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.

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.

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.

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…

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.

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 ...

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.

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.

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)

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...

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.

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.

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

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

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

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

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

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.

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

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.

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

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.

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.

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.

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

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.

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.

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

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

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

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

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.

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...

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

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

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)

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.

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

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.

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.

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.

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.

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

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....

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.

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™.

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

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.

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.

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...

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

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

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.

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

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

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.

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...

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.)

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.

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.

Nonradiological groundwater quality at low-level radioactive waste disposal sites

International Nuclear Information System (INIS)

Goode, D.J.

1986-04-01

The NRC is investigating appropriate regulatory options for disposal of low-level radioactive waste containing nonradiological hazardous constituents, as defined by EPA regulations. Standard EPA/RCRA procedures to determine hazardous organics, metals, indicator parameters, and general water quality are applied to samples from groundwater monitoring wells at two commercial low-level radioactive waste disposal sites. At the Sheffield, IL site (nonoperating), several typical organic solvents are identified in elevated concentrations in onsite wells and in an offsite area exhibiting elevated tritium concentrations. At the Barnwell, SC site (operating), only very low concentrations of three organics are found in wells adjacent to disposal units. Hydrocarbons associated with petroleum products are detected at both sites. Hazardous constituents associated with previosuly identified major LLW mixed waste streams, toluene, xylene, chromium, and lead, are at or below detection limits or at background levels in all samples. Review of previously collected data also supports the conclusion that organic solvents are the primary nonradiological contaminants associated with LLW disposal

Quantitative chemoproteomics for site-specific analysis of protein alkylation by 4-hydroxy-2-nonenal in cells.

Science.gov (United States)

Yang, Jing; Tallman, Keri A; Porter, Ned A; Liebler, Daniel C

2015-03-03

Protein alkylation by 4-hydroxy-2-nonenal (HNE), an endogenous lipid derived electrophile, contributes to stress signaling and cellular toxicity. Although previous work has identified protein targets for HNE alkylation, the sequence specificity of alkylation and dynamics in a cellular context remain largely unexplored. We developed a new quantitative chemoproteomic platform, which uses isotopically tagged, photocleavable azido-biotin reagents to selectively capture and quantify the cellular targets labeled by the alkynyl analogue of HNE (aHNE). Our analyses site-specifically identified and quantified 398 aHNE protein alkylation events (386 cysteine sites and 12 histidine sites) in intact cells. This data set expands by at least an order of magnitude the number of such modification sites previously reported. Although adducts formed by Michael addition are thought to be largely irreversible, we found that most aHNE modifications are lost rapidly in situ. Moreover, aHNE adduct turnover occurs only in intact cells and loss rates are site-selective. This quantitative chemoproteomics platform provides a versatile general approach to map bioorthogonal-chemically engineered post-translational modifications and their cellular dynamics in a site-specific and unbiased manner.

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 .

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.

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.

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

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.

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

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.

Siting Study for the Remote-Handled Low-Level Waste Disposal Project

Energy Technology Data Exchange (ETDEWEB)

Lisa Harvego; Joan Connolly; Lance Peterson; Brennon Orr; Bob Starr

2010-10-01

The U.S. Department of Energy has identified a mission need for continued disposal capacity for remote-handled low-level waste (LLW) generated at the Idaho National Laboratory (INL). An alternatives analysis that was conducted to evaluate strategies to achieve this mission need identified two broad options for disposal of INL generated remote-handled LLW: (1) offsite disposal and (2) onsite disposal. The purpose of this study is to identify candidate sites or locations within INL boundaries for the alternative of an onsite remote handled LLW disposal facility and recommend the highest-ranked locations for consideration in the National Environmental Policy Act process. The study implements an evaluation based on consideration of five key elements: (1) regulations, (2) key assumptions, (3) conceptual design, (4) facility performance, and (5) previous INL siting study criteria, and uses a five-step process to identify, screen, evaluate, score, and rank 34 separate sites located across INL. The result of the evaluation is identification of two recommended alternative locations for siting an onsite remote-handled LLW disposal facility. The two alternative locations that best meet the evaluation criteria are (1) near the Advanced Test Reactor Complex and (2) west of the Idaho Comprehensive Environmental Response, Compensation, and Liability Act Disposal Facility.

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...

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.

Reactive Oxygen Species (ROS)-Activated ATM-Dependent Phosphorylation of Cytoplasmic Substrates Identified by Large-Scale Phosphoproteomics Screen*

Science.gov (United States)

Kozlov, Sergei V.; Waardenberg, Ashley J.; Engholm-Keller, Kasper; Arthur, Jonathan W.; Graham, Mark E.; Lavin, Martin

2016-01-01

Ataxia-telangiectasia, mutated (ATM) protein plays a central role in phosphorylating a network of proteins in response to DNA damage. These proteins function in signaling pathways designed to maintain the stability of the genome and minimize the risk of disease by controlling cell cycle checkpoints, initiating DNA repair, and regulating gene expression. ATM kinase can be activated by a variety of stimuli, including oxidative stress. Here, we confirmed activation of cytoplasmic ATM by autophosphorylation at multiple sites. Then we employed a global quantitative phosphoproteomics approach to identify cytoplasmic proteins altered in their phosphorylation state in control and ataxia-telangiectasia (A-T) cells in response to oxidative damage. We demonstrated that ATM was activated by oxidative damage in the cytoplasm as well as in the nucleus and identified a total of 9,833 phosphorylation sites, including 6,686 high-confidence sites mapping to 2,536 unique proteins. A total of 62 differentially phosphorylated peptides were identified; of these, 43 were phosphorylated in control but not in A-T cells, and 19 varied in their level of phosphorylation. Motif enrichment analysis of phosphopeptides revealed that consensus ATM serine glutamine sites were overrepresented. When considering phosphorylation events, only observed in control cells (not observed in A-T cells), with predicted ATM sites phosphoSerine/phosphoThreonine glutamine, we narrowed this list to 11 candidate ATM-dependent cytoplasmic proteins. Two of these 11 were previously described as ATM substrates (HMGA1 and UIMCI/RAP80), another five were identified in a whole cell extract phosphoproteomic screens, and the remaining four proteins had not been identified previously in DNA damage response screens. We validated the phosphorylation of three of these proteins (oxidative stress responsive 1 (OSR1), HDGF, and ccdc82) as ATM dependent after H2O2 exposure, and another protein (S100A11) demonstrated ATM

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.

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.

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.

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)".

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

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

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.

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

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

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

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.

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

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

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.

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.

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

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

Directory of Open Access Journals (Sweden)

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.

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

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.

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

Wetland survey of selected areas in the K-24 Site Area of responsibility

Energy Technology Data Exchange (ETDEWEB)

Rosensteel, B.A.; Awl, D.J. [JAYCOR, Environmental Division, Oak Ridge, TN (United States)

1995-07-01

In accordance with DOE Regulations for Compliance with Floodplain/Wetlands Environmental Review Requirements, wetland surveys were conducted in selected areas within the K-25 Area of Responsibility during the summer of 1994. These areas are Mitchell Branch, Poplar Creek, the K-770 OU, Duct Island Peninsula, the Powerhouse area, and the K-25 South Corner. Previously surveyed areas included in this report are the main plant area of the K-25 Site, the K-901 OU, the AVLIS site, and the K-25 South Site. Wetland determinations were based on the USACE methodology. Forty-four separate wetland areas, ranging in size from 0.13 to 4.23 ha, were identified. Wetlands were identified in all of the areas surveyed with the exception of the interior of the Duct Island Peninsula and the main plant area of the K-25 Site. Wetlands perform functions such as floodflow alteration, sediment stabilization, sediment and toxicant retention, nutrient transformation, production export, and support of aquatic species and wildlife diversity and abundance. The forested, scrub-shrub, and emergent wetlands identified in the K-25 area perform some or all of these functions to varying degrees.

Wetland survey of selected areas in the K-24 Site Area of responsibility

International Nuclear Information System (INIS)

Rosensteel, B.A.; Awl, D.J.

1995-07-01

In accordance with DOE Regulations for Compliance with Floodplain/Wetlands Environmental Review Requirements, wetland surveys were conducted in selected areas within the K-25 Area of Responsibility during the summer of 1994. These areas are Mitchell Branch, Poplar Creek, the K-770 OU, Duct Island Peninsula, the Powerhouse area, and the K-25 South Corner. Previously surveyed areas included in this report are the main plant area of the K-25 Site, the K-901 OU, the AVLIS site, and the K-25 South Site. Wetland determinations were based on the USACE methodology. Forty-four separate wetland areas, ranging in size from 0.13 to 4.23 ha, were identified. Wetlands were identified in all of the areas surveyed with the exception of the interior of the Duct Island Peninsula and the main plant area of the K-25 Site. Wetlands perform functions such as floodflow alteration, sediment stabilization, sediment and toxicant retention, nutrient transformation, production export, and support of aquatic species and wildlife diversity and abundance. The forested, scrub-shrub, and emergent wetlands identified in the K-25 area perform some or all of these functions to varying degrees

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

Regulatory elements of the floral homeotic gene AGAMOUS identified by phylogenetic footprinting and shadowing.

Energy Technology Data Exchange (ETDEWEB)

Hong, R. L., Hamaguchi, L., Busch, M. A., and Weigel, D.

2003-06-01

OAK-B135 In Arabidopsis thaliana, cis-regulatory sequences of the floral homeotic gene AGAMOUS (AG) are located in the second intron. This 3 kb intron contains binding sites for two direct activators of AG, LEAFY (LFY) and WUSCHEL (WUS), along with other putative regulatory elements. We have used phylogenetic footprinting and the related technique of phylogenetic shadowing to identify putative cis-regulatory elements in this intron. Among 29 Brassicaceae, several other motifs, but not the LFY and WUS binding sites previously identified, are largely invariant. Using reporter gene analyses, we tested six of these motifs and found that they are all functionally important for activity of AG regulatory sequences in A. thaliana. Although there is little obvious sequence similarity outside the Brassicaceae, the intron from cucumber AG has at least partial activity in A. thaliana. Our studies underscore the value of the comparative approach as a tool that complements gene-by-gene promoter dissection, but also highlight that sequence-based studies alone are insufficient for a complete identification of cis-regulatory sites.

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.

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...

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.

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.

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...

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

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.

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/.

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.

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.

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.

Conversion of agonist site to metal-ion chelator site in the beta(2)-adrenergic receptor

DEFF Research Database (Denmark)

Elling, C E; Thirstrup, K; Holst, Birgitte

1999-01-01

Previously metal-ion sites have been used as structural and functional probes in seven transmembrane receptors (7TM), but as yet all the engineered sites have been inactivating. Based on presumed agonist interaction points in transmembrane III (TM-III) and -VII of the beta(2)-adrenergic receptor,...... as generic, pharmacologic tools to switch 7TM receptors with engineered metal-ion sites on or off at will.......Previously metal-ion sites have been used as structural and functional probes in seven transmembrane receptors (7TM), but as yet all the engineered sites have been inactivating. Based on presumed agonist interaction points in transmembrane III (TM-III) and -VII of the beta(2)-adrenergic receptor......, in this paper we construct an activating metal-ion site between the amine-binding Asp-113 in TM-III-or a His residue introduced at this position-and a Cys residue substituted for Asn-312 in TM-VII. No increase in constitutive activity was observed in the mutant receptors. Signal transduction was activated...

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...

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  

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

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

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)

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.

Transcriptional activation of transforming growth factor alpha by estradiol: requirement for both a GC-rich site and an estrogen response element half-site.

