects identified in the Closure Plan, a risk assessment of normal operations and potential accidents was recently prepared to provide an updated baseline of the cumulative impacts to the worker, public and environment due to the Site's operations, activities, and environmental conditions in light of the Site's change in mission, and of future closure projects. This paper summarizes the risk assessment approach, results, and conclusions

  18. Effect of site conditions on ground motion and damage

    Science.gov (United States)

    Borcherdt, R.; Glassmoyer, G.; Andrews, M.; Cranswick, E.

    1989-01-01

    Results of seismologic studies conducted by the U.S. reconnaissance team in conjunction with Soviet colleagues following the tragic earthquakes of December 7, 1988, suggest that site conditions may have been a major factor in contributing to increased damage levels in Leninakan. As the potential severity of these effects in Leninakan had not been previously identified, this chapter presents results intended to provide a preliminary quantification of these effects on both damage and levels of ground motion observed in Leninakan. The article describes the damage distribution geologic setting, ground motion amplification in Leninakan, including analog amplifications and spectral amplifications. Preliminary model estimates for site response are presented. It is concluded that ground motion amplification in the 0.5-2.5-second period range was a major contributing factor to increased damage in Leninakan as compared with Kirovakan. Leninakan is located on thick water saturated alluvial deposits.

  19. The frequency of previously undetectable deletions involving 3' Exons of the PMS2 gene.

    Science.gov (United States)

    Vaughn, Cecily P; Baker, Christine L; Samowitz, Wade S; Swensen, Jeffrey J

    2013-01-01

    Lynch syndrome is characterized by mutations in one of four mismatch repair genes, MLH1, MSH2, MSH6, or PMS2. Clinical mutation analysis of these genes includes sequencing of exonic regions and deletion/duplication analysis. However, detection of deletions and duplications in PMS2 has previously been confined to Exons 1-11 due to gene conversion between PMS2 and the pseudogene PMS2CL in the remaining 3' exons (Exons 12-15). We have recently described an MLPA-based method that permits detection of deletions of PMS2 Exons 12-15; however, the frequency of such deletions has not yet been determined. To address this question, we tested for 3' deletions in 58 samples that were reported to be negative for PMS2 mutations using previously available methods. All samples were from individuals whose tumors exhibited loss of PMS2 immunohistochemical staining without concomitant loss of MLH1 immunostaining. We identified seven samples in this cohort with deletions in the 3' region of PMS2, including three previously reported samples with deletions of Exons 13-15 (two samples) and Exons 14-15. Also detected were deletions of Exons 12-15, Exon 13, and Exon 14 (two samples). Breakpoint analysis of the intragenic deletions suggests they occurred through Alu-mediated recombination. Our results indicate that ∼12% of samples suspected of harboring a PMS2 mutation based on immunohistochemical staining, for which mutations have not yet been identified, would benefit from testing using the new methodology. Copyright © 2012 Wiley Periodicals, Inc.

  20. Protein Supplement Usage Among Male University Students: Comparisons Between Current and Previous Users.

    Science.gov (United States)

    Sung, Youngmo; Choi, Jinkyung

    2018-02-01

    Interest in specialized dietary supplements is leading market growth, and protein supplements are popular for increasing muscle mass among young males. Therefore, this study investigated the attitudes toward and satisfaction with protein supplements to identify detailed consumer behaviors related to the consumption of protein supplements. The study sample includes male university students in their 20s in South Korea. In total, 223 responses were entered for analysis. Questions related to attitudes, satisfaction, and future behavioral intentions were asked using 5-point Likert scales. The responses were divided into two groups, current and previous users, to identify significant differences in terms of attitudes, satisfaction, and future behavioral intentions. A descriptive analysis, analysis of variance (ANOVA), and multiple regression were run. The majority of respondents prefer the powdered form of supplements in bulk with a price range between 30,000 won and 60,000 won. Online shopping was preferred, while word of mouth and friends/family were considered credible information sources. The most common side effects experienced were problems with digestion and hives, although more than 78% did not experience side effects. In comparison between current and previous users in terms of attitudes and satisfaction, the following areas showed significances. Regarding attitudes, the importance of brand, preference for products from overseas, the search for nutritional facts, and reading carefully all product information were significant, while regarding satisfaction, price, effectiveness, and ease of consumption were significant. All significances showed that current users had more positive attitudes and greater satisfaction. Overall, consumers' satisfaction regarding ease of consumption influenced future behavioral intentions. The market for protein supplements has been growing, so measuring consumers' attitudes and satisfaction would help attract potential consumers. In

  1. Hazardous waste site assessment: Inactive landfill, Site 300, Lawrence Livermore National Laboratory

    Energy Technology Data Exchange (ETDEWEB)

    1985-01-01

    This report presents the results of an investigation of an inactive landfill (Pit 6) at Lawrence Livermore National Laboratory's (LLNL) Site 300. The primary objectives were to: collect and review background information pertaining to past waste disposal practices and previous environmental characterization studies; conduct a geophysical survey of the landfill area to locate the buried wastes; conduct a hydrogeologic investigation to provide additional data on the rate and direction of groundwater flow, the extent of any groundwater contamination, and to investigate the connection, if any, of the shallow groundwater beneath the landfill with the local drinking water supply; conduct a risk assessment to identify the degree of threat posed by the landfill to the public health and environment; compile a preliminary list of feasible long-term remedial action alternatives for the landfill; and develop a list of recommendations for any interim measures necessary at the landfill should the long-term remedial action plan be needed.

  2. Hazardous waste site assessment: Inactive landfill, Site 300, Lawrence Livermore National Laboratory

    International Nuclear Information System (INIS)

    1985-01-01

    This report presents the results of an investigation of an inactive landfill (Pit 6) at Lawrence Livermore National Laboratory's (LLNL) Site 300. The primary objectives were to: collect and review background information pertaining to past waste disposal practices and previous environmental characterization studies; conduct a geophysical survey of the landfill area to locate the buried wastes; conduct a hydrogeologic investigation to provide additional data on the rate and direction of groundwater flow, the extent of any groundwater contamination, and to investigate the connection, if any, of the shallow groundwater beneath the landfill with the local drinking water supply; conduct a risk assessment to identify the degree of threat posed by the landfill to the public health and environment; compile a preliminary list of feasible long-term remedial action alternatives for the landfill; and develop a list of recommendations for any interim measures necessary at the landfill should the long-term remedial action plan be needed

  3. Double tracks test site characterization report

    International Nuclear Information System (INIS)

    1996-05-01

    This report presents the results of site characterization activities performed at the Double Tracks Test Site, located on Range 71 North, of the Nellis Air Force Range (NAFR) in southern Nevada. Site characterization activities included reviewing historical data from the Double Tracks experiment, previous site investigation efforts, and recent site characterization data. The most recent site characterization activities were conducted in support of an interim corrective action to remediate the Double Tracks Test Site to an acceptable risk to human health and the environment. Site characterization was performed using a phased approach. First, previously collected data and historical records sere compiled and reviewed. Generalized scopes of work were then prepared to fill known data gaps. Field activities were conducted and the collected data were then reviewed to determine whether data gaps were filled and whether other areas needed to be investigated. Additional field efforts were then conducted, as required, to adequately characterize the site. Characterization of the Double Tracks Test Site was conducted in accordance with the US Department of Energy's (DOE) Streamlined Approach for Environmental Restoration (SAFER)

  4. Catalysis on singly dispersed bimetallic sites

    Science.gov (United States)

    Zhang, Shiran; Nguyen, Luan; Liang, Jin-Xia; Shan, Junjun; Liu, Jingyue; Frenkel, Anatoly I.; Patlolla, Anitha; Huang, Weixin; Li, Jun; Tao, Franklin

    2015-08-01

    A catalytic site typically consists of one or more atoms of a catalyst surface that arrange into a configuration offering a specific electronic structure for adsorbing or dissociating reactant molecules. The catalytic activity of adjacent bimetallic sites of metallic nanoparticles has been studied previously. An isolated bimetallic site supported on a non-metallic surface could exhibit a distinctly different catalytic performance owing to the cationic state of the singly dispersed bimetallic site and the minimized choices of binding configurations of a reactant molecule compared with continuously packed bimetallic sites. Here we report that isolated Rh1Co3 bimetallic sites exhibit a distinctly different catalytic performance in reduction of nitric oxide with carbon monoxide at low temperature, resulting from strong adsorption of two nitric oxide molecules and a nitrous oxide intermediate on Rh1Co3 sites and following a low-barrier pathway dissociation to dinitrogen and an oxygen atom. This observation suggests a method to develop catalysts with high selectivity.

  5. Multiple binding modes of ibuprofen in human serum albumin identified by absolute binding free energy calculations

    KAUST Repository

    Evoli, Stefania

    2016-11-10

    Human serum albumin possesses multiple binding sites and transports a wide range of ligands that include the anti-inflammatory drug ibuprofen. A complete map of the binding sites of ibuprofen in albumin is difficult to obtain in traditional experiments, because of the structural adaptability of this protein in accommodating small ligands. In this work, we provide a set of predictions covering the geometry, affinity of binding and protonation state for the pharmaceutically most active form (S-isomer) of ibuprofen to albumin, by using absolute binding free energy calculations in combination with classical molecular dynamics (MD) simulations and molecular docking. The most favorable binding modes correctly reproduce several experimentally identified binding locations, which include the two Sudlow\\'s drug sites (DS2 and DS1) and the fatty acid binding sites 6 and 2 (FA6 and FA2). Previously unknown details of the binding conformations were revealed for some of them, and formerly undetected binding modes were found in other protein sites. The calculated binding affinities exhibit trends which seem to agree with the available experimental data, and drastically degrade when the ligand is modeled in a protonated (neutral) state, indicating that ibuprofen associates with albumin preferentially in its charged form. These findings provide a detailed description of the binding of ibuprofen, help to explain a wide range of results reported in the literature in the last decades, and demonstrate the possibility of using simulation methods to predict ligand binding to albumin.