Science.gov (United States)

Vyhlidal, C; Samudio, I; Kladde, M P; Safe, S

2000-06-01

17beta-Estradiol (E2) induces transforming growth factor alpha (TGFalpha) gene expression in MCF-7 cells and previous studies have identified a 53 bp (-252 to -200) sequence containing two imperfect estrogen responsive elements (EREs) that contribute to E2 responsiveness. Deletion analysis of the TGFalpha gene promoter in this study identified a second upstream region of the promoter (-623 to -549) that is also E2 responsive. This sequence contains three GC-rich sites and an imperfect ERE half-site, and the specific cis-elements and trans-acting factors were determined by promoter analysis in transient transfection experiments, gel mobility shift assays and in vitro DNA footprinting. The results are consistent with an estrogen receptor alpha (ERalpha)/Sp1 complex interacting with an Sp1(N)(30) ERE half-site ((1/2)) motif in which both ERalpha and Sp1 bind promoter DNA. The ER/Sp1-DNA complex is formed using nuclear extracts from MCF-7 cells but not with recombinant human ERalpha or Sp1 proteins, suggesting that other nuclear factor(s) are required for complex stabilization. The E2-responsive Sp1(N)(x)ERE(1/2) motif identified in the TGFalpha gene promoter has also been characterized in the cathepsin D and heat shock protein 27 gene promoters; however, in the latter two promoters the numbers of intervening nucleotides are 23 and 10 respectively.

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.

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.

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

Extreme heterogeneity of polyadenylation sites in mRNAs encoding chloroplast RNA-binding proteins in Nicotiana plumbaginifolia.

Science.gov (United States)

Klahre, U; Hemmings-Mieszczak, M; Filipowicz, W

1995-06-01

We have previously characterized nuclear cDNA clones encoding two RNA binding proteins, CP-RBP30 and CP-RBP-31, which are targeted to chloroplasts in Nicotiana plumbaginifolia. In this report we describe the analysis of the 3'-untranslated regions (3'-UTRs) in 22 CP-RBP30 and 8 CP-RBP31 clones which reveals that mRNAs encoding both proteins have a very complex polyadenylation pattern. Fourteen distinct poly(A) sites were identified among CP-RBP30 clones and four sites among the CP-RBP31 clones. The authenticity of the sites was confirmed by RNase A/T1 mapping of N. plumbaginifolia RNA. CP-RBP30 provides an extreme example of the heterogeneity known to be a feature of mRNA polyadenylation in higher plants. Using PCR we have demonstrated that CP-RBP genes in N. plumbaginifolia and N. sylvestris, in addition to the previously described introns interrupting the coding region, contain an intron located in the 3' non-coding part of the gene. In the case of the CP-RBP31, we have identified one polyadenylation event occurring in this intron.

TAPDANCE: An automated tool to identify and annotate transposon insertion CISs and associations between CISs from next generation sequence data

Directory of Open Access Journals (Sweden)

Sarver Aaron L

2012-06-01

Full Text Available Abstract Background Next generation sequencing approaches applied to the analyses of transposon insertion junction fragments generated in high throughput forward genetic screens has created the need for clear informatics and statistical approaches to deal with the massive amount of data currently being generated. Previous approaches utilized to 1 map junction fragments within the genome and 2 identify Common Insertion Sites (CISs within the genome are not practical due to the volume of data generated by current sequencing technologies. Previous approaches applied to this problem also required significant manual annotation. Results We describe Transposon Annotation Poisson Distribution Association Network Connectivity Environment (TAPDANCE software, which automates the identification of CISs within transposon junction fragment insertion data. Starting with barcoded sequence data, the software identifies and trims sequences and maps putative genomic sequence to a reference genome using the bowtie short read mapper. Poisson distribution statistics are then applied to assess and rank genomic regions showing significant enrichment for transposon insertion. Novel methods of counting insertions are used to ensure that the results presented have the expected characteristics of informative CISs. A persistent mySQL database is generated and utilized to keep track of sequences, mappings and common insertion sites. Additionally, associations between phenotypes and CISs are also identified using Fisher’s exact test with multiple testing correction. In a case study using previously published data we show that the TAPDANCE software identifies CISs as previously described, prioritizes them based on p-value, allows holistic visualization of the data within genome browser software and identifies relationships present in the structure of the data. Conclusions The TAPDANCE process is fully automated, performs similarly to previous labor intensive approaches

Diversity of reductive dehalogenase genes from environmental samples and enrichment cultures identified with degenerate primer PCR screens.

Directory of Open Access Journals (Sweden)

Laura Audrey Hug

2013-11-01

Full Text Available Reductive dehalogenases are the critical enzymes for anaerobic organohalide respiration, a microbial metabolic process that has been harnessed for bioremediation efforts to resolve chlorinated solvent contamination in groundwater and is implicated in the global halogen cycle. Reductive dehalogenase sequence diversity is informative for the dechlorination potential of the site or enrichment culture. A suite of degenerate PCR primers targeting a comprehensive curated set of reductive dehalogenase genes was designed and applied to twelve DNA samples extracted from contaminated and pristine sites, as well as six enrichment cultures capable of reducing chlorinated compounds to non-toxic end-products. The amplified gene products from four environmental sites and two enrichment cultures were sequenced using Illumina HiSeq, and the reductive dehalogenase complement of each sample determined. The results indicate that the diversity of the reductive dehalogenase gene family is much deeper than is currently accounted for: one-third of the translated proteins have less than 70% pairwise amino acid identity to database sequences. Approximately 60% of the sequenced reductive dehalogenase genes were broadly distributed, being identified in four or more samples, and often in previously sequenced genomes as well. In contrast, 17% of the sequenced reductive dehalogenases were unique, present in only a single sample and bearing less than 90% pairwise amino acid identity to any previously identified proteins. Many of the broadly distributed reductive dehalogenases are uncharacterized in terms of their substrate specificity, making these intriguing targets for further biochemical experimentation. Finally, comparison of samples from a contaminated site and an enrichment culture derived from the same site eight years prior allowed examination of the effect of the enrichment process.

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.

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

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

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

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.

A trans-ethnic genome-wide association study identifies gender-specific loci influencing pediatric aBMD and BMC at the distal radius.

Science.gov (United States)

Chesi, Alessandra; Mitchell, Jonathan A; Kalkwarf, Heidi J; Bradfield, Jonathan P; Lappe, Joan M; McCormack, Shana E; Gilsanz, Vicente; Oberfield, Sharon E; Hakonarson, Hakon; Shepherd, John A; Kelly, Andrea; Zemel, Babette S; Grant, Struan F A

2015-09-01

Childhood fractures are common, with the forearm being the most common site. Genome-wide association studies (GWAS) have identified more than 60 loci associated with bone mineral density (BMD) in adults but less is known about genetic influences specific to bone in childhood. To identify novel genetic factors that influence pediatric bone strength at a common site for childhood fractures, we performed a sex-stratified trans-ethnic genome-wide association study of areal BMD (aBMD) and bone mineral content (BMC) Z-scores measured by dual energy X-ray absorptiometry at the one-third distal radius, in a cohort of 1399 children without clinical abnormalities in bone health. We tested signals with P BMC-Z). Signals at the CPED1-WNT16-FAM3C locus have been previously associated with BMD at other skeletal sites in adults and children. Our result at the distal radius underscores the importance of this locus at multiple skeletal sites. The 9p21.3 locus is within a gene desert, with the nearest gene flanking each side being MIR31HG and MTAP, neither of which has been implicated in BMD or BMC previously. These findings suggest that genetic determinants of childhood bone accretion at the radius, a skeletal site that is primarily cortical bone, exist and also differ by sex. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

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

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

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.

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.

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

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.

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.

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)

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.

Mine tailings composition in a historic site: implications for ecological restoration.

Science.gov (United States)

Courtney, R

2013-02-01

Ecological restoration, using tolerant plant species and nutrient additions, is a low-cost option to decrease environmental risks associated with mine tailings. An attempt was previously made to establish such a vegetation cover on an abandoned tailings facility in Southern Ireland. Historically, the tailings site has been prone to dusting and is a potential source of contamination to the surrounding environment. The site was examined to determine the success of the previous restoration plan used to revegetate the site and to determine its suitability for further restoration. Three distinct floristic areas were identified (grassland, poor grassland and bare area) based on herbage compositions and elemental analysis. Surface and subsurface samples were taken to characterise tailings from within these areas of the tailings site. The pH of bare surface tailings (pH, 2.7) was significantly more acidic (p tailings being hostile to plant growth. Total metal concentrations in tailings were high (c. 10,000 mg kg(-1) for Pb and up to 20,000 mg kg(-1) for Zn). DTPA-extractable Zn and Pb were 16 and 11 % of the total amount, respectively. Metal content in grasses growing on some areas of the tailings were elevated and demonstrated the inability of the tailings to support sustainable plant growth. Due to the inherently hostile characteristics of these areas, future restoration work will employ capping with a barrier layer.

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.

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

Identifying three-dimensional structures of autophosphorylation complexes in crystals of protein kinases

Science.gov (United States)

Xu, Qifang; Malecka, Kimberly L.; Fink, Lauren; Jordan, E. Joseph; Duffy, Erin; Kolander, Samuel; Peterson, Jeffrey; Dunbrack, Roland L.

2016-01-01

Protein kinase autophosphorylation is a common regulatory mechanism in cell signaling pathways. Crystal structures of several homomeric protein kinase complexes have a serine, threonine, or tyrosine autophosphorylation site of one kinase monomer located in the active site of another monomer, a structural complex that we call an “autophosphorylation complex.” We developed and applied a structural bioinformatics method to identify all such autophosphorylation kinase complexes in X-ray crystallographic structures in the Protein Data Bank (PDB). We identified 15 autophosphorylation complexes in the PDB, of which 5 complexes had not previously been described in the publications describing the crystal structures. These 5 consist of tyrosine residues in the N-terminal juxtamembrane regions of colony stimulating factor 1 receptor (CSF1R, Tyr561) and EPH receptor A2 (EPHA2, Tyr594), tyrosine residues in the activation loops of the SRC kinase family member LCK (Tyr394) and insulin-like growth factor 1 receptor (IGF1R, Tyr1166), and a serine in a nuclear localization signal region of CDC-like kinase 2 (CLK2, Ser142). Mutations in the complex interface may alter autophosphorylation activity and contribute to disease; therefore we mutated residues in the autophosphorylation complex interface of LCK and found that two mutations impaired autophosphorylation (T445V and N446A) and mutation of Pro447 to Ala, Gly, or Leu increased autophosphorylation. The identified autophosphorylation sites are conserved in many kinases, suggesting that, by homology, these complexes may provide insight into autophosphorylation complex interfaces of kinases that are relevant drug targets. PMID:26628682

SITE-2, Power Plant Siting, Cost, Environment, Seismic and Meteorological Effects

International Nuclear Information System (INIS)

Frigerio, N.A.; Habegger, L.J.; King, R.F.; Hoover, L.J.; Clark, N.A.; Cobian, J.M.

1977-01-01

1 - Description of problem or function: SITE2 is designed to (1) screen candidate energy facility sites or areas within an electric utility region, based on the region's physical and socioeconomic attributes, the planned facility's characteristics, and impact assessments, and (2) evaluate the cumulative regional impacts associated with alternate energy supply options and inter-regional energy import/export practices, specifically, comparison of different energy technologies and their regional distribution in clustered or dispersed patterns. 2 - Method of solution: The SITE2 methodology is based on the quantification of three major site-related vectors. A cost vector is determined which identifies site-specific costs, such as transmission costs, cooling costs as related to water availability, and costs of specific controls needed to protect the surrounding environment. An impact vector is also computed for each potential site, using models of health and environmental impacts incurred in areas adjacent to the site. Finally, a site attribute vector is developed which reflects such characteristics as population, seismic conditions, meteorology, land use, and local ecological systems. This vector can be used to eliminate certain sites because of their inability to satisfy specific constraints. These three vectors can be displayed as density maps and combined in a simple overlay approach, similar to that developed by I. L. McHarg in reference 2, to identify candidate sites. Alternatively, the vector elements can be computationally combined into a weighted sum to obtain quantitative indicators of site suitability

SITE-2, Power Plant Siting, Cost, Environment, Seismic and Meteorological Effects

Energy Technology Data Exchange (ETDEWEB)

Frigerio, N A [Environmental Impact Studies, Argonne National Laboratory 9700 South Cass Avenue, Argonne, Illinois 60439 (United States); Habegger, L J; King, R F; Hoover, L J [Energy and Environmental Systems Division, Argonne National Laboratory 9700 South Cass Avenue, Argonne, Illinois 60439 (United States); Clark, N A [Applied Mathematics Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439 (United States); Cobian, J M [Northwestern University, Evanston, Illinois 60201 (United States)

1977-08-01

1 - Description of problem or function: SITE2 is designed to (1) screen candidate energy facility sites or areas within an electric utility region, based on the region's physical and socioeconomic attributes, the planned facility's characteristics, and impact assessments, and (2) evaluate the cumulative regional impacts associated with alternate energy supply options and inter-regional energy import/export practices, specifically, comparison of different energy technologies and their regional distribution in clustered or dispersed patterns. 2 - Method of solution: The SITE2 methodology is based on the quantification of three major site-related vectors. A cost vector is determined which identifies site-specific costs, such as transmission costs, cooling costs as related to water availability, and costs of specific controls needed to protect the surrounding environment. An impact vector is also computed for each potential site, using models of health and environmental impacts incurred in areas adjacent to the site. Finally, a site attribute vector is developed which reflects such characteristics as population, seismic conditions, meteorology, land use, and local ecological systems. This vector can be used to eliminate certain sites because of their inability to satisfy specific constraints. These three vectors can be displayed as density maps and combined in a simple overlay approach, similar to that developed by I. L. McHarg in reference 2, to identify candidate sites. Alternatively, the vector elements can be computationally combined into a weighted sum to obtain quantitative indicators of site suitability.

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 ...

ASSESSING AEROBIC NATURAL ATTENUATION OF TRICHLOROETHENE AT FOUR DOE SITES

International Nuclear Information System (INIS)

Koelsch, Michael C.; Starr, Robert C.; Sorenson, Kent S. Jr.

2005-01-01

A 3-year Department of Energy Environmental Science Management Program (EMSP) project is currently investigating natural attenuation of trichloroethane (TCE) in aerobic groundwater. This presentation summarizes the results of a screening process to identify TCE plumes at DOE facilities that are suitable for assessing the rate of TCE cometabolism under aerobic conditions. In order to estimate aerobic degradation rates, plumes had to meet the following criteria: TCE must be present in aerobic groundwater, a conservative co-contaminant must be present and have approximately the same source as TCE, and the groundwater velocity must be known. A total of 127 TCE plumes were considered across 24 DOE sites. The four sites retained for the assessment were: (1) Brookhaven National Laboratory, OU III; (2) Paducah Gaseous Diffusion Plant, Northwest Plume; (3) Rocky Flats Environmental Technology Site, Industrialized Area--Southwest Plume and 903 Pad South Plume; and (4) Savannah River Site, A/M Area Plume. For each of these sites, a co-contaminant derived from the same source area as TCE was used as a nonbiodegrading tracer. The tracer determined the extent to which concentration decreases in the plume can be accounted for solely by abiotic processes such as dispersion and dilution. Any concentration decreases not accounted for by these processes must be explained by some other natural attenuation mechanism. Thus, ''half-lives'' presented herein are in addition to attenuation that occurs due to hydrologic mechanisms. This ''tracer-corrected method'' has previously been used at the DOE's Idaho National Engineering and Environmental Laboratory in conjunction with other techniques to document the occurrence of intrinsic aerobic cometabolism. Application of this method to other DOE sites is the first step to determining whether this might be a significant natural attenuation mechanism on a broader scale. Application of the tracer-corrected method to data from the Brookhaven

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

Intrasteric control of AMPK via the gamma1 subunit AMP allosteric regulatory site.

Science.gov (United States)

Adams, Julian; Chen, Zhi-Ping; Van Denderen, Bryce J W; Morton, Craig J; Parker, Michael W; Witters, Lee A; Stapleton, David; Kemp, Bruce E

2004-01-01

AMP-activated protein kinase (AMPK) is a alphabetagamma heterotrimer that is activated in response to both hormones and intracellular metabolic stress signals. AMPK is regulated by phosphorylation on the alpha subunit and by AMP allosteric control previously thought to be mediated by both alpha and gamma subunits. Here we present evidence that adjacent gamma subunit pairs of CBS repeat sequences (after Cystathionine Beta Synthase) form an AMP binding site related to, but distinct from the classical AMP binding site in phosphorylase, that can also bind ATP. The AMP binding site of the gamma(1) CBS1/CBS2 pair, modeled on the structures of the CBS sequences present in the inosine monophosphate dehydrogenase crystal structure, contains three arginine residues 70, 152, and 171 and His151. The yeast gamma homolog, snf4 contains a His151Gly substitution, and when this is introduced into gamma(1), AMP allosteric control is substantially lost and explains why the yeast snf1p/snf4p complex is insensitive to AMP. Arg70 in gamma(1) corresponds to the site of mutation in human gamma(2) and pig gamma(3) genes previously identified to cause an unusual cardiac phenotype and glycogen storage disease, respectively. Mutation of any of AMP binding site Arg residues to Gln substantially abolishes AMP allosteric control in expressed AMPK holoenzyme. The Arg/Gln mutations also suppress the previously described inhibitory properties of ATP and render the enzyme constitutively active. We propose that ATP acts as an intrasteric inhibitor by bridging the alpha and gamma subunits and that AMP functions to derepress AMPK activity.

An Iterative Approach to Ground Penetrating Radar at the Maya Site of Pacbitun, Belize

Directory of Open Access Journals (Sweden)

Sheldon Skaggs

2016-09-01

Full Text Available Ground penetrating radar (GPR surveys provide distinct advantages for archaeological prospection in ancient, complex, urban Maya sites, particularly where dense foliage or modern debris may preclude other remote sensing or geophysical techniques. Unidirectional GPR surveys using a 500 MHz shielded antenna were performed at the Middle Preclassic Maya site of Pacbitun, Belize. The survey in 2012 identified numerous linear and circular anomalies between 1 m and 2 m deep. Based on these anomalies, one 1 m × 4 m unit and three smaller units were excavated in 2013. These test units revealed a curved plaster surface not previously found at Pacbitun. Post-excavation, GPR data were reprocessed to best match the true nature of excavated features. Additional GPR surveys oriented perpendicular to the original survey confirmed previously detected anomalies and identified new anomalies. The excavations provided information on the sediment layers in the survey area, which allowed better identification of weak radar reflections of the surfaces of a burnt, Middle Preclassic temple in the northern end of the survey area. Additional excavations of the area in 2014 and 2015 revealed it to be a large square structure, which was named El Quemado.

Mutations that silence constitutive signaling activity in the allosteric ligand-binding site of the thyrotropin receptor.

Science.gov (United States)

Haas, Ann-Karin; Kleinau, Gunnar; Hoyer, Inna; Neumann, Susanne; Furkert, Jens; Rutz, Claudia; Schülein, Ralf; Gershengorn, Marvin C; Krause, Gerd

2011-01-01

The thyrotropin receptor (TSHR) exhibits elevated cAMP signaling in the basal state and becomes fully activated by thyrotropin. Previously we presented evidence that small-molecule ligands act allosterically within the transmembrane region in contrast to the orthosteric extracellular hormone-binding sites. Our goal in this study was to identify positions that surround the allosteric pocket and that are sensitive for inactivation of TSHR. Homology modeling combined with site-directed mutagenesis and functional characterization revealed seven mutants located in the allosteric binding site that led to a decrease of basal cAMP signaling activity. The majority of these silencing mutations, which constrain the TSHR in an inactive conformation, are found in two clusters when mapped onto the 3D structural model. We suggest that the amino acid positions identified herein are indicating locations where small-molecule antagonists, both neutral antagonists and inverse agonists, might interfere with active TSHR conformations.

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%.

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.

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

VISPA2: a scalable pipeline for high-throughput identification and annotation of vector integration sites.

Science.gov (United States)

Spinozzi, Giulio; Calabria, Andrea; Brasca, Stefano; Beretta, Stefano; Merelli, Ivan; Milanesi, Luciano; Montini, Eugenio

2017-11-25

Bioinformatics tools designed to identify lentiviral or retroviral vector insertion sites in the genome of host cells are used to address the safety and long-term efficacy of hematopoietic stem cell gene therapy applications and to study the clonal dynamics of hematopoietic reconstitution. The increasing number of gene therapy clinical trials combined with the increasing amount of Next Generation Sequencing data, aimed at identifying integration sites, require both highly accurate and efficient computational software able to correctly process "big data" in a reasonable computational time. Here we present VISPA2 (Vector Integration Site Parallel Analysis, version 2), the latest optimized computational pipeline for integration site identification and analysis with the following features: (1) the sequence analysis for the integration site processing is fully compliant with paired-end reads and includes a sequence quality filter before and after the alignment on the target genome; (2) an heuristic algorithm to reduce false positive integration sites at nucleotide level to reduce the impact of Polymerase Chain Reaction or trimming/alignment artifacts; (3) a classification and annotation module for integration sites; (4) a user friendly web interface as researcher front-end to perform integration site analyses without computational skills; (5) the time speedup of all steps through parallelization (Hadoop free). We tested VISPA2 performances using simulated and real datasets of lentiviral vector integration sites, previously obtained from patients enrolled in a hematopoietic stem cell gene therapy clinical trial and compared the results with other preexisting tools for integration site analysis. On the computational side, VISPA2 showed a > 6-fold speedup and improved precision and recall metrics (1 and 0.97 respectively) compared to previously developed computational pipelines. These performances indicate that VISPA2 is a fast, reliable and user-friendly tool for

Remaining Sites Verification Package for the 600-233 Waste Site, Vertical Pipe Near 100-B Electrical Laydown Area. Attachment to Waste Site Reclassification Form 2005-041

International Nuclear Information System (INIS)

Carlson, R.A.

2005-01-01

The 600-233 waste site consisted of three small-diameter pipelines within the 600-232 waste site, including previously unknown diesel fuel supply lines discovered during site remediation. The 600-233 waste site has been remediated to achieve the remedial action objectives specified in the Remaining Sites ROD. The results of verification sampling show that residual contaminant concentrations do not preclude any future uses and allow for unrestricted use of shallow zone soils. The results also demonstrate that residual contaminant concentrations are protective of groundwater and the Columbia River

The disposal of Canada's nuclear fuel waste: site screening and site evaluation technology

International Nuclear Information System (INIS)

Davison, C.C.; Brown, A.; Everitt, R.A.; Gascoyne, M.; Kozak, E.T.; Lodha, G.S.; Martin, C.D.; Soonawala, N.M.; Stevenson, D.R.; Thorne, G.A.; Whitaker, S.H.

1994-06-01

The concept for the disposal of Canada's nuclear fuel waste is to dispose of the waste in an underground vault, nominally at 500 m to 1000 m depth, at a suitable site in plutonic rock of the Canadian Shield. The feasibility of this concept and assessments of its impact on the environment and human health, will be documented by AECL in an Environmental Impact Statement (EIS). This report is one of nine primary references for the EIS. It describes the approach and methods that would be used during the siting stage of the disposal project to identify a preferred candidate disposal site and to confirm its suitability for constructing a disposal facility. The siting stage is divided into two distinct but closely related substages, site screening and site evaluation. Site screening would mainly involve reconnaissance investigations of siting regions of the Shield to identify potential candidate areas where suitable vault locations are likely to exist. Site screening would identify a small number of candidate areas where further detailed investigations were warranted. Site evaluation would involve progressively more detailed surface and subsurface investigations of the candidate areas to first identify potentially suitable vault locations within the candidate areas, and then characterize these potential disposal sites to identify the preferred candidate location for constructing the disposal vault. Site evaluation would conclude with the construction of exploratory shafts and tunnels at the preferred vault location, and underground characterization would be done to confirm the suitability of the preferred candidate site. An integrated program of geological, geophysical, hydrogeological, geochemical and geomechanical investigations would be implemented to obtain the geoscience information needed to assess the suitability of the candidate siting areas and candidate sites for locating a disposal vault. The candidate siting areas and candidate disposal vault sites would be

Selection criteria for a radioactive waste disposal site in the Republic of South Africa

International Nuclear Information System (INIS)

Toens, P.D.; Hambleton-Jones, B.B.