  6. Supplemental site inspection for Air Force Plant 59, Johnson City, New York, Volume 1: Investigation report

    Energy Technology Data Exchange (ETDEWEB)

    Nashold, B.; Rosenblatt, D.; Hau, J. [and others

    1995-08-01

    This summary describes a Supplemental Site Inspection (SSI) conducted by Argonne National Laboratory (ANL) at Air Force Plant 59 (AFP 59) in Johnson City, New York. All required data pertaining to this project were entered by ANL into the Air Force-wide Installation Restoration Program Information System (IRPIMS) computer format and submitted to an appropriate authority. The work was sponsored by the United States Air Force as part of its Installation Restoration Program (IRP). Previous studies had revealed the presence of contaminants at the site and identified several potential contaminant sources. Argonne`s study was conducted to answer questions raised by earlier investigations.

  7. Environmental assessment: Richton Dome site, Mississippi

    International Nuclear Information System (INIS)

    1986-05-01

    In February 1983, the US Department of Energy (DOE) identified the Richton Dome site in Mississippi as one of the nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high-level radioactive waste. To determine their suitability, the Richton Dome site and the eight other potentially acceptable sites have been evaluated in accordance with the DOE's General Guidelines for the Recommendation of Sites for the Nuclear Waste Repositories. These evaluations were reported in draft environmental assessments (EAs), which were issued for public review and comment. After considering the comments received on the draft EAs, the DOE prepared the final EAs. The site is in the Gulf interior region, which is one of five distinct geohydrologic settings considered for the first repository. This setting contains two other potentially acceptable sites--the Cypress Creek Dome site in Mississippi and the Vacherie Dome site in Louisiana. Although the Cypress Creek Dome and the Vacherie Dome sites are suitable for site characterization, the DOE has concluded that the Richton Dome site is the preferred site in the Gulf interior region. On the basis of the evaluations reported in this EA, the DOE has found that the Richton Dome site is not disqualified under the guidelines

  8. Environmental assessment: Richton Dome Site, Mississippi

    Energy Technology Data Exchange (ETDEWEB)

    none,

    1986-05-01

    In February 1983, the US Department of Energy (DOE) identified the Richton Dome site in Mississippi as one of the nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high-level radioactive waste. To determine their suitability, the Richton Dome site and the eight other potentially acceptable sites have been evaluated in accordance with the DOE's General Guidelines for the Recommendation of Sites for the Nuclear Waste Repositories. These evaluations were reported in draft environmental assessments (EAs), which were issued for public review and comment. After considering the comments received on the draft EAs, the DOE prepared the final EAs. The site is in the Gulf interior region, which is one of five distinct geohydrologic settings considered for the first repository. This setting contains two other potentially acceptable sites--the Cypress Creek Dome site in Mississippi and the Vacherie Dome site in Louisiana. Although the Cypress Creek Dome and the Vacherie Dome sites are suitable for site characterization, the DOE has concluded that the Richton Dome site is the preferred site in the Gulf interior region. On the basis of the evaluations reported in this EA, the DOE has found that the Richton Dome site is not disqualified under the guidelines.

  9. Environmental assessment: Richton Dome site, Mississippi

    Energy Technology Data Exchange (ETDEWEB)

    none,

    1986-05-01

    In February 1983, the US Department of Energy (DOE) identified the Richton Dome site in Mississippi as one of the nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high-level radioactive waste. To determine their suitability, the Richton Dome site and the eight other potentially acceptable sites have been evaluated in accordance with the DOE's General Guidelines for the Recommendation of Sites for the Nuclear Waste Repositories. These evaluations were reported in draft environmental assessments (EAs), which were issued for public review and comment. After considering the comments received on the draft EAs, the DOE prepared the final EAs. The site is in the Gulf interior region, which is one of five distinct geohydrologic settings considered for the first repository. This setting contains two other potentially acceptable sites--the Cypress Creek Dome site in Mississippi and the Vacherie Dome site in Louisiana. Although the Cypress Creek Dome and the Vacherie Dome sites are suitable for site characterization, the DOE has concluded that the Richton Dome site is the preferred site in the Gulf interior region. On the basis of the evaluations reported in this EA, the DOE has found that the Richton Dome site is not disqualified under the guidelines.

  10. Environmental assessment: Richton Dome Site, Mississippi

    International Nuclear Information System (INIS)

    1986-05-01

    In February 1983, the US Department of Energy (DOE) identified the Richton Dome site in Mississippi as one of the nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high-level radioactive waste. To determine their suitability, the Richton Dome site and the eight other potentially acceptable sites have been evaluated in accordance with the DOE's General Guidelines for the Recommendation of Sites for the Nuclear Waste Repositories. These evaluations were reported in draft environmental assessments (EAs), which were issued for public review and comment. After considering the comments received on the draft EAs, the DOE prepared the final EAs. The site is in the Gulf interior region, which is one of five distinct geohydrologic settings considered for the first repository. This setting contains two other potentially acceptable sites--the Cypress Creek Dome site in Mississippi and the Vacherie Dome site in Louisiana. Although the Cypress Creek Dome and the Vacherie Dome sites are suitable for site characterization, the DOE has concluded that the Richton Dome site is the preferred site in the Gulf interior region. On the basis of the evaluations reported in this EA, the DOE has found that the Richton Dome site is not disqualified under the guidelines

  11. Antimetabolites in cataract surgery to prevent failure of a previous trabeculectomy.

    Science.gov (United States)

    Thomas, Roger E; Crichton, Andrew; Thomas, Bennett C

    2014-07-28

    Patients having cataract surgery have often earlier undergone a trabeculectomy for glaucoma. However, cataract surgery may be associated with failure of the previous glaucoma surgery and antimetabolites may be used with cataract surgery to prevent such failure. There is no systematic review on whether antimetabolites with cataract surgery prevent failure of a previous trabeculectomy. To assess the effects of antimetabolites with cataract surgery on functioning of a previous trabeculectomy. We searched CENTRAL (which contains the Cochrane Eyes and Vision Group Trials Register) (2014, Issue 5), Ovid MEDLINE, Ovid MEDLINE In-Process and Other Non-Indexed Citations, Ovid MEDLINE Daily, Ovid OLDMEDLINE (January 1946 to June 2014), EMBASE (January 1980 to June 2014), Latin American and Caribbean Health Sciences Literature Database (LILACS) (January 1982 to June 2014), the metaRegister of Controlled Trials (mRCT) (www.controlled-trials.com), ClinicalTrials.gov (www.clinicaltrials.gov) and the World Health Organization (WHO) International Clinical Trials Registry Platform (ICTRP) (www.who.int/ictrp/search/en). We did not use any date or language restrictions in the electronic searches for trials. We last searched the electronic databases on 10 June 2014. We also searched the Science Citation Index database (July 2013) and reference lists of potentially relevant studies. Randomised controlled trials (RCTs) of antimetabolites with cataract surgery in people with a functioning trabeculectomy. Two review authors independently reviewed the titles and abstracts from the electronic searches. Two review authors independently assessed relevant full-text articles and entered data. We identified no RCTs to test the effectiveness of antimetabolites with cataract surgery in individuals with the intention of preventing failure of a previous trabeculectomy. There are no RCTs of antimetabolites with cataract surgery in people with a functioning trabeculectomy. Appropriately powered RCTs

  12. Anaerobic carboxydotrophic bacteria in geothermal springs identified using stable isotope probing

    Directory of Open Access Journals (Sweden)

    Allyson Lee Brady

    2015-09-01

    Full Text Available Carbon monoxide (CO is a potential energy and carbon source for thermophilic bacteria in geothermal environments. Geothermal sites ranging in temperature from 45–65°C were investigated for the presence and activity of anaerobic CO-oxidizing bacteria. Anaerobic CO oxidation potentials were measured at up to 48.9 µmoles CO day-1 g (wet weight-1 within 5 selected sites. Active anaerobic carboxydotrophic bacteria were identified using 13CO DNA stable isotope probing (SIP combined with pyrosequencing of 16S rRNA genes amplified from labeled DNA. Bacterial communities identified in heavy DNA fractions were predominated by Firmicutes, which comprised up to 95% of all sequences in 13CO incubations. The predominant bacteria that assimilated 13C derived from CO were closely related (>98% to genera of known carboxydotrophs including Thermincola, Desulfotomaculum, Thermolithobacter and Carboxydocella, although a few species with lower similarity to known bacteria were also found that may represent previously unconfirmed CO-oxidizers. While the distribution was variable, many of the same OTUs were identified across sample sites from different temperature regimes. These results show that bacteria capable of using CO as a carbon source are common in geothermal springs, and that thermophilic carboxydotrophs are probably already quite well known from cultivation studies.

  13. [Meningitis and white matter lesions due to Streptococcus mitis in a previously healthy child].