1986-01-01

A program commenced in 1978 to select a suitable site for the disposal of nuclear waste in South Africa. This entailed the examination of a variety of socio-economic and earthscience related parameters over large parts of South Africa. The site selection program, for which the Geology Department of the Atomic Energy Corporation of South Africa Ltd (AEC) (previously the Nuclear Development Corporation (NUCOR)) accepted responsibility, commenced with an initial screening phase and led to the identification of potentially suitable areas by mid 1980. A site suitability phase involving regional, and subsequently detailed socio-economic, geological, geohydrological and geophysical studies in the areas identified by the screening phase was completed in December 1982. As a result of very positive indications that the district of Namaqualand was the most suitable candidate area it was possible, after further detailed investigations, to identify and purchase a site judged to be suitable for the disposal of low- and intermediate-level waste by February 1983. The area acquired measures some 10 000ha in extent and is situated 100km southeast of Springbok in the northwestern Cape and 600km north of the Koeberg nuclear power station near Cape Town

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

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 ...

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

High-resolution detection of DNA binding sites of the global transcriptional regulator GlxR in Corynebacterium glutamicum

DEFF Research Database (Denmark)

Jungwirth, Britta; Sala, Claudia; Kohl, Thomas A

2013-01-01

of the 6C non-coding RNA gene and to non-canonical DNA binding sites within protein-coding regions. The present study underlines the dynamics within the GlxR regulon by identifying in vivo targets during growth on glucose and contributes to the expansion of knowledge of this important transcriptional......The transcriptional regulator GlxR has been characterized as a global hub within the gene-regulatory network of Corynebacterium glutamicum. Chromatin immunoprecipitation with a specific anti-GlxR antibody and subsequent high-throughput sequencing (ChIP-seq) was applied to C. glutamicum to get new...... mapping of these data on the genome sequence of C. glutamicum, 107 enriched DNA fragments were detected from cells grown with glucose as carbon source. GlxR binding sites were identified in the sequence of 79 enriched DNA fragments, of which 21 sites were not previously reported. Electrophoretic mobility...

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.

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.

A model-based approach for identifying signatures of ancient balancing selection in genetic data.

Science.gov (United States)

DeGiorgio, Michael; Lohmueller, Kirk E; Nielsen, Rasmus

2014-08-01

While much effort has focused on detecting positive and negative directional selection in the human genome, relatively little work has been devoted to balancing selection. This lack of attention is likely due to the paucity of sophisticated methods for identifying sites under balancing selection. Here we develop two composite likelihood ratio tests for detecting balancing selection. Using simulations, we show that these methods outperform competing methods under a variety of assumptions and demographic models. We apply the new methods to whole-genome human data, and find a number of previously-identified loci with strong evidence of balancing selection, including several HLA genes. Additionally, we find evidence for many novel candidates, the strongest of which is FANK1, an imprinted gene that suppresses apoptosis, is expressed during meiosis in males, and displays marginal signs of segregation distortion. We hypothesize that balancing selection acts on this locus to stabilize the segregation distortion and negative fitness effects of the distorter allele. Thus, our methods are able to reproduce many previously-hypothesized signals of balancing selection, as well as discover novel interesting candidates.

A model-based approach for identifying signatures of ancient balancing selection in genetic data.

Directory of Open Access Journals (Sweden)

Michael DeGiorgio

2014-08-01

Full Text Available While much effort has focused on detecting positive and negative directional selection in the human genome, relatively little work has been devoted to balancing selection. This lack of attention is likely due to the paucity of sophisticated methods for identifying sites under balancing selection. Here we develop two composite likelihood ratio tests for detecting balancing selection. Using simulations, we show that these methods outperform competing methods under a variety of assumptions and demographic models. We apply the new methods to whole-genome human data, and find a number of previously-identified loci with strong evidence of balancing selection, including several HLA genes. Additionally, we find evidence for many novel candidates, the strongest of which is FANK1, an imprinted gene that suppresses apoptosis, is expressed during meiosis in males, and displays marginal signs of segregation distortion. We hypothesize that balancing selection acts on this locus to stabilize the segregation distortion and negative fitness effects of the distorter allele. Thus, our methods are able to reproduce many previously-hypothesized signals of balancing selection, as well as discover novel interesting candidates.

Tonal response on the stairway of the main pyramid at La Ciudadela, Teotihuacan archaeological site

Science.gov (United States)

Beristain, Sergio; Coss, Cecilia; Aquino, Gabriela; Negrete, Jose; Lizana, Pablo

2002-11-01

This paper presents new research on the very interesting audible effects produced by the stairways of many archaeological sites in Mexico. This investigation was made at the main stairway of the pyramid at La Ciudadela, Teotihuacan archaeological site. The effect previously studied was a chirped echo reflected from the stairway at normal incidence, which resembles the singing of the Quetzal. Now it is presented with the impulsive sound source and the listeners located at different angles, where apart from the characteristic chirped sound, several musical notes could be obtained and identified, covering a range of at least one half an octave. This evaluation was made at the site, where the effect is clearly audible, and it is supported with simple mathematics.

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.

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

Site Selection for the Salt Disposition Facility at the Savannah River Site

International Nuclear Information System (INIS)

Gladden, J.B.; Rueter, K.J.; Morin, J.P.

2000-01-01

A site selection study was conducted to identify a suitable location for the construction and operation of a new Salt Disposition Facility (SDF) at the Savannah River Site (SRS). The facility to be sited is a single processing facility and support buildings that could house either of three technology alternatives being developed by the High Level Waste Systems Engineering Team: Small Tank Tetraphenylborate Precipitation, Crystalline Silicotitanate Non-Elutable Ion Exchange or Caustic Side Solvent Extraction. A fourth alternative, Direct Disposal in grout, is not part of the site selection study because a location has been identified that is unique to this technology (i.e., Z-Area). Facility site selection at SRS is a formal, documented process that seeks to optimize siting of new facilities with respect to facility-specific engineering requirements, sensitive environmental resources, and applicable regulatory requirements. In this manner, the prime objectives of cost minimization, environmental protection, and regulatory compliance are achieved. The results from this geotechnical characterization indicated that continued consideration be given to Site B for the proposed SDF. Suitable topography, the lack of surface hydrology and floodplain issues, no significant groundwater contamination, the presence of minor soft zones along the northeast portion of footprint, and no apparent geological structure in the Gordon Aquitard support this recommendation

Environmental Regulatory Compliance Plan for site: Draft characterization of the Yucca Mountain site:Draft

International Nuclear Information System (INIS)

1988-01-01

The objective of the EMMP is to document compliance with the NWPA. To do so, a summary description of site characterization activites is provided, based on the consultation draft of the SCP. Subsequent chpaters identify those technical areas having the potential to be impacted by site characterization activities and the monitoring plans proposed to identify whether those impacts acutally occur. Should monitoring confirm the potential for significant adverse impact, mitigative measures will be developed. In the context of site characterization, mitigation is defined as those changes in site characterization activities that serve to avoid or minimize, to the maximum extent practicle, any significant adverse environmental impacts. Although site characterization activies involve both surface and subsurface activities, it is the surface-based aspect of site characterization that is addressed in detailed by the EMMP. The schedule and duration of these activities is given in the consultation draft of the SCP. A breif summary of all proposed activities is given in the EMMP. 10 refs., 8 figs

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.

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.

Haiti: Feasibility of Waste-to-Energy Options at the Trutier Waste Site

Energy Technology Data Exchange (ETDEWEB)

Conrad, M. D.; Hunsberger, R.; Ness, J. E.; Harris, T.; Raibley, T.; Ursillo, P.

2014-08-01

This report provides further analysis of the feasibility of a waste-to-energy (WTE) facility in the area near Port-au-Prince, Haiti. NREL's previous analysis and reports identified anaerobic digestion (AD) as the optimal WTE technology at the facility. Building on the prior analyses, this report evaluates the conceptual financial and technical viability of implementing a combined waste management and electrical power production strategy by constructing a WTE facility at the existing Trutier waste site north of Port-au-Prince.

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

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.

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.

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.

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.

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.

Revised corrective action plan for underground storage tank 2331-U at the Building 9201-1 Site

International Nuclear Information System (INIS)

Bohrman, D.E.; Ingram, E.M.

1993-09-01

This document represents the Corrective Action Plan for underground storage tank (UST) 2331-U, previously located at Building 9201-1, Oak Ridge Y-12 Plant, Oak Ridge, Tennessee. Tank 2331-U, a 560-gallon UST, was removed on December 14, 1988. This document presents a comprehensive summary of all environmental assessment investigations conducted at the Building 9201-1 Site and the corrective action measures proposed for remediation of subsurface petroleum product contamination identified at the site. This document is written in accordance with the regulatory requirements of the Tennessee Department of Environment and Conservation (TDEC) Rule 1200-1-15-.06(7)

Supplemental site inspection for Air Force Plant 59, Johnson City, New York, Volume 3: Appendices F-Q

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. This volume consists of appendices F-Q, which contain the analytical data from the site characterization.

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

Reconnaissance survey of site 7 of the proposed Three Rivers Regional Landfill and Technology Center, Savannah River Site, Aiken County, South Carolina

Energy Technology Data Exchange (ETDEWEB)

Cabak, M.A.; Beck, M.L.; Gillam, C.; Sassaman, K.E.

1996-02-01

This report documents the archaeological investigation of Site 7 of the proposed Three Rivers Regional Landfill and Technology Center in Aiken County on the United States Department of Energy`s Savannah River Site (SRS) in Aiken and Barnwell Counties, South Carolina. Pedestrian and subsurface survey techniques were used to investigate the 1,403-acre project area. Survey resulted in the discovery of 23 previously unrecorded sites and 11 occurrences; six previously recorded sites were also investigated. These sites consist of six prehistoric sites, nine historic sites, and 14 sites with both prehistoric and historic components. Sites locations and project area boundaries are provided on a facsimile of a USGS 7.5 topographic map. The prehistoric components consist of very small, low-density lithic and ceramic scatters; most contain less than 10 artifacts. Six of the prehistoric components are of unknown cultural affiliation, the remaining prehistoric sites were occupied predominately in the Woodland period. The historic sites are dominated by postbellum/modem home places of tenant and yeoman farmers but four historic sites were locations of antebellum house sites (38AK136, 38AK613, 38AK660, and 38AK674). The historic sites also include an African-American school (38AK677).

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

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

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.

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.

Mosquito-borne arbovirus surveillance at selected sites in diverse ecological zones of Kenya; 2007 – 2012

Science.gov (United States)

2013-01-01

Background Increased frequency of arbovirus outbreaks in East Africa necessitated the determination of distribution of risk by entomologic arbovirus surveillance. A systematic vector surveillance programme spanning 5 years and covering 11 sites representing seven of the eight provinces in Kenya and located in diverse ecological zones was carried out. Methods Mosquitoes were sampled bi-annually during the wet seasons and screened for arboviruses. Mosquitoes were identified to species, pooled by species, collection date and site and screened for arboviruses by isolation in cell culture and/or RT-PCR screening and sequencing. Results Over 450,000 mosquitoes in 15,890 pools were screened with 83 viruses being detected/isolated that include members of the alphavirus, flavivirus and orthobunyavirus genera many of which are known to be of significant public health importance in the East African region. These include West Nile, Ndumu, Sindbis, Bunyamwera, Pongola and Usutu viruses detected from diverse sites. Ngari virus, which was associated with hemorrhagic fever in northern Kenya in 1997/98 was isolated from a pool of Anopheles funestus sampled from Tana-delta and from Aedes mcintoshi from Garissa. Insect only flaviviruses previously undescribed in Kenya were also isolated in the coastal site of Rabai. A flavivirus most closely related to the Chaoyang virus, a new virus recently identified in China and two isolates closely related to Quang Binh virus previously unreported in Kenya were also detected. Conclusion Active transmission of arboviruses of public health significance continues in various parts of the country with possible undetermined human impact. Arbovirus activity was highest in the pastoralist dominated semi-arid to arid zones sites of the country where 49% of the viruses were isolated suggesting a role of animals as amplifiers and indicating the need for improved arbovirus disease diagnosis among pastoral communities. PMID:23663381

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.

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

Site study plan for Transportation, Deaf Smith County Site, Texas: Preliminary draft

International Nuclear Information System (INIS)

1987-06-01

This site study plan describes transportation field studies to be conducted during the characterization of the Deaf Smith County, Texas, site for the US Department of Energy's Salt Repository Project. The studies are needed to identify and assess potential project impacts to transportation infrastructure and systems in the project vicinity and along potential transportation routes to the site across the State of Texas. The studies are also needed to locate and design project transportation facilities, and to evaluate and design impact mitigation. After identifying the transportation information requirements needed to comply with Federal, State, and local regulations and repository program requirements, the site study plan describes the study design and rationale, the field data collection procedures and equipment, the data analysis methods and application of results, the data management strategy, the schedule of field activities, the management of the study, and the study's quality assurance program. The field data collection activities are organized into programs for the characterization of site vicinity rail corridors and highway corridors, characterization of alternative statewide transportation routes, monitoring of site characterization effects on transportation, characterization of aircraft overflight patterns and hazardous material transportation patterns, and assessment of emergency response preparedness along alternative statewide transportation routes. 34 refs., 10 figs., 2 tabs

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...

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

Site enforcement tracking system (SETS): PRP listing by site for region 9

International Nuclear Information System (INIS)

1993-04-01

When expending Superfund monies at a CERCLA (Comprehensive Environmental Response, Compensation and Liability Act) site, EPA must conduct a search to identify parties with potential financial responsibility for remediation of uncontrolled hazardous waste sites. EPA regional Superfund Waste Management Staff issue a notice letter to the potentially responsible party (PRP). Data from the notice letter is used to form the Site Enforcement Tracking System (SETS). The data includes PRP name and address, a company contact person, the date the notice was issued, and the related CERCLA site name and identification number

Site enforcement tracking system (SETS): PRP listing by site for region 8

International Nuclear Information System (INIS)

1993-04-01

When expending Superfund monies at a CERCLA (Comprehensive Environmental Response, Compensation and Liability Act) site, EPA must conduct a search to identify parties with potential financial responsibility for remediation of uncontrolled hazardous waste sites. EPA regional Superfund Waste Management Staff issue a notice letter to the potentially responsible party (PRP). Data from the notice letter is used to form the Site Enforcement Tracking System (SETS). The data includes PRP name and address, a company contact person, the date the notice was issued, and the related CERCLA site name and identification number

Site enforcement tracking system (SETS): PRP listing by site for region 10

International Nuclear Information System (INIS)

1993-04-01

When expending Superfund monies at a CERCLA (Comprehensive Environmental Response, Compensation and Liability Act) site, EPA must conduct a search to identify parties with potential financial responsibility for remediation of uncontrolled hazardous waste sites. EPA regional Superfund Waste Management Staff issue a notice letter to the potentially responsible party (PRP). Data from the notice letter is used to form the Site Enforcement Tracking System (SETS). The data includes PRP name and address, a company contact person, the date the notice was issued, and the related CERCLA site name and identification number

Site enforcement tracking system (SETS): PRP listing by site for region 3

International Nuclear Information System (INIS)

1993-04-01

When expending Superfund monies at a CERCLA (Comprehensive Environmental Response, Compensation and Liability Act) site, EPA must conduct a search to identify parties with potential financial responsibility for remediation of uncontrolled hazardous waste sites. EPA regional Superfund Waste Management Staff issue a notice letter to the potentially responsible party (PRP). Data from the notice letter is used to form the Site Enforcement Tracking System (SETS). The data includes PRP name and address, a company contact person, the date the notice was issued, and the related CERCLA site name and identification number

Site enforcement tracking system (SETS): PRP listing by site for region 2

International Nuclear Information System (INIS)

1993-04-01

When expending Superfund monies at a CERCLA (Comprehensive Environmental Response, Compensation and Liability Act) site, EPA must conduct a search to identify parties with potential financial responsibility for remediation of uncontrolled hazardous waste sites. EPA regional Superfund Waste Management Staff issue a notice letter to the potentially responsible party (PRP). Data from the notice letter is used to form the Site Enforcement Tracking System (SETS). The data includes PRP name and address, a company contact person, the date the notice was issued, and the related CERCLA site name and identification number

Site enforcement tracking system (SETS): PRP listing by site for region 5

International Nuclear Information System (INIS)

1993-04-01

When expending Superfund monies at a CERCLA (Comprehensive Environmental Response, Compensation and Liability Act) site, EPA must conduct a search to identify parties with potential financial responsibility for remediation of uncontrolled hazardous waste sites. EPA regional Superfund Waste Management Staff issue a notice letter to the potentially responsible party (PRP). Data from the notice letter is used to form the Site Enforcement Tracking System (SETS). The data includes PRP name and address, a company contact person, the date the notice was issued, and the related CERCLA site name and identification number

Site enforcement tracking system (SETS): PRP listing by site for region 6

International Nuclear Information System (INIS)

1993-04-01

When expending Superfund monies at a CERCLA (Comprehensive Environmental Response, Compensation and Liability Act) site, EPA must conduct a search to identify parties with potential financial responsibility for remediation of uncontrolled hazardous waste sites. EPA regional Superfund Waste Management Staff issue a notice letter to the potentially responsible party (PRP). Data from the notice letter is used to form the Site Enforcement Tracking System (SETS). The data includes PRP name and address, a company contact person, the date the notice was issued, and the related CERCLA site name and identification number

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- ...

Identification of the quinolinedione inhibitor binding site in Cdc25 phosphatase B through docking and molecular dynamics simulations

Science.gov (United States)

Ge, Yushu; van der Kamp, Marc; Malaisree, Maturos; Liu, Dan; Liu, Yi; Mulholland, Adrian J.

2017-11-01

Cdc25 phosphatase B, a potential target for cancer therapy, is inhibited by a series of quinones. The binding site and mode of quinone inhibitors to Cdc25B remains unclear, whereas this information is important for structure-based drug design. We investigated the potential binding site of NSC663284 [DA3003-1 or 6-chloro-7-(2-morpholin-4-yl-ethylamino)-quinoline-5, 8-dione] through docking and molecular dynamics simulations. Of the two main binding sites suggested by docking, the molecular dynamics simulations only support one site for stable binding of the inhibitor. Binding sites in and near the Cdc25B catalytic site that have been suggested previously do not lead to stable binding in 50 ns molecular dynamics (MD) simulations. In contrast, a shallow pocket between the C-terminal helix and the catalytic site provides a favourable binding site that shows high stability. Two similar binding modes featuring protein-inhibitor interactions involving Tyr428, Arg482, Thr547 and Ser549 are identified by clustering analysis of all stable MD trajectories. The relatively flexible C-terminal region of Cdc25B contributes to inhibitor binding. The binding mode of NSC663284, identified through MD simulation, likely prevents the binding of protein substrates to Cdc25B. The present results provide useful information for the design of quinone inhibitors and their mechanism of inhibition.

Identification of the quinolinedione inhibitor binding site in Cdc25 phosphatase B through docking and molecular dynamics simulations.

Science.gov (United States)

Ge, Yushu; van der Kamp, Marc; Malaisree, Maturos; Liu, Dan; Liu, Yi; Mulholland, Adrian J

2017-11-01

Cdc25 phosphatase B, a potential target for cancer therapy, is inhibited by a series of quinones. The binding site and mode of quinone inhibitors to Cdc25B remains unclear, whereas this information is important for structure-based drug design. We investigated the potential binding site of NSC663284 [DA3003-1 or 6-chloro-7-(2-morpholin-4-yl-ethylamino)-quinoline-5, 8-dione] through docking and molecular dynamics simulations. Of the two main binding sites suggested by docking, the molecular dynamics simulations only support one site for stable binding of the inhibitor. Binding sites in and near the Cdc25B catalytic site that have been suggested previously do not lead to stable binding in 50 ns molecular dynamics (MD) simulations. In contrast, a shallow pocket between the C-terminal helix and the catalytic site provides a favourable binding site that shows high stability. Two similar binding modes featuring protein-inhibitor interactions involving Tyr428, Arg482, Thr547 and Ser549 are identified by clustering analysis of all stable MD trajectories. The relatively flexible C-terminal region of Cdc25B contributes to inhibitor binding. The binding mode of NSC663284, identified through MD simulation, likely prevents the binding of protein substrates to Cdc25B. The present results provide useful information for the design of quinone inhibitors and their mechanism of inhibition.

Distinct roles of beta1 metal ion-dependent adhesion site (MIDAS), adjacent to MIDAS (ADMIDAS), and ligand-associated metal-binding site (LIMBS) cation-binding sites in ligand recognition by integrin alpha2beta1.

Science.gov (United States)

Valdramidou, Dimitra; Humphries, Martin J; Mould, A Paul

2008-11-21

Integrin-ligand interactions are regulated in a complex manner by divalent cations, and previous studies have identified ligand-competent, stimulatory, and inhibitory cation-binding sites. In collagen-binding integrins, such as alpha2beta1, ligand recognition takes place exclusively at the alpha subunit I domain. However, activation of the alphaI domain depends on its interaction with a structurally similar domain in the beta subunit known as the I-like or betaI domain. The top face of the betaI domain contains three cation-binding sites: the metal-ion dependent adhesion site (MIDAS), the ADMIDAS (adjacent to MIDAS), and LIMBS (ligand-associated metal-binding site). The role of these sites in controlling ligand binding to the alphaI domain has yet to be elucidated. Mutation of the MIDAS or LIMBS completely blocked collagen binding to alpha2beta1; in contrast mutation of the ADMIDAS reduced ligand recognition but this effect could be overcome by the activating monoclonal antibody TS2/16. Hence, the MIDAS and LIMBS appear to be essential for the interaction between alphaI and betaI, whereas occupancy of the ADMIDAS has an allosteric effect on the conformation of betaI. An activating mutation in the alpha2 I domain partially restored ligand binding to the MIDAS and LIMBS mutants. Analysis of the effects of Ca(2+), Mg(2+), and Mn(2+) on ligand binding to these mutants showed that the MIDAS is a ligand-competent site through which Mn(2+) stimulates ligand binding, whereas the LIMBS is a stimulatory Ca(2+)-binding site, occupancy of which increases the affinity of Mg(2+) for the MIDAS.

AutoSite: an automated approach for pseudo-ligands prediction—from ligand-binding sites identification to predicting key ligand atoms

Science.gov (United States)

Ravindranath, Pradeep Anand; Sanner, Michel F.

2016-01-01

Motivation: The identification of ligand-binding sites from a protein structure facilitates computational drug design and optimization, and protein function assignment. We introduce AutoSite: an efficient software tool for identifying ligand-binding sites and predicting pseudo ligand corresponding to each binding site identified. Binding sites are reported as clusters of 3D points called fills in which every point is labelled as hydrophobic or as hydrogen bond donor or acceptor. From these fills AutoSite derives feature points: a set of putative positions of hydrophobic-, and hydrogen-bond forming ligand atoms. Results: We show that AutoSite identifies ligand-binding sites with higher accuracy than other leading methods, and produces fills that better matches the ligand shape and properties, than the fills obtained with a software program with similar capabilities, AutoLigand. In addition, we demonstrate that for the Astex Diverse Set, the feature points identify 79% of hydrophobic ligand atoms, and 81% and 62% of the hydrogen acceptor and donor hydrogen ligand atoms interacting with the receptor, and predict 81.2% of water molecules mediating interactions between ligand and receptor. Finally, we illustrate potential uses of the predicted feature points in the context of lead optimization in drug discovery projects. Availability and Implementation: http://adfr.scripps.edu/AutoDockFR/autosite.html Contact: sanner@scripps.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27354702

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.