    Science.gov (United States)

    Yiş, Reyhan; Yüksel, Ciğdem Nükhet; Derundere, Umit; Yiş, Uluç

    2011-10-01

    Streptococcus mitis, an important member of viridans streptococci, is found in the normal flora of the oropharynx, gastrointestinal tract, female genital tract and skin. Although it is of low pathogenicity and virulence, it may cause serious infections in immunocompromised patients. Meningitis caused by S.mitis has been described in patients with previous spinal anesthesia, neurosurgical procedure, malignancy, bacterial endocarditis with neurological complications and alcoholics, but it is rare in patients who are previously healthy. In this report, a rare case of meningoencephalitis caused by S.mitis developed in a previously healthy child has been presented. A previously healthy eight-year-old girl who presented with fever, altered state of consciousness, and headache was hospitalized in intensive care unit with the diagnosis of meningitis. Past history revealed that she was treated with amoxicillin-clavulanate for acute sinusitis ten days before her admission. Whole blood count revealed the followings: hemoglobin 13 g/dl, white blood cell count 18.6 x 109/L (90% neutrophils), platelet count 200 x 109/L and 150 leucocytes were detected on cerebrospinal fluid (CSF) examination. Protein and glucose levels of CSF were 80 mg/dl and 40 mg/dl (concomitant blood glucose 100 mg/dl), respectively. Brain magnetic resonance imaging (MRI) revealed widespread white matter lesions, and alpha-hemolytic streptococci were grown in CSF culture. The isolate was identified as S.mitis with conventional methods, and also confirmed by VITEK2 (bioMerieux, France) and API 20 STREP (bioMerieux, France) systems. Isolate was found susceptible to penicillin, erythromycin, clindamycin, tetracycline, cefotaxime, vancomycin and chloramphenicol. Regarding the etiology, echocardiography revealed no vegetation nor valve pathology, and peripheral blood smear showed no abnormality. Immunoglobulin and complement levels were within normal limits. Ongoing inflammation in maxillary sinuses detected in

  14. Genomic analysis identifies masqueraders of full-term cerebral palsy.

    Science.gov (United States)

    Takezawa, Yusuke; Kikuchi, Atsuo; Haginoya, Kazuhiro; Niihori, Tetsuya; Numata-Uematsu, Yurika; Inui, Takehiko; Yamamura-Suzuki, Saeko; Miyabayashi, Takuya; Anzai, Mai; Suzuki-Muromoto, Sato; Okubo, Yukimune; Endo, Wakaba; Togashi, Noriko; Kobayashi, Yasuko; Onuma, Akira; Funayama, Ryo; Shirota, Matsuyuki; Nakayama, Keiko; Aoki, Yoko; Kure, Shigeo

    2018-05-01

    Cerebral palsy is a common, heterogeneous neurodevelopmental disorder that causes movement and postural disabilities. Recent studies have suggested genetic diseases can be misdiagnosed as cerebral palsy. We hypothesized that two simple criteria, that is, full-term births and nonspecific brain MRI findings, are keys to extracting masqueraders among cerebral palsy cases due to the following: (1) preterm infants are susceptible to multiple environmental factors and therefore demonstrate an increased risk of cerebral palsy and (2) brain MRI assessment is essential for excluding environmental causes and other particular disorders. A total of 107 patients-all full-term births-without specific findings on brain MRI were identified among 897 patients diagnosed with cerebral palsy who were followed at our center. DNA samples were available for 17 of the 107 cases for trio whole-exome sequencing and array comparative genomic hybridization. We prioritized variants in genes known to be relevant in neurodevelopmental diseases and evaluated their pathogenicity according to the American College of Medical Genetics guidelines. Pathogenic/likely pathogenic candidate variants were identified in 9 of 17 cases (52.9%) within eight genes: CTNNB1 , CYP2U1 , SPAST , GNAO1 , CACNA1A , AMPD2 , STXBP1 , and SCN2A . Five identified variants had previously been reported. No pathogenic copy number variations were identified. The AMPD2 missense variant and the splice-site variants in CTNNB1 and AMPD2 were validated by in vitro functional experiments. The high rate of detecting causative genetic variants (52.9%) suggests that patients diagnosed with cerebral palsy in full-term births without specific MRI findings may include genetic diseases masquerading as cerebral palsy.

  15. Identification and pathway analysis of microRNAs with no previous involvement in breast cancer.

    Directory of Open Access Journals (Sweden)

    Sandra Romero-Cordoba

    Full Text Available microRNA expression signatures can differentiate normal and breast cancer tissues and can define specific clinico-pathological phenotypes in breast tumors. In order to further evaluate the microRNA expression profile in breast cancer, we analyzed the expression of 667 microRNAs in 29 tumors and 21 adjacent normal tissues using TaqMan Low-density arrays. 130 miRNAs showed significant differential expression (adjusted P value = 0.05, Fold Change = 2 in breast tumors compared to the normal adjacent tissue. Importantly, the role of 43 of these microRNAs has not been previously reported in breast cancer, including several evolutionary conserved microRNA*, showing similar expression rates to that of their corresponding leading strand. The expression of 14 microRNAs was replicated in an independent set of 55 tumors. Bioinformatic analysis of mRNA targets of the altered miRNAs, identified oncogenes like ERBB2, YY1, several MAP kinases, and known tumor-suppressors like FOXA1 and SMAD4. Pathway analysis identified that some biological process which are important in breast carcinogenesis are affected by the altered microRNA expression, including signaling through MAP kinases and TP53 pathways, as well as biological processes like cell death and communication, focal adhesion and ERBB2-ERBB3 signaling. Our data identified the altered expression of several microRNAs whose aberrant expression might have an important impact on cancer-related cellular pathways and whose role in breast cancer has not been previously described.

  16. Environmental assessment: Deaf Smith County site, Texas

    International Nuclear Information System (INIS)

    1986-05-01

    In February 1983, the US Department of Energy (DOE) identified a location in Deaf Smith County, Texas, as one of nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high-level radioactive waste. To determine their suitability, the Deaf Smith County site and the eight other potentially sites have been evaluated in accordance with the DOE's General Guidelines for the Recommendation of Sites for the Nuclear Waste Repositories. The Deaf Smith County site is in the Permian Basin, which is one of five distinct geohydrologic settings considered for the first repository. On the basis of the evaluations reported in this EA, the DOE has found that the Deaf Smith County site is not disqualified under the guidelines. On the basis of these findings, the DOE is nominating the Deaf Smith County site as one of the five sites suitable for characterization. 591 refs., 147 figs., 173 tabs

  17. Environmental assessment: Deaf Smith County site, Texas

    Energy Technology Data Exchange (ETDEWEB)

    1986-05-01

    In February 1983, the US Department of Energy (DOE) identified a location in Deaf Smith County, Texas, as one of nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high-level radioactive waste. To determine their suitability, the Deaf Smith County site and the eight other potentially sites have been evaluated in accordance with the DOE's General Guidelines for the Recommendation of Sites for the Nuclear Waste Repositories. The Deaf Smith County site is in the Permian Basin, which is one of five distinct geohydrologic settings considered for the first repository. On the basis of the evaluations reported in this EA, the DOE has found that the Deaf Smith County site is not disqualified under the guidelines. On the basis of these findings, the DOE is nominating the Deaf Smith County site as one of the five sites suitable for characterization. 591 refs., 147 figs., 173 tabs.

  18. SITE COMPREHENSIVE LISTING (CERCLIS) (Superfund) - NPL Sites

    Data.gov (United States)

    U.S. Environmental Protection Agency — National Priorities List (NPL) Sites - The Comprehensive Environmental Response, Compensation and Liability Information System (CERCLIS) (Superfund) Public Access...

  19. Superfund Site Information - Site Sampling Data

    Data.gov (United States)

    U.S. Environmental Protection Agency — This asset includes Superfund site-specific sampling information including location of samples, types of samples, and analytical chemistry characteristics of...

  20. Site Closure Strategy Model for Creosote Site

    International Nuclear Information System (INIS)

    Coll, F.R.; Gray, D.R.

    2009-01-01

    In conjunction with RCRA site corrective action at an active wood preserving facility, a risk-based site closure strategy was developed and incorporated the performance of a dense non-aqueous phase liquid (DNAPL) source recovery remedy, a monitored natural attenuation (MNA) remedy for dissolved phase groundwater, and institutional controls. Innovative creosote DNAPL source recovery has been undertaken at the Site since 1998. Pooled creosote DNAPL is present 90 feet below ground within a transmissive sand and gravel aquifer with a saturated thickness of approximately 80 feet. The creosote DNAPL source is situated on the property boundary of the site and has generated a 1/2 mile off-site dissolved phase plume, creating significant NAPL management and remedial technology verification issues. To date, over 120,000 gallons of creosote DNAPL have been recovered from the subsurface utilizing a modified circulation well technology. A mass discharge flux protocol was developed to serve as a major performance metrics for the continuation of source removal efforts and to support the application of monitored natural attenuation as an associated remedial technology for groundwater. The mass removal success has supported the MNA remedy for dissolved phase groundwater and the associated development of institutional controls. The enacted site management strategy outlines the current and future risk management activities for the Site and represents an appropriate site closure strategy for the Site. (authors)

  1. SPARQL-enabled identifier conversion with Identifiers.org

    Science.gov (United States)

    Wimalaratne, Sarala M.; Bolleman, Jerven; Juty, Nick; Katayama, Toshiaki; Dumontier, Michel; Redaschi, Nicole; Le Novère, Nicolas; Hermjakob, Henning; Laibe, Camille

    2015-01-01

    Motivation: On the semantic web, in life sciences in particular, data is often distributed via multiple resources. Each of these sources is likely to use their own International Resource Identifier for conceptually the same resource or database record. The lack of correspondence between identifiers introduces a barrier when executing federated SPARQL queries across life science data. Results: We introduce a novel SPARQL-based service to enable on-the-fly integration of life science data. This service uses the identifier patterns defined in the Identifiers.org Registry to generate a plurality of identifier variants, which can then be used to match source identifiers with target identifiers. We demonstrate the utility of this identifier integration approach by answering queries across major producers of life science Linked Data. Availability and implementation: The SPARQL-based identifier conversion service is available without restriction at http://identifiers.org/services/sparql. Contact: sarala@ebi.ac.uk PMID:25638809

  2. SPARQL-enabled identifier conversion with Identifiers.org.

    Science.gov (United States)

    Wimalaratne, Sarala M; Bolleman, Jerven; Juty, Nick; Katayama, Toshiaki; Dumontier, Michel; Redaschi, Nicole; Le Novère, Nicolas; Hermjakob, Henning; Laibe, Camille

    2015-06-01

    On the semantic web, in life sciences in particular, data is often distributed via multiple resources. Each of these sources is likely to use their own International Resource Identifier for conceptually the same resource or database record. The lack of correspondence between identifiers introduces a barrier when executing federated SPARQL queries across life science data. We introduce a novel SPARQL-based service to enable on-the-fly integration of life science data. This service uses the identifier patterns defined in the Identifiers.org Registry to generate a plurality of identifier variants, which can then be used to match source identifiers with target identifiers. We demonstrate the utility of this identifier integration approach by answering queries across major producers of life science Linked Data. The SPARQL-based identifier conversion service is available without restriction at http://identifiers.org/services/sparql. © The Author 2015. Published by Oxford University Press.