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

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.

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.

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.

Dual binding mode of the nascent polypeptide-associated complex reveals a novel universal adapter site on the ribosome.

Science.gov (United States)

Pech, Markus; Spreter, Thomas; Beckmann, Roland; Beatrix, Birgitta

2010-06-18

Nascent polypeptide-associated complex (NAC) was identified in eukaryotes as the first cytosolic factor that contacts the nascent polypeptide chain emerging from the ribosome. NAC is present as a homodimer in archaea and as a highly conserved heterodimer in eukaryotes. Mutations in NAC cause severe embryonically lethal phenotypes in mice, Drosophila melanogaster, and Caenorhabditis elegans. In the yeast Saccharomyces cerevisiae NAC is quantitatively associated with ribosomes. Here we show that NAC contacts several ribosomal proteins. The N terminus of betaNAC, however, specifically contacts near the tunnel exit ribosomal protein Rpl31, which is unique to eukaryotes and archaea. Moreover, the first 23 amino acids of betaNAC are sufficient to direct an otherwise non-associated protein to the ribosome. In contrast, alphaNAC (Egd2p) contacts Rpl17, the direct neighbor of Rpl31 at the ribosomal tunnel exit site. Rpl31 was also recently identified as a contact site for the SRP receptor and the ribosome-associated complex. Furthermore, in Escherichia coli peptide deformylase (PDF) interacts with the corresponding surface area on the eubacterial ribosome. In addition to the previously identified universal adapter site represented by Rpl25/Rpl35, we therefore refer to Rpl31/Rpl17 as a novel universal docking site for ribosome-associated factors on the eukaryotic ribosome.

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.

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

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.

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.

Site study plan for cultural resources, Deaf Smith County site, Texas: Environmental Field Program: Preliminary draft

International Nuclear Information System (INIS)

1987-06-01

The Cultural Resources Site Study Plan describes a field program to identify and evaluate the archaeological, historical, and Native American Indian resources of the site on local and regional perspectives; monitor and manage discovered cultural resources; and establish a worker education program. The archaeological field program consists of three pedestrian surveys: Survey 1 includes two EDBH seismic survey lines and the area within the exploratory shaft facility (ESF); Survey 2 includes the remainder of the site plus a 1/4 to 3/4-mi border area; and Survey 3 includes an assortment of offsite areas. The historical studies will identify and evaluate known and discovered historical sites and structures and the Native American Indian will identify and evaluate cultural and religious concerns expressed by Indian tribal groups. Prehistoric and historic sites will be evaluated to determine if they meet eligibility criteria for listing on the National Register of Historic Places. This site study plan describes the need for each study; its design and design rationale; analysis, management, and use of data; schedule of field activities; organization of field personnel and sample management; and quality assurance requirements. The cultural resource studies will provide data for satisfying the Programmatic Agreement, engineering design needs, and SRP requirements for permits and approvals, and for minimizing effects to any cultural properties discovered during site characterization. 75 refs., 10 figs., 2 tabs

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/.

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.

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

Hanford site transuranic waste sampling plan

International Nuclear Information System (INIS)

GREAGER, T.M.

1999-01-01

This sampling plan (SP) describes the selection of containers for sampling of homogeneous solids and soil/gravel and for visual examination of transuranic and mixed transuranic (collectively referred to as TRU) waste generated at the U.S. Department of Energy (DOE) Hanford Site. The activities described in this SP will be conducted under the Hanford Site TRU Waste Certification Program. This SP is designed to meet the requirements of the Transuranic Waste Characterization Quality Assurance Program Plan (CAO-94-1010) (DOE 1996a) (QAPP), site-specific implementation of which is described in the Hanford Site Transuranic Waste Characterization Program Quality Assurance Project Plan (HNF-2599) (Hanford 1998b) (QAPP). The QAPP defines the quality assurance (QA) requirements and protocols for TRU waste characterization activities at the Hanford Site. In addition, the QAPP identifies responsible organizations, describes required program activities, outlines sampling and analysis strategies, and identifies procedures for characterization activities. The QAPP identifies specific requirements for TRU waste sampling plans. Table 1-1 presents these requirements and indicates sections in this SP where these requirements are addressed

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.

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.

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.

The yule approximation for the site frequency spectrum after a selective sweep.

Directory of Open Access Journals (Sweden)

Sebastian Bossert

Full Text Available In the area of evolutionary theory, a key question is which portions of the genome of a species are targets of natural selection. Genetic hitchhiking is a theoretical concept that has helped to identify various such targets in natural populations. In the presence of recombination, a severe reduction in sequence diversity is expected around a strongly beneficial allele. The site frequency spectrum is an important tool in genome scans for selection and is composed of the numbers S(1,...,S(n-1, where S(k is the number of single nucleotide polymorphisms (SNPs present in k from n individuals. Previous work has shown that both the number of low- and high-frequency variants are elevated relative to neutral evolution when a strongly beneficial allele fixes. Here, we follow a recent investigation of genetic hitchhiking using a marked Yule process to obtain an analytical prediction of the site frequency spectrum in a panmictic population at the time of fixation of a highly beneficial mutation. We combine standard results from the neutral case with the effects of a selective sweep. As simulations show, the resulting formula produces predictions that are more accurate than previous approaches for the whole frequency spectrum. In particular, the formula correctly predicts the elevation of low- and high-frequency variants and is significantly more accurate than previously derived formulas for intermediate frequency variants.

Site Selection for Surplus Plutonium Disposition Facilities at the Savannah River Site

International Nuclear Information System (INIS)

Wike, L.D.

2000-01-01

A site selection study was conducted to evaluate locations for the proposed Surplus Plutonium Disposition Facilities. Facilities to be located include the Mixed Oxide (MOX) Fuel Fabrication Facility, the Pit Disassembly and Conversion Facility (PDCF), and the Plutonium Immobilization Project (PIP) facility. Objectives of the study include: (1) Confirm that the Department of Energy (DOE) selected locations for the MOX and PDCF were suitable based on selected siting criteria, (2) Recommend a site in the vicinity of F Area that is suitable for the PIP, and (3) Identify alternative suitable sites for one or more of these facilities in the event that further geotechnical characterization or other considerations result in disqualification of a currently proposed site

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.

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

Nevada Test Site Environmental Report 2008

Energy Technology Data Exchange (ETDEWEB)

Cathy A. Wills

2009-09-01

The Nevada Test Site Environmental Report (NTSER) 2008 was prepared to meet the information needs of the public and the requirements and guidelines of the U.S. Department of Energy (DOE) for annual site environmental reports. It was prepared by National Security Technologies, LLC (NSTec), for the U.S. Department of Energy, National Nuclear Security Administration Nevada Site Office (NNSA/NSO). This and previous years’ NTSERs are posted on the NNSA/NSO website at http://www.nv.doe.gov/library/publications/aser.aspx.

Functional characterization of autophosphorylation sites of the activated insulin receptor-tyrosine kinase

International Nuclear Information System (INIS)

Flores-Riveros, J.R.; Lane, M.D.

1987-01-01

Insulin receptor, solubilized from 3T3-L1 cellular membranes and then purified, was autophosphorylated with [γ- 32 P]ATP in the absence or presence of insulin. Specific phosphopeptides generated by trypsin digestion of the 32 P-labeled β-subunit were identified and separated by reverse phase HPLC. In the absence of insulin, radioactivity of the phosphopeptides is evenly distributed among four major peaks designated as sites I, II, III and IV, according to their order of elution. This pattern is maintained for at least the first 30 min of autophosphorylation. When the reaction is carried out in the presence of insulin, > 50% of the total 32 P radioactivity is found in site I and the rate of 32 P incorporation into this site is markedly higher than into sites II, III and IV. Maximal activation of tyrosine kinase activity, as estimated by substrate phosphorylation, is coincident with the nearly complete phosphorylation of site I. Delayed activation of previously autophosphorylated receptor by insulin, but not by EGF or IGF-I, produced a similar pattern where phosphorylated site I predominates. These observations indicate that one major insulin-regulated autophosphorylation site in the β-subunit is responsible for activation of the insulin receptor tyrosine kinase. The isolation of this phosphopeptide on a preparative scale and its characterization are now in progress

Remediation of 20,000 m3 of hydrocarbon-impacted soil at a former well site using the biopile process

Energy Technology Data Exchange (ETDEWEB)

Bedard, G. [Biogenie Inc., Calgary, AB (Canada)

2006-07-01

The remediation of 20,000 m{sup 3} of hydrocarbon-impacted soil at a former well site using the biopile process was discussed. The site involved was an abandoned site located southwest from Red Deer, Alberta in an agricultural area. The presentation provided background on the site history and discussed an additional site assessment. The objectives of this assessment were to complete the delineation of the hydrocarbon plume; confirm the depth of impact identified in a previous environmental assessment; and, select the most efficient remediation strategy. The presentation also discussed findings of the Environmental Services Association (ESA). Site specific challenges that were addressed included proximity of land owners; lease slopes to a nearby river; large volume of impacted material; depth of impact; limited space available on-site; high concentrations of petroleum hydrocarbons (PHCs); segregation of impacted soil; and winter installation and start-up. The proposed strategy and its advantages as well as the methodology for the remediation strategy were all discussed. 5 tabs., 5 figs.

Structural Fingerprints of Transcription Factor Binding Site Regions

Directory of Open Access Journals (Sweden)

Peter Willett

2009-03-01

Full Text Available Fourier transforms are a powerful tool in the prediction of DNA sequence properties, such as the presence/absence of codons. We have previously compiled a database of the structural properties of all 32,896 unique DNA octamers. In this work we apply Fourier techniques to the analysis of the structural properties of human chromosomes 21 and 22 and also to three sets of transcription factor binding sites within these chromosomes. We find that, for a given structural property, the structural property power spectra of chromosomes 21 and 22 are strikingly similar. We find common peaks in their power spectra for both Sp1 and p53 transcription factor binding sites. We use the power spectra as a structural fingerprint and perform similarity searching in order to find transcription factor binding site regions. This approach provides a new strategy for searching the genome data for information. Although it is difficult to understand the relationship between specific functional properties and the set of structural parameters in our database, our structural fingerprints nevertheless provide a useful tool for searching for function information in sequence data. The power spectrum fingerprints provide a simple, fast method for comparing a set of functional sequences, in this case transcription factor binding site regions, with the sequences of whole chromosomes. On its own, the power spectrum fingerprint does not find all transcription factor binding sites in a chromosome, but the results presented here show that in combination with other approaches, this technique will improve the chances of identifying functional sequences hidden in genomic data.

Savannah River Site`s Site Specific Plan. Environmental restoration and waste management, fiscal year 1992

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.

Identifying the source, transport path and sinks of sewage derived organic matter

International Nuclear Information System (INIS)

Mudge, Stephen M.; Duce, Caroline E.

2005-01-01

Since sewage discharges can significantly contribute to the contaminant loadings in coastal areas, it is important to identify sources, pathways and environmental sinks. Sterol and fatty alcohol biomarkers were quantified in source materials, suspended sediments and settling matter from the Ria Formosa Lagoon. Simple ratios between key biomarkers including 5β-coprostanol, cholesterol and epi-coprostanol were able to identify the sewage sources and effected deposition sites. Multivariate methods (PCA) were used to identify co-varying sites. PLS analysis using the sewage discharge as the signature indicated ∼ 25% of the variance in the sites could be predicted by the sewage signature. A new source of sewage derived organic matter was found with a high sewage predictable signature. The suspended sediments had relatively low sewage signatures as the material was diluted with other organic matter from in situ production. From a management viewpoint, PLS provides a useful tool in identifying the pathways and accumulation sites for such contaminants. - Multivariate statistical analysis was used to identify pathways and accumulation sites for contaminants in coastal waters

5' diversity of human hepatic PXR (NR1I2) transcripts and identification of the major transcription initiation site.

Science.gov (United States)

Kurose, Kouichi; Koyano, Satoru; Ikeda, Shinobu; Tohkin, Masahiro; Hasegawa, Ryuichi; Sawada, Jun-Ichi

2005-05-01

The human pregnane X receptor (PXR) is a crucial regulator of the genes encoding several major cytochrome P450 enzymes and transporters, such as CYP3A4 and MDR1, but its own transcriptional regulation remains unclear. To elucidate the transcriptional mechanisms of human PXR gene, we first endeavored to identify the transcription initiation site of human PXR using 5'-RACE. Five types of 5'-variable transcripts (a, b, c, d, and e) with common exon 2 sequence were found, and comparison of these sequences with the genomic sequence suggested that their 5' diversity is derived from initiation by alternative promoters and alternative splicing. None of the exons found in our study contain any new in-frame coding regions. Newly identified introns IVS-a and IVS-b were found to have CT-AC splice sites that do not follow the GT-AG rule of conventional donor and acceptor splice sites. Of the five types of 5' variable transcripts identified, RT-PCR showed that type-a was the major transcript type. Four transcription initiation sites (A-D) for type-a transcript were identified by 5'-RACE using GeneRacer RACE Ready cDNA (human liver) constructed by the oligo-capping method. Putative TATA boxes were located approximately 30 bp upstream from the transcriptional start sites of the major transcript (C) and the longest minor transcript (A) expressed in the human liver. These results indicate that the initiation of transcription of human PXR is more complex than previously reported.

Relative contributions of microbial and infrastructure heat at a crude oil-contaminated site

Science.gov (United States)

Warren, Ean; Bekins, Barbara A.

2018-04-01

Biodegradation of contaminants can increase the temperature in the subsurface due to heat generated from exothermic reactions, making temperature observations a potentially low-cost approach for determining microbial activity. For this technique to gain more widespread acceptance, it is necessary to better understand all the factors affecting the measured temperatures. Biodegradation has been occurring at a crude oil-contaminated site near Bemidji, Minnesota for 39 years, creating a quasi-steady-state plume of contaminants and degradation products. A model of subsurface heat generation and transport helps elucidate the contribution of microbial and infrastructure heating to observed temperature increases at this site. We created a steady-state, two-dimensional, heat transport model using previous-published parameter values for physical, chemical and biodegradation properties. Simulated temperature distributions closely match the observed average annual temperatures measured in the contaminated area at the site within less than 0.2 °C in the unsaturated zone and 0.4 °C in the saturated zone. The model results confirm that the observed subsurface heat from microbial activity is due primarily to methane oxidation in the unsaturated zone resulting in a 3.6 °C increase in average annual temperature. Another important source of subsurface heat is from the active, crude-oil pipelines crossing the site. The pipelines impact temperatures for a distance of 200 m and contribute half the heat. Model results show that not accounting for the heat from the pipelines leads to overestimating the degradation rates by a factor of 1.7, demonstrating the importance of identifying and quantifying all heat sources. The model results also highlighted a zone where previously unknown microbial activity is occurring at the site.

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.

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.

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

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...

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

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...

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

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.

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

MNAtoolbox: A Monitored Natural Attenuation Site Screening Program

Energy Technology Data Exchange (ETDEWEB)

Borns, David J.; Brady, Patrick V.; Brady, Warren D.; Krupka, Kenneth M.; Spalding, Brian P.; Waters, Robert D.; Zhang, Pengchu

1999-07-12

Screening of sites for the potential application and reliance upon monitored natural attenuation (MNA) can be done using MNAtoolbox, a web-based tool for estimating extent of biodegradation, chemical transformation, and dilution. MNAtoolbox uses site-specific input data, where available (default parameters are taken from the literature), to roughly quantify the nature and extent of attenuation at a particular site. Use of MNAtoolbox provides 3 important elements of site evaluation: (1) Identifies likely attenuation pathways, (2) Clearly identifies sites where MNA is inappropriate, and (3) Evaluates data requirements for subsequent reliance on MNA as a sole or partial corrective action.

Comprehensive profiling of retroviral integration sites using target enrichment methods from historical koala samples without an assembled reference genome

Directory of Open Access Journals (Sweden)

Pin Cui

2016-03-01

Full Text Available Background. Retroviral integration into the host germline results in permanent viral colonization of vertebrate genomes. The koala retrovirus (KoRV is currently invading the germline of the koala (Phascolarctos cinereus and provides a unique opportunity for studying retroviral endogenization. Previous analysis of KoRV integration patterns in modern koalas demonstrate that they share integration sites primarily if they are related, indicating that the process is currently driven by vertical transmission rather than infection. However, due to methodological challenges, KoRV integrations have not been comprehensively characterized. Results. To overcome these challenges, we applied and compared three target enrichment techniques coupled with next generation sequencing (NGS and a newly customized sequence-clustering based computational pipeline to determine the integration sites for 10 museum Queensland and New South Wales (NSW koala samples collected between the 1870s and late 1980s. A secondary aim of this study sought to identify common integration sites across modern and historical specimens by comparing our dataset to previously published studies. Several million sequences were processed, and the KoRV integration sites in each koala were characterized. Conclusions. Although the three enrichment methods each exhibited bias in integration site retrieval, a combination of two methods, Primer Extension Capture and hybridization capture is recommended for future studies on historical samples. Moreover, identification of integration sites shows that the proportion of integration sites shared between any two koalas is quite small.

Technical summary of groundwater quality protection program at the Savannah River Site, 1952--1986. Volume 1, Site geohydrology and waste sites

Energy Technology Data Exchange (ETDEWEB)

Heffner, J.D. [ed.] [Exploration Resources, Inc., Athens, GA (United States)

1991-11-01

This report provides information regarding the status of and groundwater quality at the waste sites at the Department of Energy`s (DOE) Savannah River Site (SRS). Specific information provided for each waste site at SRS includes its location, size, inventory (when known), and history. Many waste sites at SRS are considered to be of little environmental concern because they contain nontoxic or inert material such as construction rubble and debris. Other waste sites, however, either are known to have had an effect on groundwater quality or are suspected of having the potential to affect groundwater. Monitoring wells have been installed at most of these sites; monitoring wells are scheduled for installation at the remaining sites. Results of the groundwater analyses from these monitoring wells, presented in the appendices, are used in the report to help identify potential contaminants of concern, if any, at each waste site. The list of actions proposed for each waste site in Christensen and Gordon`s 1983 report are summarized, and an update is provided for each site. Planned actions for the future are also outlined.

kmer-SVM: a web server for identifying predictive regulatory sequence features in genomic data sets

Science.gov (United States)

Fletez-Brant, Christopher; Lee, Dongwon; McCallion, Andrew S.; Beer, Michael A.

2013-01-01

Massively parallel sequencing technologies have made the generation of genomic data sets a routine component of many biological investigations. For example, Chromatin immunoprecipitation followed by sequence assays detect genomic regions bound (directly or indirectly) by specific factors, and DNase-seq identifies regions of open chromatin. A major bottleneck in the interpretation of these data is the identification of the underlying DNA sequence code that defines, and ultimately facilitates prediction of, these transcription factor (TF) bound or open chromatin regions. We have recently developed a novel computational methodology, which uses a support vector machine (SVM) with kmer sequence features (kmer-SVM) to identify predictive combinations of short transcription factor-binding sites, which determine the tissue specificity of these genomic assays (Lee, Karchin and Beer, Discriminative prediction of mammalian enhancers from DNA sequence. Genome Res. 2011; 21:2167–80). This regulatory information can (i) give confidence in genomic experiments by recovering previously known binding sites, and (ii) reveal novel sequence features for subsequent experimental testing of cooperative mechanisms. Here, we describe the development and implementation of a web server to allow the broader research community to independently apply our kmer-SVM to analyze and interpret their genomic datasets. We analyze five recently published data sets and demonstrate how this tool identifies accessory factors and repressive sequence elements. kmer-SVM is available at http://kmersvm.beerlab.org. PMID:23771147

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

SITE: a methodology for assessment of energy facility siting patterns. Regional studies program

International Nuclear Information System (INIS)

Frigerio, N.A.; Habegger, L.J.; King, R.F.; Hoover, L.J.; Clark, N.A.; Cobian, J.M.

1975-08-01

The timely development of the nation's energy production capacity in a manner that minimizes potential adverse local and regional impacts associated with energy facilities requires the use of sophisticated techniques for evaluation of siting alternatives and fuel cycle options. This report is a documentation of the computerized SITE methodology that has been developed for evaluating health, environmental, and socioeconomic impacts related to utilization of alternate sites for energy production within a region of interest. The cost, impact, and attribute vectors, which are generated and displayed on density maps, can be used in a multiparameter overlay process to identify preferable siting areas. The assessment of clustered facilities in energy centers is also possible within the SITE analysis framework. An application of the SITE methodology to Northern Illinois is presented. Also included is a description of the ongoing extension of SITE for the accumulative evaluation of alternative regional energy siting patterns and fuel cycle options. An appendix provides documentation and user information for the SITE computer program

Quality of breast cancer sites on the World Wide Web.

Science.gov (United States)

Hoffman-Goetz, L; Clarke, J N

2000-01-01

The Internet is a powerful tool for accessing information about complex health topics. The purpose of this study was to evaluate breast cancer Internet sites using published criteria about website structure. Two searches were undertaken (November 1998 and June 1999) using the Yahoo search engine, providing a sample of 136 unique addresses. The results showed 1) owner's credentials were identified in 31.6% of sites, 2) financial charges were stated in 10.3% of sites, 3) less than 14.0% identified site creation date, 4) 33.1% identified content posting update, 5) 30.1% identified information sources, and 6) just under 88% of sites provided e-mail interactivity. The results indicate variability in breast cancer Internet sites with respect to framework criteria of accountability. We suggest that websites that lack fundamental indicators (such as dating and sources) do not provide the user with fundamental information that could enable informed decision making about site quality.

Comparing Potential Unstable Sites and Stable Sites on Revegetated Cut-Slopes of Mountainous Terrain in Korea

Directory of Open Access Journals (Sweden)

Sung-Ho Kil

2015-11-01

Full Text Available This study employs a diverse set of variables to explain slope stabilization on stable versus failure-prone revegetated cut-slopes in Korea. A field survey was conducted at potential unstable sites and stable sites using 23 variables. Through a non-parametric test of the field survey results, 15 variables were identified as primary determinants of slope failure. Of these variables, one described physical characteristics (elapsed year; four variables described vegetation properties (plant community, vegetation coverage rate, number of trees, and number of herbs; and 10 variables represented soil properties (porosity, soil hardness, water content, sand ratio and silt ratio of soil texture, tensile strength, permeability coefficient, soil depth, soil acidity, salt concentration, and organic matter. Slope angle, which was mainly considered in previous studies, of variables in physical characteristics was not statistically selected as one of the 15 variables because most of sites were located on steep slopes. The vegetation community, vegetation coverage, and number of trees influence slope stabilization. Vegetation coverage is highly correlated with other soil and vegetation variables, making it a major indicator of slope stabilization. All soil variables were related to slope failure such that subsequent slope failure was related to the method of slope revegetation rather than the environmental condition of the slope. Slope failure did not occur in revegetated slopes that matched the characteristics of the surrounding landscape and contained a large number of native trees. Most soil and vegetation variables showed differing values for whether a revegetated slope is potentially unstable or stable.

Early Site Permit Demonstration Program, plant parameters envelopes: Comparison with ranges of values for four hypothetical sites

International Nuclear Information System (INIS)

1992-09-01

The purpose of this volume is to report the results of the comparison of the ALWR plan parameters envelope with values of site characteristics developed for our hypothetical sites that generally represent conditions encountered within the United States. This effort is not intended to identify or address the suitability of any existing site, site area, or region in the United States. Also included in this volume is Appendix F, SERCH Summaries Regarding Siting

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.