  3. Report of early site suitability evaluation of the potential repository site at Yucca Mountain, Nevada; Yucca Mountain Site Characterization Project

    Energy Technology Data Exchange (ETDEWEB)

    Younker, J.L.; Andrews, W.B.; Fasano, G.A.; Herrington, C.C.; Mattson, S.R.; Murray, R.C. [Science Applications International Corp., Las Vegas, NV (United States); Ballou, L.B.; Revelli, M.A. [Lawrence Livermore National Lab., CA (United States); Ducharme, A.R.; Shephard, L.E. [Sandia National Labs., Albuquerque, NM (United States); Dudley, W.W.; Hoxie, D.T. [Geological Survey, Denver, CO (United States); Herbst, R.J.; Patera, E.A. [Los Alamos National Lab., NM (United States); Judd, B.R. [Decision Analysis Co., Portola Valley, CA (United States); Docka, J.A.; Rickertsen, L.D. [Weston Technical Associates, Washington, DC (United States)

    1992-01-01

    This study evaluated the technical suitability of Yucca Mountain, Nevada, as a potential site for a mined geologic repository for the permanent disposal of radioactive waste. The evaluation was conducted primarily to determine early in the site characterization program if there are any features or conditions at the site that indicate it is unsuitable for repository development. A secondary purpose was to determine the status of knowledge in the major technical areas that affect the suitability of the site. This early site suitability evaluation (ESSE) was conducted by a team of technical personnel at the request of the Associate Director of the US Department of Energy (DOE) Office of Geologic Disposal, a unit within the DOE`s Office of Civilian Radioactive Waste Management. The Yucca Mountain site has been the subject of such evaluations for over a decade. In 1983, the site was evaluated as part of a screening process to identify potentially acceptable sites. The site was evaluated in greater detail and found suitable for site characterization as part of the Environmental Assessment (EA) (DOE, 1986) required by the Nuclear Waste Policy Act of 1982 (NWPA). Additional site data were compiled during the preparation of the Site Characterization Plan (SCP) (DOE, 1988a). This early site suitability evaluation has considered information that was used in preparing both-documents, along with recent information obtained since the EA and SCP were published. This body of information is referred to in this report as ``current information`` or ``available evidence.``

  4. Site specific information in site selection

    International Nuclear Information System (INIS)

    Aeikaes, T.; Hautojaervi, A.

    1998-01-01

    The programme for the siting of a deep repository for final disposal of spent nuclear fuel was started already in 1983 and is carried out today by Posiva Oy which continues the work started by Teollisuuden Voima Oy. The programme aims at site selection by the end of the year 2000. The programme has progressed in successive interim stages with defined goals. After an early phase for site identification, five sites were selected in 1987 for preliminary site characterisation. Three of these were selected and judged to be best suited for the more detailed characterisation in 1992. An additional new site was included into the programme based on a separate feasibility study in the beginning of 1997. Since the year 1983 several safety assessments together with technical plans of the facility have been completed. When approaching the site selection the needs for more detailed consideration of the site specific properties in the safety assessment have been increased. The Finnish regulator STUK has published a proposal for general safety requirements for the final disposal of spent nuclear fuel in Finland. This set of requirements has been projected to be used in conjunction of the decision making by the end 2000. Based on the site evaluation all sites can provide a stable environment and there is evidence that the requirements for the longevity of the canister can be fulfilled at each site. In this manner the four candidate sites do not differ too much from each other. The main difference between the sites is in the salinity of the deep groundwater. The significance of differences in the salinity for the long-term safety cannot be defined yet. The differences may contribute to the discussion of the longevity of the bentonite buffer and also to the modelling of the groundwater flow and transport. The use of the geosphere as a transport barrier is basically culminated on the questions about sparse but fast flow routes and 'how bad channeling can be'. To answer these questions

  5. Fear and anxiety previous to dental treatment in children from Acaraú-CE

    Directory of Open Access Journals (Sweden)

    Karyne Barreto Gonçalves Marques

    2010-12-01

    Full Text Available Objective: To identify the main causing factors of fear and anxiety of children previously to dental treatment. Methods: A descriptive and qualitative study held in the municipal district of Acaraú - CE with 10 children aged 4 to 6 years old, who did not present strong pain between August and September, 2006. At first, we applied the modified VPT (Venham Picture Test, an instrument containing a set of figures of children in different emotional states, which were presented to each child so that he pointed to what he considered to be further identified at the time. The second test, held before the consultation, consisted in asking to the children to free-hand draw the dental office, the dentist and auxiliary personnel asking to each child: what do you think about the dental office and the dentist? The drawings were submitted to idiographic analysis and categorized in units of significance for interpretation. Results: Three children on VPT and nine children on the drawings presented an increased level of anxiety. Causing factors such as the motor (high speed rotation, tooth extraction and white clothes could be found. Final considerations: By means of drawing we were able to efficiently obtain results in identifying some factors that cause fear and anxiety to the child patient. The modified VPT showed to be quick, easy to apply and acceptable to children, but sometimes was contradictory with the drawings.

  6. Multicenter Study of Pin Site Infections and Skin Complications Following Pinning of Pediatric Supracondylar Humerus Fractures.

    Science.gov (United States)

    Combs, Kristen; Frick, Steven; Kiebzak, Gary

    2016-12-03

    Pediatric supracondylar humerus fractures are the most common elbow fractures in pediatric patients. Surgical fixation using pins is the primary treatment for displaced fractures. Pin site infections may follow supracondylar humerus fracture fixation; the previously reported incidence rate in the literature is 2.34%, but there is significant variability in reported incidence rates of pin site infection. This study aims to define the incidence rate and determine pre-, peri-, and postoperative factors that may contribute to pin site infection following operative reduction, pinning, and casting. A retrospective chart analysis was performed over a one-year period on patients that developed pin site infection. A cast care form was added to Nemours' electronic medical records (EMR) system (Epic Systems Corp., Verona, WI) to identify pin site infections for retrospective review. The cast care form noted any inflamed or infected pins. Patients with inflamed or infected pin sites underwent a detailed chart review. Preoperative antibiotic use, number and size of pins used, method of postoperative immobilization, pin dressings, whether postoperative immobilization was changed prior to pin removal, and length of time pins were in place was recorded. A total of 369 patients underwent operative reduction, pinning, and casting. Three patients developed a pin site infection. The pin site infection incidence rate was 3/369=0.81%. Descriptive statistics were reported for the three patients that developed pin site infections and three patients that developed pin site complications. Pin site infection development is low. Factors that may contribute to the development of pin site infection include preoperative antibiotic use, length of time pins are left in, and changing the cast prior to pin removal.

  7. Regulation of CCL2 expression by an upstream TALE homeodomain protein-binding site that synergizes with the site created by the A-2578G SNP.

    Science.gov (United States)

    Page, Stephen H; Wright, Edward K; Gama, Lucio; Clements, Janice E

    2011-01-01

    CC Chemokine Ligand 2 (CCL2) is a potent chemoattractant produced by macrophages and activated astrocytes during periods of inflammation within the central nervous system. Increased CCL2 expression is correlated with disease progression and severity, as observed in pulmonary tuberculosis, HCV-related liver disease, and HIV-associated dementia. The CCL2 distal promoter contains an A/G polymorphism at position -2578 and the homozygous -2578 G/G genotype is associated with increased CCL2 production and inflammation. However, the mechanisms that contribute to the phenotypic differences in CCL2 expression are poorly understood. We previously demonstrated that the -2578 G polymorphism creates a TALE homeodomain protein binding site (TALE binding site) for PREP1/PBX2 transcription factors. In this study, we identified the presence of an additional TALE binding site 22 bp upstream of the site created by the -2578 G polymorphism and demonstrated the synergistic effects of the two sites on the activation of the CCL2 promoter. Using chromatin immunoprecipitation (ChIP) assays, we demonstrated increased binding of the TALE proteins PREP1 and PBX2 to the -2578 G allele, and binding of IRF1 to both the A and G alleles. The presence of TALE binding sites that form inverted repeats within the -2578 G allele results in increased transcriptional activation of the CCL2 distal promoter while the presence of only the upstream TALE binding site within the -2578 A allele exerts repression of promoter activity.

  8. American National Standard: guidelines for evaluating site-related geotechnical parameters at nuclear power sites

    International Nuclear Information System (INIS)

    Anon.

    1978-01-01

    This standard presents guidelines for evaluating site-related geotechnical parameters for nuclear power sites. Aspects considered include geology, ground water, foundation engineering, and earthwork engineering. These guidelines identify the basic geotechnical parameters to be considered in site evaluation, and in the design, construction, and performance of foundations and earthwork aspects for nuclear power plants. Also included are tabulations of typical field and laboratory investigative methods useful in identifying geotechnical parameters. Those areas where interrelationships with other standards may exist are indicated

  9. Environmental assessment: Davis Canyon site, Utah

    International Nuclear Information System (INIS)

    1986-05-01

    In February 1983, the US Department of Energy (DOE) identified the Davis Canyon site in Utah as one of the nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high-level radioactive waste. To determine their suitability, the Davis Canyon site and the eight other potentially acceptable sites have been evaluated in accordance with the DOE's General Guidelines for the Recommendation of Sites for the Nuclear Waste Repositories. These evaluations were reported in draft environmental assessments (EAs), which were issued for public review and comment. After considering the comments received on the draft EAs, the DOE prepared the final EA. The Davis Canyon site is in the Paradox Basin, which is one of five distinct geohydrologic settings considered for the first repository. This setting contains one other potentially acceptable site -- the Lavender Canyon site. Although the Lavender Canyon site is suitable for site characterization, the DOE has concluded that the Davis Canyon site is the preferred site in the Paradox Basin. On the basis of the evaluations reported in this EA, the DOE has found that the Davis Canyon site is not disqualified under the guidelines. Furthermore, the DOE has fond that the site is suitable for site characterization because the evidence does not support a conclusion that the site will not be able to meet each of the qualifying conditions specified in the guidelines. On the basis of these findings, the DOE is nominating the Davis Canyon site as one of five sites suitable for characterization. 181 figs., 175 tabs

  10. Environmental assessment: Davis Canyon site, Utah

    Energy Technology Data Exchange (ETDEWEB)

    none,

    1986-05-01

    In February 1983, the US Department of Energy (DOE) identified the Davis Canyon site in Utah as one of the nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high-level radioactive waste. To determine their suitability, the Davis Canyon site and the eight other potentially acceptable sites have been evaluated in accordance with the DOE's General Guidelines for the Recommendation of Sites for the Nuclear Waste Repositories. These evaluations were reported in draft environmental assessments (EAs), which were issued for public review and comment. After considering the comments received on the draft EAs, the DOE prepared the final EA. The Davis Canyon site is in the Paradox Basin, which is one of five distinct geohydrologic settings considered for the first repository. This setting contains one other potentially acceptable site -- the Lavender Canyon site. Although the Lavender Canyon site is suitable for site characterization, the DOE has concluded that the Davis Canyon site is the preferred site in the Paradox Basin. On the basis of the evaluations reported in this EA, the DOE has found that the Davis Canyon site is not disqualified under the guidelines. Furthermore, the DOE has fond that the site is suitable for site characterization because the evidence does not support a conclusion that the site will not be able to meet each of the qualifying conditions specified in the guidelines. On the basis of these findings, the DOE is nominating the Davis Canyon site as one of five sites suitable for characterization. 181 figs., 175 tabs.

  11. Baseline report - tall upland shrubland at the Rocky Flats Environmental Technology Site

    International Nuclear Information System (INIS)

    1997-03-01

    Rocky Flats Environmental Technology Site (Site) is located on the Colorado Piedmont east of the Front Range between Boulder and Golden. At an elevation of approximately 6,000 feet, the Site contains a unique ecotonal mixture of mountain and prairie plant species, resulting from the topography and close proximity to the mountain front. The Buffer Zone surrounding the Industrial Area is one of the largest remaining undeveloped areas of its kind along the Colorado Piedmont. A number of plant communities at the Site have been identified as increasingly rare and unique by Site ecologists and the Colorado Natural Heritage Program (CNHP). These include the xeric tallgrass prairie, tall upland shrubland, wetlands, and Great Plains riparian woodland communities. Many of these communities support populations of increasingly rare animals as well, including the Preble's meadow jumping mouse, grasshopper sparrow, loggerhead shrike, Merriam's shrew, black crowned night heron, and Hops blue and Argos skipper butterflies. One of the more interesting and important plant communities at the Site is the tall upland shrubland community. It has been generally overlooked by previous Site ecological studies, probably due to its relatively small size; only 34 acres total. Although mentioned in a plant community ordination study conducted by Clark et al. and also in the Site baseline ecological study, few data were available on this plant community before the present study

  12. Baseline report - tall upland shrubland at the Rocky Flats Environmental Technology Site

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-03-01

    Rocky Flats Environmental Technology Site (Site) is located on the Colorado Piedmont east of the Front Range between Boulder and Golden. At an elevation of approximately 6,000 feet, the Site contains a unique ecotonal mixture of mountain and prairie plant species, resulting from the topography and close proximity to the mountain front. The Buffer Zone surrounding the Industrial Area is one of the largest remaining undeveloped areas of its kind along the Colorado Piedmont. A number of plant communities at the Site have been identified as increasingly rare and unique by Site ecologists and the Colorado Natural Heritage Program (CNHP). These include the xeric tallgrass prairie, tall upland shrubland, wetlands, and Great Plains riparian woodland communities. Many of these communities support populations of increasingly rare animals as well, including the Preble`s meadow jumping mouse, grasshopper sparrow, loggerhead shrike, Merriam`s shrew, black crowned night heron, and Hops blue and Argos skipper butterflies. One of the more interesting and important plant communities at the Site is the tall upland shrubland community. It has been generally overlooked by previous Site ecological studies, probably due to its relatively small size; only 34 acres total. Although mentioned in a plant community ordination study conducted by Clark et al. and also in the Site baseline ecological study, few data were available on this plant community before the present study.

  13. Features generated for computational splice-site prediction correspond to functional elements

    Directory of Open Access Journals (Sweden)

    Wilbur W John

    2007-10-01

    Full Text Available Abstract Background Accurate selection of splice sites during the splicing of precursors to messenger RNA requires both relatively well-characterized signals at the splice sites and auxiliary signals in the adjacent exons and introns. We previously described a feature generation algorithm (FGA that is capable of achieving high classification accuracy on human 3' splice sites. In this paper, we extend the splice-site prediction to 5' splice sites and explore the generated features for biologically meaningful splicing signals. Results We present examples from the observed features that correspond to known signals, both core signals (including the branch site and pyrimidine tract and auxiliary signals (including GGG triplets and exon splicing enhancers. We present evidence that features identified by FGA include splicing signals not found by other methods. Conclusion Our generated features capture known biological signals in the expected sequence interval flanking splice sites. The method can be easily applied to other species and to similar classification problems, such as tissue-specific regulatory elements, polyadenylation sites, promoters, etc.

  14. Hanford Site Development Plan

    International Nuclear Information System (INIS)

    Hathaway, H.B.; Daly, K.S.; Rinne, C.A.; Seiler, S.W.

    1993-05-01

    The Hanford Site Development Plan (HSDP) provides an overview of land use, infrastructure, and facility requirements to support US Department of Energy (DOE) programs at the Hanford Site. The HSDP's primary purpose is to inform senior managers and interested parties of development activities and issues that require a commitment of resources to support the Hanford Site. The HSDP provides an existing and future land use plan for the Hanford Site. The HSDP is updated annually in accordance with DOE Order 4320.1B, Site Development Planning, to reflect the mission and overall site development process. Further details about Hanford Site development are defined in individual area development plans

  15. Residential customer-sited photovoltaics markets 1999

    International Nuclear Information System (INIS)

    Herig, C.; Thomas, H.; Perez, R.; Wenger, H.

    1999-01-01

    Nearly three years ago, the authors published the paper, Niche Markets for Grid Connected Photovoltaics. The paper identified target market niches for Customer-Sited Photovoltaics (CSPV), on a state-by-state basis for the US. The paper demonstrated cost-effective, grid-connected, domestic markets existed and identified those showing the most near-term promise. Many financial and policy attributes effecting the economics of CSPV have changed since the previous paper was published. Incorporating these policy changes into the analysis expands the CSPV market from a niche status to an era of significance. The number of states with break-even turnkey costs (BTC) above four dollars per watt expanded from five to fifteen. The top five state market values are now above a break-even cost of seven dollars per watt, a value at which the domestic CSPV market moves beyond a break-even status to consumer savings or industry profit, depending on system price. Emissions mitigation values were also included in the paper, but did not significantly effect the break-even market value results. The paper presents the details of the data, analysis, and results

  16. Assessing hypotheses about nesting site occupancy dynamics

    Science.gov (United States)

    Bled, Florent; Royle, J. Andrew; Cam, Emmanuelle

    2011-01-01

    Hypotheses about habitat selection developed in the evolutionary ecology framework assume that individuals, under some conditions, select breeding habitat based on expected fitness in different habitat. The relationship between habitat quality and fitness may be reflected by breeding success of individuals, which may in turn be used to assess habitat quality. Habitat quality may also be assessed via local density: if high-quality sites are preferentially used, high density may reflect high-quality habitat. Here we assessed whether site occupancy dynamics vary with site surrogates for habitat quality. We modeled nest site use probability in a seabird subcolony (the Black-legged Kittiwake, Rissa tridactyla) over a 20-year period. We estimated site persistence (an occupied site remains occupied from time t to t + 1) and colonization through two subprocesses: first colonization (site creation at the timescale of the study) and recolonization (a site is colonized again after being deserted). Our model explicitly incorporated site-specific and neighboring breeding success and conspecific density in the neighborhood. Our results provided evidence that reproductively "successful'' sites have a higher persistence probability than "unsuccessful'' ones. Analyses of site fidelity in marked birds and of survival probability showed that high site persistence predominantly reflects site fidelity, not immediate colonization by new owners after emigration or death of previous owners. There is a negative quadratic relationship between local density and persistence probability. First colonization probability decreases with density, whereas recolonization probability is constant. This highlights the importance of distinguishing initial colonization and recolonization to understand site occupancy. All dynamics varied positively with neighboring breeding success. We found evidence of a positive interaction between site-specific and neighboring breeding success. We addressed local

  17. A critical evaluation of Web sites offering patient information on tinnitus.

    LENUS (Irish Health Repository)

    Kieran, Stephen M

    2012-02-01

    The Internet is a vast information resource for both patients and healthcare professionals. However, the quality and content often lack formal scrutiny, so we examined the quality of patient information regarding tinnitus on the Internet. Using the three most popular search engines (google.com, yahoo.com, and msn.com), we found pertinent Web sites using the search term tinnitus. Web sites\\' accountability and authorship were evaluated using previously published criteria. The quality of patient information about tinnitus was assessed using a new 10-point scale, the Tinnitus Information Value (TIV). Statistical analysis was performed using the independent sample t-test (p sites was constructed using the first 30 English-language Web sites identified by each search engine. After duplicates and sites only containing links to other Web sites were eliminated, 39 remained. The mean score for accountability was 2.13 on scale of 0 to 7. The mean TIV was 5.0 on a scale of 0 to 10. Only 12 sites (30.8%) had their authors clearly identified. Twenty-two (56.4%) sites were sponsored by commercial interests or represented private practices. The mean TIV was significantly higher (p = 0.037) for noncommercial (personal, academic institution, or charity) sites (5.88 +\\/- 2.39 SD) than those representing commercial interests (4.32 +\\/- 2.10 SD). Tinnitus information available on the Internet is indeed variable, and care should be taken in recommending tinnitus Web sites to patients.

  18. Fungal community structure under goat willows (Salix caprea L.) growing at metal polluted site: the potential of screening in a model phytostabilisation study

    Science.gov (United States)

    Marjana Regvar; Matevz Likar; Andrej Piltaver; Nives Kugonic; Jane E. Smith

    2010-01-01

    Goat willow (Salix caprea L.) was selected in a previous vegetation screening study as a potential candidate for the later-stage phytostabilisation efforts at a heavily metal polluted site in Slovenia. The aims of this study were to identify the fungi colonising roots of S. caprea along the gradient of vegetation succession and...

  19. LIBRA: LIgand Binding site Recognition Application.

    Science.gov (United States)

    Hung, Le Viet; Caprari, Silvia; Bizai, Massimiliano; Toti, Daniele; Polticelli, Fabio

    2015-12-15

    In recent years, structural genomics and ab initio molecular modeling activities are leading to the availability of a large number of structural models of proteins whose biochemical function is not known. The aim of this study was the development of a novel software tool that, given a protein's structural model, predicts the presence and identity of active sites and/or ligand binding sites. The algorithm implemented by ligand binding site recognition application (LIBRA) is based on a graph theory approach to find the largest subset of similar residues between an input protein and a collection of known functional sites. The algorithm makes use of two predefined databases for active sites and ligand binding sites, respectively, derived from the Catalytic Site Atlas and the Protein Data Bank. Tests indicate that LIBRA is able to identify the correct binding/active site in 90% of the cases analyzed, 90% of which feature the identified site as ranking first. As far as ligand binding site recognition is concerned, LIBRA outperforms other structure-based ligand binding sites detection tools with which it has been compared. The application, developed in Java SE 7 with a Swing GUI embedding a JMol applet, can be run on any OS equipped with a suitable Java Virtual Machine (JVM), and is available at the following URL: http://www.computationalbiology.it/software/LIBRAv1.zip. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  20. National Ignition Facility Project Site Safety Program

    International Nuclear Information System (INIS)

    Dun, C

    2003-01-01

    This Safety Program for the National Ignition Facility (NIF) presents safety protocols and requirements that management and workers shall follow to assure a safe and healthful work environment during activities performed on the NIF Project site. The NIF Project Site Safety Program (NPSSP) requires that activities at the NIF Project site be performed in accordance with the ''LLNL ES and H Manual'' and the augmented set of controls and processes described in this NIF Project Site Safety Program. Specifically, this document: (1) Defines the fundamental NIF site safety philosophy. (2) Defines the areas covered by this safety program (see Appendix B). (3) Identifies management roles and responsibilities. (4) Defines core safety management processes. (5) Identifies NIF site-specific safety requirements. This NPSSP sets forth the responsibilities, requirements, rules, policies, and regulations for workers involved in work activities performed on the NIF Project site. Workers are required to implement measures to create a universal awareness that promotes safe practice at the work site and will achieve NIF management objectives in preventing accidents and illnesses. ES and H requirements are consistent with the ''LLNL ES and H Manual''. This NPSSP and implementing procedures (e.g., Management Walkabout, special work procedures, etc.,) are a comprehensive safety program that applies to NIF workers on the NIF Project site. The NIF Project site includes the B581/B681 site and support areas shown in Appendix B

  1. Region 9 NPL Sites (Superfund Sites 2013)

    Science.gov (United States)

    NPL site POINT locations for the US EPA Region 9. NPL (National Priorities List) sites are hazardous waste sites that are eligible for extensive long-term cleanup under the Superfund program. Eligibility is determined by a scoring method called Hazard Ranking System. Sites with high scores are listed on the NPL. The majority of the locations are derived from polygon centroids of digitized site boundaries. The remaining locations were generated from address geocoding and digitizing. Area covered by this data set include Arizona, California, Nevada, Hawaii, Guam, American Samoa, Northern Marianas and Trust Territories. Attributes include NPL status codes, NPL industry type codes and environmental indicators. Related table, NPL_Contaminants contains information about contaminated media types and chemicals. This is a one-to-many relate and can be related to the feature class using the relationship classes under the Feature Data Set ENVIRO_CONTAMINANT.

  2. EZID: Long term identifiers made easy (Invited)

    Science.gov (United States)

    Starr, J.

    2013-12-01

    Scholarly research is producing ever increasing amounts of digital research data, and this data should be managed throughout the research life cycle both as part of good scientific practice, but also to comply with funder mandates, such as the 2013 OSTP Public Access Memo (http://www.whitehouse.gov/sites/default/files/microsites/ostp/ostp_public_access_memo_2013.pdf). By assigning unique and persistent identifiers to data objects, data managers can gain control and flexibility over what can be a daunting task. This is due to the fact that the objects can be moved to new locations without disruption to links, as long as the identifier target is maintained. EZID is a tool that makes assigning and maintaining unique, persistent identifiers easy. It was designed and built by California Digital Library (CDL) and has both a user interface and a RESTful API. EZID currently offers services for two globally unique, persistent identifier schemes: Digital Object Identifiers (DOIs) and Archival Resource Keys (ARKs). DOIs are identifiers originating from the publishing world and are in widespread use for journal articles. CDL is able to offer DOIs because of being a founding member of DataCite (http://www.datacite.org/), an international consortium established to provide easier access to scientific research data on the Internet. ARKs are identifiers originating from the library, archive and museum community. Like DOIs, they become persistent when the objects and identifier forwarding information is maintained. DOIs and ARKs have a key role in data management and, therefore, in data management plans. DOIs are the recommended identifier for use in data citation, and ARKs provide the maximum flexibility needed for data documentation and management throughout the early phases of a project. The two identifier schemes are able to be used together, and EZID is made to work with both. EZID clients, coming from education, research, government, and the private sector, are utilizing the

  3. Impact of previous virological treatment failures and adherence on the outcome of antiretroviral therapy in 2007.

    Directory of Open Access Journals (Sweden)

    Marie Ballif

    Full Text Available BACKGROUND: Combination antiretroviral treatment (cART has been very successful, especially among selected patients in clinical trials. The aim of this study was to describe outcomes of cART on the population level in a large national cohort. METHODS: Characteristics of participants of the Swiss HIV Cohort Study on stable cART at two semiannual visits in 2007 were analyzed with respect to era of treatment initiation, number of previous virologically failed regimens and self reported adherence. Starting ART in the mono/dual era before HIV-1 RNA assays became available was counted as one failed regimen. Logistic regression was used to identify risk factors for virological failure between the two consecutive visits. RESULTS: Of 4541 patients 31.2% and 68.8% had initiated therapy in the mono/dual and cART era, respectively, and been on treatment for a median of 11.7 vs. 5.7 years. At visit 1 in 2007, the mean number of previous failed regimens was 3.2 vs. 0.5 and the viral load was undetectable (4 previous failures compared to 1 were 0.9 (95% CI 0.4-1.7, 0.8 (0.4-1.6, 1.6 (0.8-3.2, 3.3 (1.7-6.6 respectively, and 2.3 (1.1-4.8 for >2 missed cART doses during the last month, compared to perfect adherence. From the cART era, odds ratios with a history of 1, 2 and >2 previous failures compared to none were 1.8 (95% CI 1.3-2.5, 2.8 (1.7-4.5 and 7.8 (4.5-13.5, respectively, and 2.8 (1.6-4.8 for >2 missed cART doses during the last month, compared to perfect adherence. CONCLUSIONS: A higher number of previous virologically failed regimens, and imperfect adherence to therapy were independent predictors of imminent virological failure.

  4. Salmon Site Remedial Investigation Report

    International Nuclear Information System (INIS)

    1999-01-01

    This Salmon Site Remedial Investigation Report provides the results of activities initiated by the U.S. Department of Energy (DOE) to determine if contamination at the Salmon Site poses a current or future risk to human health and the environment. These results were used to develop and evaluate a range of risk-based remedial alternatives. Located in Lamar County, Mississippi, the Salmon Site was used by the U.S. Atomic Energy Commission (predecessor to the DOE) between 1964 and 1970 for two nuclear and two gas explosions conducted deep underground in a salt dome. The testing resulted in the release of radionuclides into the salt dome. During reentry drilling and other site activities, liquid and solid wastes containing radioactivity were generated resulting in surface soil and groundwater contamination. Most of the waste and contaminated soil and water were disposed of in 1993 during site restoration either in the cavities left by the tests or in an injection well. Other radioactive wastes were transported to the Nevada Test Site for disposal. Nonradioactive wastes were disposed of in pits at the site and capped with clean soil and graded. The preliminary investigation showed residual contamination in the Surface Ground Zero mud pits below the water table. Remedial investigations results concluded the contaminant concentrations detected present no significant risk to existing and/or future land users, if surface institutional controls and subsurface restrictions are maintained. Recent sampling results determined no significant contamination in the surface or shallow subsurface. The test cavity resulting from the experiments is contaminated and cannot be economically remediated with existing technologies. The ecological sampling did not detect biological uptake of contaminants in the plants or animals sampled. Based on the current use of the Salmon Site, the following remedial actions were identified to protect both human health and the environment: (1) the

  5. PROCOV: maximum likelihood estimation of protein phylogeny under covarion models and site-specific covarion pattern analysis

    Directory of Open Access Journals (Sweden)

    Wang Huai-Chun

    2009-09-01

    Full Text Available Abstract Background The covarion hypothesis of molecular evolution holds that selective pressures on a given amino acid or nucleotide site are dependent on the identity of other sites in the molecule that change throughout time, resulting in changes of evolutionary rates of sites along the branches of a phylogenetic tree. At the sequence level, covarion-like evolution at a site manifests as conservation of nucleotide or amino acid states among some homologs where the states are not conserved in other homologs (or groups of homologs. Covarion-like evolution has been shown to relate to changes in functions at sites in different clades, and, if ignored, can adversely affect the accuracy of phylogenetic inference. Results PROCOV (protein covarion analysis is a software tool that implements a number of previously proposed covarion models of protein evolution for phylogenetic inference in a maximum likelihood framework. Several algorithmic and implementation improvements in this tool over previous versions make computationally expensive tree searches with covarion models more efficient and analyses of large phylogenomic data sets tractable. PROCOV can be used to identify covarion sites by comparing the site likelihoods under the covarion process to the corresponding site likelihoods under a rates-across-sites (RAS process. Those sites with the greatest log-likelihood difference between a 'covarion' and an RAS process were found to be of functional or structural significance in a dataset of bacterial and eukaryotic elongation factors. Conclusion Covarion models implemented in PROCOV may be especially useful for phylogenetic estimation when ancient divergences between sequences have occurred and rates of evolution at sites are likely to have changed over the tree. It can also be used to study lineage-specific functional shifts in protein families that result in changes in the patterns of site variability among subtrees.

  6. New Site Coefficients and Site Classification System Used in Recent Building Seismic Code Provisions

    Science.gov (United States)

    Dobry, R.; Borcherdt, R.D.; Crouse, C.B.; Idriss, I.M.; Joyner, W.B.; Martin, G.R.; Power, M.S.; Rinne, E.E.; Seed, R.B.

    2000-01-01

    Recent code provisions for buildings and other structures (1994 and 1997 NEHRP Provisions, 1997 UBC) have adopted new site amplification factors and a new procedure for site classification. Two amplitude-dependent site amplification factors are specified: Fa for short periods and Fv for longer periods. Previous codes included only a long period factor S and did not provide for a short period amplification factor. The new site classification system is based on definitions of five site classes in terms of a representative average shear wave velocity to a depth of 30 m (V?? s). This definition permits sites to be classified unambiguously. When the shear wave velocity is not available, other soil properties such as standard penetration resistance or undrained shear strength can be used. The new site classes denoted by letters A - E, replace site classes in previous codes denoted by S1 - S4. Site classes A and B correspond to hard rock and rock, Site Class C corresponds to soft rock and very stiff / very dense soil, and Site Classes D and E correspond to stiff soil and soft soil. A sixth site class, F, is defined for soils requiring site-specific evaluations. Both Fa and Fv are functions of the site class, and also of the level of seismic hazard on rock, defined by parameters such as Aa and Av (1994 NEHRP Provisions), Ss and S1 (1997 NEHRP Provisions) or Z (1997 UBC). The values of Fa and Fv decrease as the seismic hazard on rock increases due to soil nonlinearity. The greatest impact of the new factors Fa and Fv as compared with the old S factors occurs in areas of low-to-medium seismic hazard. This paper summarizes the new site provisions, explains the basis for them, and discusses ongoing studies of site amplification in recent earthquakes that may influence future code developments.

  7. Incidence of cancer in adolescent idiopathic scoliosis patients treated 25 years previously

    DEFF Research Database (Denmark)

    Simony, Ane; Hansen, Emil Jesper; Christensen, Steen Bach

    2016-01-01

    , is comparable to modern equipment. This is to our knowledge the first study to report increased rates of endometrial cancers in a cohort of AIS patients, and future attention is needed to reduce the radiation dose distributed to the AIS patients both pre-operatively and during surgery.......PURPOSE: To report the incidence of cancer in a cohort of adolescent idiopathic scoliosis (AIS) patients treated 25 years previously. METHODS: 215 consecutive AIS patients treated between 1983 and 1990 were identified and requested to return for clinical and radiographic examination. The incidence....... RESULTS: From the original cohort of 215 consecutive AIS patients, radiation information was available in 211 of the patients, and medical charts were available in 209 AIS patients. 170 (83 %) of the 205 AIS patients participated in the follow-up study with questionnaires. The calculated mean total...

  8. Laparoscopic assisted ventriculoperitoneal shunt revisions as an option for pediatric patients with previous intraabdominal complications

    Directory of Open Access Journals (Sweden)

    Fernanda O. de Carvalho

    2014-04-01

    Full Text Available Multiple shunt failure is a challenge in pediatric neurosurgery practice and one of the most feared complications of hydrocephalus. Objective: To demonstrate that laparoscopic procedures for distal ventriculoperitoneal shunt failure may be an effective option for patients who underwent multiple revisions due to repetitive manipulation of the peritoneal cavity, abdominal pseudocyst, peritonitis or other situations leading to a “non reliable” peritoneum. Method: From March 2012 to February 2013, the authors reviewed retrospectively the charts of six patients born and followed up at our institution, which presented with previous intra-peritoneal complications and underwent ventriculoperitoneal shunt revision assisted by video laparoscopy. Results: After a mean follow-up period of nine months, all patients are well and no further shunt failure was identified so far. Conclusion: Laparoscopy assisted shunt revision in children may be, in selected cases, an effective option for patients with multiple peritoneal complications due to ventriculo-peritoneal shunting.

  9. Outcome after arthroscopic labral surgery in patients previously treated with periacetabular osteotomy

    DEFF Research Database (Denmark)

    Hartig-Andreasen, Charlotte; Nielsen, Torsten G; Lund, Bent

    2017-01-01

    To identify factors predicting failure after hip arthroscopy in patients with previous periacetabular osteotomy (PAO) defined as a conversion to total hip replacement (THR) and to evaluate the patient reported outcome scores. Of 55 hips treated with hip arthroscopy after PAO from Aug 2008 to 2012....... Nine hips were converted to a THR. Kaplan-Meier survival rate was 52.8% (95% CI, 10%-83.8%) at 6.5 years follow-up. Statistically significant predictors of failure: joint space width after PAO ...% of the hips. In 42% of the hips cartilage lesions of Becks grade >3 were found. Mean mHHS and HOS were 65.7 and 68.8 respectively at follow-up. A NRS pain score of >3 in rest and during activity were present in respectively, 43% and 62% of the patients. Hip arthroscopy after PAO demonstrated limited clinical...

  10. Wildlife studies on the Hanford site: 1994 Highlights report

    Energy Technology Data Exchange (ETDEWEB)

    Cadwell, L.L. [ed.

    1995-04-01

    The purposes of the project are to monitor and report trends in wildlife populations; conduct surveys to identify, record, and map populations of threatened, endangered, and sensitive plant and animal species; and cooperate with Washington State and federal and private agencies to help ensure the protection afforded by law to native species and their habitats. Census data and results of surveys and special study topics are shared freely among cooperating agencies. Special studies are also conducted as needed to provide additional information that may be required to assess, protect, or manage wildlife resources at Hanford. This report describes highlights of wildlife studies on the Site in 1994. Redd counts of fall chinook salmon in the Hanford Reach suggest that harvest restrictions directed at protecting Snake River salmon may have helped Columbia River stocks as well. The 1994 count (5619) was nearly double that of 1993 and about 63% of the 1989 high of approximately 9000. A habitat map showing major vegetation and land use cover types for the Hanford Site was completed in 1993. During 1994, stochastic simulation was used to estimate shrub characteristics (height, density, and canopy cover) across the previously mapped Hanford landscape. The information provided will be available for use in determining habitat quality for sensitive wildlife species. Mapping Site locations of plant species of concern continued during 1994. Additional sensitive plant species data from surveys conducted by TNC were archived. The 10 nesting pairs of ferruginous hawks that used the Hanford Site in 1993 represented approximately 25% of the Washington State population.

  11. Wildlife studies on the Hanford site: 1994 Highlights report

    International Nuclear Information System (INIS)

    Cadwell, L.L.

    1995-04-01

    The purposes of the project are to monitor and report trends in wildlife populations; conduct surveys to identify, record, and map populations of threatened, endangered, and sensitive plant and animal species; and cooperate with Washington State and federal and private agencies to help ensure the protection afforded by law to native species and their habitats. Census data and results of surveys and special study topics are shared freely among cooperating agencies. Special studies are also conducted as needed to provide additional information that may be required to assess, protect, or manage wildlife resources at Hanford. This report describes highlights of wildlife studies on the Site in 1994. Redd counts of fall chinook salmon in the Hanford Reach suggest that harvest restrictions directed at protecting Snake River salmon may have helped Columbia River stocks as well. The 1994 count (5619) was nearly double that of 1993 and about 63% of the 1989 high of approximately 9000. A habitat map showing major vegetation and land use cover types for the Hanford Site was completed in 1993. During 1994, stochastic simulation was used to estimate shrub characteristics (height, density, and canopy cover) across the previously mapped Hanford landscape. The information provided will be available for use in determining habitat quality for sensitive wildlife species. Mapping Site locations of plant species of concern continued during 1994. Additional sensitive plant species data from surveys conducted by TNC were archived. The 10 nesting pairs of ferruginous hawks that used the Hanford Site in 1993 represented approximately 25% of the Washington State population

  12. Systematic Analysis of Splice-Site-Creating Mutations in Cancer

    Directory of Open Access Journals (Sweden)

    Reyka G. Jayasinghe

    2018-04-01

    Full Text Available Summary: For the past decade, cancer genomic studies have focused on mutations leading to splice-site disruption, overlooking those having splice-creating potential. Here, we applied a bioinformatic tool, MiSplice, for the large-scale discovery of splice-site-creating mutations (SCMs across 8,656 TCGA tumors. We report 1,964 originally mis-annotated mutations having clear evidence of creating alternative splice junctions. TP53 and GATA3 have 26 and 18 SCMs, respectively, and ATRX has 5 from lower-grade gliomas. Mutations in 11 genes, including PARP1, BRCA1, and BAP1, were experimentally validated for splice-site-creating function. Notably, we found that neoantigens induced by SCMs are likely several folds more immunogenic compared to missense mutations, exemplified by the recurrent GATA3 SCM. Further, high expression of PD-1 and PD-L1 was observed in tumors with SCMs, suggesting candidates for immune blockade therapy. Our work highlights the importance of integrating DNA and RNA data for understanding the functional and the clinical implications of mutations in human diseases. : Jayasinghe et al. identify nearly 2,000 splice-site-creating mutations (SCMs from over 8,000 tumor samples across 33 cancer types. They provide a more accurate interpretation of previously mis-annotated mutations, highlighting the importance of integrating data types to understand the functional and the clinical implications of splicing mutations in human disease. Keywords: splicing, RNA, mutations of clinical relevance

  13. Predicting protein amidation sites by orchestrating amino acid sequence features

    Science.gov (United States)

    Zhao, Shuqiu; Yu, Hua; Gong, Xiujun

    2017-08-01

    Amidation is the fourth major category of post-translational modifications, which plays an important role in physiological and pathological processes. Identifying amidation sites can help us understanding the amidation and recognizing the original reason of many kinds of diseases. But the traditional experimental methods for predicting amidation sites are often time-consuming and expensive. In this study, we propose a computational method for predicting amidation sites by orchestrating amino acid sequence features. Three kinds of feature extraction methods are used to build a feature vector enabling to capture not only the physicochemical properties but also position related information of the amino acids. An extremely randomized trees algorithm is applied to choose the optimal features to remove redundancy and dependence among components of the feature vector by a supervised fashion. Finally the support vector machine classifier is used to label the amidation sites. When tested on an independent data set, it shows that the proposed method performs better than all the previous ones with the prediction accuracy of 0.962 at the Matthew's correlation coefficient of 0.89 and area under curve of 0.964.

  14. Optimizing Ocean Space: Co-siting Open Ocean Aquaculture

    Science.gov (United States)

    Cobb, B. L.; Wickliffe, L. C.; Morris, J. A., Jr.

    2016-12-01

    In January of 2016, NOAA's National Marine Fisheries Service released the Gulf Aquaculture Plan (GAP) to manage the development of environmentally sound and economically sustainable open ocean finfish aquaculture in the Gulf of Mexico (inside the U.S. Exclusive Economic Zone [EEZ]). The GAP provides the first regulatory framework for aquaculture in federal waters with estimated production of 64 million pounds of finfish, and an estimated economic impact of $264 million annually. The Gulf of Mexico is one of the most industrialized ocean basins in the world, with many existing ocean uses including oil and natural gas production, shipping and commerce, commercial fishing operations, and many protected areas to ensure conservation of valuable ecosystem resources and services. NOAA utilized spatial planning procedures and tools identifying suitable sites for establishing aquaculture through exclusion analyses using authoritative federal and state data housed in a centralized geodatabase. Through a highly collaborative, multi-agency effort a mock permitting exercise was conducted to illustrate the regulatory decision-making process for the Gulf. Further decision-making occurred through exploring co-siting opportunities with oil and natural gas platforms. Logistical co-siting was conducted to reduce overall operational costs by looking at distance to major port and commodity tonnage at each port. Importantly, the process of co-siting allows aquaculture to be coupled with other benefits, including the availability of previously established infrastructure and the reduction of environmental impacts.

  15. Structural Identifiability of Dynamic Systems Biology Models.

    Science.gov (United States)

    Villaverde, Alejandro F; Barreiro, Antonio; Papachristodoulou, Antonis

    2016-10-01

    A powerful way of gaining insight into biological systems is by creating a nonlinear differential equation model, which usually contains many unknown parameters. Such a model is called structurally identifiable if it is possible to determine the values of its parameters from measurements of the model outputs. Structural identifiability is a prerequisite for parameter estimation, and should be assessed before exploiting a model. However, this analysis is seldom performed due to the high computational cost involved in the necessary symbolic calculations, which quickly becomes prohibitive as the problem size increases. In this paper we show how to analyse the structural identifiability of a very general class of nonlinear models by extending methods originally developed for studying observability. We present results about models whose identifiability had not been previously determined, report unidentifiabilities that had not been found before, and show how to modify those unidentifiable models to make them identifiable. This method helps prevent problems caused by lack of identifiability analysis, which can compromise the success of tasks such as experiment design, parameter estimation, and model-based optimization. The procedure is called STRIKE-GOLDD (STRuctural Identifiability taKen as Extended-Generalized Observability with Lie Derivatives and Decomposition), and it is implemented in a MATLAB toolbox which is available as open source software. The broad applicability of this approach facilitates the analysis of the increasingly complex models used in systems biology and other areas.

  16. Savannah River Site's Site Specific Plan

    Energy Technology Data Exchange (ETDEWEB)

    1991-08-01

    This Site Specific Plan (SSP) has been prepared by the Savannah River Site (SRS) in order to show the Environmental Restoration and Waste Management activities that were identified during the preparation of the Department of Energy-Headquarters (DOE-HQ) Environmental Restoration and Waste Management Five-Year Plan (FYP) for FY 1992--1996. The SSP has been prepared in accordance with guidance received from DOE-HQ. DOE-SR is accountable to DOE-HQ for the implementation of this plan. The purpose of the SSP is to develop a baseline for policy, budget, and schedules for the DOE Environmental Restoration and Waste Management activities. The plan explains accomplishments since the Fiscal Year (FY) 1990 plan, demonstrates how present and future activities are prioritized, identifies currently funded activities and activities that are planned to be funded in the upcoming fiscal year, and describes future activities that SRS is considering.

  17. 75 FR 20933 - Airworthiness Directives; Arrow Falcon Exporters, Inc. (previously Utah State University...

    Science.gov (United States)

    2010-04-22

    ... Hawkins and Powers Aviation, Inc.); S.M.&T. Aircraft (previously US Helicopters, Inc., UNC Helicopter, Inc... Joaquin Helicopters (previously Hawkins and Powers Aviation, Inc.); S.M.&T. Aircraft (previously US...

  18. Enhanced intensity dependence and aggression history indicate previous regular ecstasy use in abstinent polydrug users.

    Science.gov (United States)

    Wan, Li; Baldridge, Robyn M; Colby, Amanda M; Stanford, Matthew S

    2009-11-13

    Intensity dependence is an electrophysiological measure of intra-individual stability of the augmenting/reducing characteristic of N1/ P2 event-related potential amplitudes in response to stimuli of varying intensities. Abstinent ecstasy users typically show enhanced intensity dependence and higher levels of impulsivity and aggression. Enhanced intensity dependence and high impulsivity and aggression levels may be due to damage in the brain's serotonergic neurons as a result of ecstasy use. The present study investigated whether intensity dependence, impulsivity and aggression history can be used as indicators of previous chronic ecstasy usage. Forty-four abstinent polydrug users (8 women; age 19 to 61 years old) were recruited. All participants were currently residents at a local substance abuse facility receiving treatment and had been free of all drugs for a minimum of 21 days. The study found significantly enhanced intensity dependence of tangential dipole source activity and a history of more aggressive behavior in those who had previously been involved in chronic ecstasy use. Intensity dependence of the tangential dipole source and aggressive behavior history correctly identified 73.3% of those who had been regular ecstasy users and 78.3% of those who had not. Overall, 76.3% of the participants were correctly classified.

  19. Outcomes after radical prostatectomy in men receiving previous pelvic radiation for non-prostate malignancies.

    Science.gov (United States)

    Masterson, Timothy A; Wedmid, Alexei; Sandhu, Jaspreet S; Eastham, James A

    2009-08-01

    To report the perioperative and functional outcomes of nine patients treated at our institution who had radical prostatectomy (RP) after previous pelvic radiotherapy (RT) for non-prostate malignancies. From 1993 to 2007, nine patients had RP after external beam RT for testicular seminoma (six), anorectal cancer (two) and colon cancer (one). Clinical information was obtained from a prospective prostate cancer database. RP was completed with no identifiable injury to adjacent structures in all nine patients. Four patients had significant pelvic fibrosis, and three required bilateral neurovascular bundle (NVB) resection. The NVB was preserved in the remaining six patients, four with good preoperative erectile function. However, no patient recovered erectile function after RP at a median (range) follow-up of 75 (12-172) months. Of seven men continent before RP, four required one or fewer pads daily and three were completely dry, achieving complete urinary control at a median (range) time of 7.5 (2-20) months. Two patients developed an anastomotic stricture, one being associated with concomitant ureteric stricture. RP after pelvic RT for non-prostate malignancies was not associated with increased intraoperative morbidity. However, rates of anastomotic stricture, erectile dysfunction and urinary incontinence appeared to be higher than those reported after RP in men with no previous RT, and comparable with those seen in the salvage RP setting.

  20. Prevention of type 2 diabetes mellitus in women with previous gestational diabetes mellitus

    Science.gov (United States)

    Moon, Joon Ho; Kwak, Soo Heon; Jang, Hak C.

    2017-01-01

    Gestational diabetes mellitus (GDM), defined as any degree of glucose intolerance with onset or first recognition during pregnancy, is characterized by underlying maternal defects in the β-cell response to insulin during pregnancy. Women with a previous history of GDM have a greater than 7-fold higher risk of developing postpartum diabetes compared with women without GDM. Various risk factors for postpartum diabetes have been identified, including maternal age, glucose levels in pregnancy, family history of diabetes, pre-pregnancy and postpartum body mass index, dietary patterns, physical activity, and breastfeeding. Genetic studies revealed that GDM shares common genetic variants with type 2 diabetes. A number of lifestyle interventional trials that aimed to ameliorate modifiable risk factors, including diet, exercise, and breastfeeding, succeeded in reducing the incidence of postpartum diabetes, weight retention, and other obesity-related morbidities. The present review summarizes the findings of previous studies on the incidence and risk factors of postpartum diabetes and discusses recent lifestyle interventional trials that attempted to prevent postpartum diabetes. PMID:28049284