Site characterization quality assurance for the California LLRW Disposal Site Project

International Nuclear Information System (INIS)

Hanrahan, T.P.; Ench, J.E.; Serlin, C.L.; Bennett, C.B.

1988-01-01

In December of 1985 US Ecology was chosen as the license designee for the State of California's low-level radioactive waste disposal facility. In early 1987, three candidate sites were selected for characterization studies in preparation for identifying the preferred site. The geotechnical characterization activities along with studies of the ecological and archaeological attributes, as well as assessments of the socio-economic impacts and cultural resources all provide input towards selection of the proposed site. These technical studies in conjunction with comments from local citizen committees and other interested parties are used as a basis for determining the proposed site for which full site characterization as required by California licensing requirements are undertaken. The purpose of this paper is to present an overview of the program for Quality Assurance and Quality Control for the site characterization activities on the California LLRW Disposal Site Project. The focus is on three major perspectives: The composite QA Program and two of the primary characterization activities, the geotechnical and the meteorological investigations

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.

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

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

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...

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

Nuclear Energy Center Site Survey, 1975. Part V. Resource availability and site screening

International Nuclear Information System (INIS)

1976-01-01

Resource requirements for nuclear energy centers are discussed and the large land areas which meet these requirements and may contain potential sites for a nuclear energy center (NEC) are identified. Maps of the areas are included that identify seismic zones, river flow rates, and population density

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.

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.

Environmental waste site characterization utilizing aerial photographs and satellite imagery: Three sites in New Mexico, USA

International Nuclear Information System (INIS)

Van Eeckhout, E.; Pope, P.; Becker, N.; Wells, B.; Lewis, A.; David, N.

1996-01-01

The proper handling and characterization of past hazardous waste sites is becoming more and more important as world population extends into areas previously deemed undesirable. Historical photographs, past records, current aerial satellite imagery can play an important role in characterizing these sites. These data provide clear insight into defining problem areas which can be surface samples for further detail. Three such areas are discussed in this paper: (1) nuclear wastes buried in trenches at Los Alamos National Laboratory, (2) surface dumping at one site at Los Alamos National Laboratory, and (3) the historical development of a municipal landfill near Las Cruces, New Mexico

Shocking Path of Least Resistance Shines Light on Subsurface by Revealing the Paths of Water and the Presence of Faults: Stacked EM Case Studies over Barite Hills Superfund Site in South Carolina

Science.gov (United States)

Haggar, K. S.; Nelson, H. R., Jr.; Berent, L. J.

2017-12-01

The Barite Hills/Nevada Gold Fields mines are in Late Proterozoic and early Paleozoic rocks of the gold and iron sulfides rich Carolina slate belt. The mines were active from 1989 to1995. EPA and USGS site investigations in 2003 resulted in the declaration of the waste pit areas as a superfund site. The USGS and private consulting firms have evaluated subsurface water flow paths, faults & other groundwater-related features at this superfund site utilizing 2-D conductivity & 3-D electromagnetic (EM) surveys. The USGS employed conductivity to generate instantaneous 2-D profiles to evaluate shallow groundwater patterns. Porous regolith sediments, contaminated water & mine debris have high conductivity whereas bedrock is identified by its characteristic low conductivity readings. Consulting contractors integrated EM technology, magnetic & shallow well data to generate 3-D images of groundwater flow paths at given depths across the superfund site. In so doing several previously undetected faults were identified. Lighting strike data was integrated with the previously evaluated electrical and EM data to determine whether this form of natural-sourced EM data could complement and supplement the more traditional geophysical data described above. Several lightning attributes derived from 3-D lightning volumes were found to correlate to various features identified in the previous geophysical studies. Specifically, the attributes Apparent Resistivity, Apparent Permittivity, Peak Current & Tidal Gravity provided the deepest structural geological framework & provided insights into rock properties & earth tides. Most significantly, Peak Current showed remarkable coincidence with the preferred groundwater flow map identified by one of the contractors utilizing EM technology. This study demonstrates the utility of robust integrated EM technology applications for projects focused on hydrology, geohazards to dams, levees, and structures, as well as mineral and hydrocarbon exploration.

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.

Mammographic and Ultrasonographic Findings of the Chemoport Insertion Site

International Nuclear Information System (INIS)

Kim, Seun Jung; Kang, Bong Joo; Cha, Eun Suk; Park, Hye Jung; Kim, Sung Hun; Choi, Jae Jeong; Lee, Ji Hye

2010-01-01

To describe mammographic and ultrasonographic findings of previous chemoport insertion sites. We included patients who had abnormal findings at chemoport insertion sites on mammography and ultrasonography from 224 patients who underwent chemoport insertion and breast imaging at our institution between January, 2005, and December, 2007. Abnormal findings were identified in 16 mammographies and 14 ultrasonographies in 10 patients. The mean age was 50.9 years and the age range was from 44 to 67 years. Abnormal findings on mammography and ultrasonography were retrospectively analyzed according to ACR/BI-RADS. All cases were followed up with imaging studies for 2 years to confirm changes after chemoport insertion. Of the abnormal findings identified on mammography, focal asymmetry (7/16) was the most common. Other abnormal findings included mass (6/16), skin retraction (2/16), residual chemoport tip (1/16), and trabecular thickening (1/16). Of the abnormal findings seen on ultrasonography, skin thickening (12/14) was the most common. Other abnormal findings included mass (5/14), diffuse increased echogenicity of subcutaneous tissue (1/14), and a localized skin nodule (1/14). Abnormal findings on mammography and ultrasonography were located in the upper outer quadrant in 5 patients, upper inner quadrant in 3 patients, and mid upper portion in 1 patient. In 1 patient, the abnormal finding was only identified in the mediolateral oblique view of her mammography. Radiologists should be aware of potential abnormal findings on mammography and ultrasonography following chemoport insertion. In particular, ultrasonography is a very useful modality for detecting skin complications after chemoport insertion

Bedrock transport properties. Preliminary site description Simpevarp subarea - version 1.2

Energy Technology Data Exchange (ETDEWEB)

Byegaard, Johan; Gustavsson, Eva [Geosigma AB, Uppsala (Sweden); Tullborg, Eva-Lena [Terralogica AB, Graabo (Sweden); Berglund, Sten [Swedish Nuclear Fuel and Waste Management Co., Stockholm (Sweden)

2005-06-01

This report presents the site descriptive model of transport properties developed as a part of the Simpevarp 1.2 site description. The main parameters included in the model, referred to as retardation parameters, are the matrix porosity and diffusivity, and the matrix sorption coefficient K{sub d}. The model is based on the presently available site investigation data, mainly obtained from laboratory investigations of core samples from boreholes within the Simpevarp subarea, and on data from previous studies at the Aespoe Hard Rock Laboratory (Aespoe HRL). The modelling is a first attempt, based on limited data, to obtain a description of the retardation parameters. Further refinement of the model is foreseen when more data becomes available for future versions of the Simpevarp site description. The modelling work included descriptions of rock mass geology, the fractures and deformation zones, the hydrogeochemistry and also the available results from the site specific porosity, sorption and diffusivity measurements. The description of the transport related aspects of the data and models presented by other modelling disciplines is an important part of the transport description. In accordance with the strategy for the modelling of transport properties, the results are presented as a 'retardation model', in which a summary of the transport data for the different geological compartments is given. Concerning the major rock types, Aevroe granite, quartz monzodiorite and fine-grained dioritoid are identified as the rock types dominating the main rock domains identified and described in the site descriptive model of the bedrock geology. However, relatively large parts of the rock consist of altered rock and the open fracture frequency appears to be correlated to the altered/oxidised parts of the rock. This implies that transport in open fractures to a large extent takes place in the altered parts of the rock. For the fracture mineralogy, it is found that the

Defining the plasticity of transcription factor binding sites by Deconstructing DNA consensus sequences: the PhoP-binding sites among gamma/enterobacteria.

Directory of Open Access Journals (Sweden)

Oscar Harari

2010-07-01

Full Text Available Transcriptional regulators recognize specific DNA sequences. Because these sequences are embedded in the background of genomic DNA, it is hard to identify the key cis-regulatory elements that determine disparate patterns of gene expression. The detection of the intra- and inter-species differences among these sequences is crucial for understanding the molecular basis of both differential gene expression and evolution. Here, we address this problem by investigating the target promoters controlled by the DNA-binding PhoP protein, which governs virulence and Mg(2+ homeostasis in several bacterial species. PhoP is particularly interesting; it is highly conserved in different gamma/enterobacteria, regulating not only ancestral genes but also governing the expression of dozens of horizontally acquired genes that differ from species to species. Our approach consists of decomposing the DNA binding site sequences for a given regulator into families of motifs (i.e., termed submotifs using a machine learning method inspired by the "Divide & Conquer" strategy. By partitioning a motif into sub-patterns, computational advantages for classification were produced, resulting in the discovery of new members of a regulon, and alleviating the problem of distinguishing functional sites in chromatin immunoprecipitation and DNA microarray genome-wide analysis. Moreover, we found that certain partitions were useful in revealing biological properties of binding site sequences, including modular gains and losses of PhoP binding sites through evolutionary turnover events, as well as conservation in distant species. The high conservation of PhoP submotifs within gamma/enterobacteria, as well as the regulatory protein that recognizes them, suggests that the major cause of divergence between related species is not due to the binding sites, as was previously suggested for other regulators. Instead, the divergence may be attributed to the fast evolution of orthologous target

Seismic activity parameters of the Finnish potential repository sites

International Nuclear Information System (INIS)

Saari, J.

2000-10-01

Posiva Oy has started a project for estimating the possible earthquake induced rock movements on the deposition holes containing canisters of spent nuclear fuel. These estimates will be made for the four investigation sites, Romuvaara, Kivetty, Olkiluoto and Haestholmen. This study deals with the current and future seismicity associated with the above mentioned sites. Seismic belts that participate the seismic behaviour of the studied sites have been identified and the magnitude-frequency distributions of these belts have been estimated. The seismic activity parameters of the sites have been deduced from the characteristics of the seismic belts in order to forecast the seismicity during the next 100,000 years. The report discusses the possible earthquakes induced by future glaciation. The seismic interpretation seems to indicate that the previous postglacial faults in Finnish Lapland have been generated in compressional environment. The orientation of the rather uniform compression has been NW-SE, which coincide with the current stress field. It seems that, although the impact of postglacial crustal rebound must have been significant, the impact of plate tectonics has been dominant. A major assumption of this study has been that future seismicity will generally resemble the current seismicity. However, when the postglacial seismicity is concerned, the magnitude-frequency distribution is likely different and the expected maximum magnitude will be higher. Maximum magnitudes of future postglacial earthquakes have been approximated by strain release examinations. Seismicity has been examined within the framework of the lineament maps, in order to associate the future significant earthquakes with active fault zones in the vicinity of the potential repository sites. (orig.)

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

Review of institutional and socioeconomic issues for radioactive waste repository siting

International Nuclear Information System (INIS)

Copenhaver, E.D.; Carnes, S.A.; Soderstrom, E.J.; Sorensen, J.H.; Peelle, E.; Bjornstad, D.J.

1982-01-01

In recent years, the importance of social and institutional issues in the siting of radioactive waste management repositories has been recognized. This study deals with the possibility of using incentives to assist in siting repositories and outlines some of their uses, limitations, and preconditions. Limited survey data and other studies indicate that incentives may help encourage people to formulate positive positions on radioactive waste repositories. In an overall siting strategy, incentives are just one part of a structured process involving the creation of a mutually acceptable set of arrangements that make certain guarantees and confer certain benefits in exchange for the acceptance of the proposed facility. Because the range of needs to be fulfilled is varied, a package of incentives is likely to be more acceptable than any one single incentive. The purpose of incentives is to encourage local approval by minimizing and redressing costs and providing missing benefits. Most previous discussions of incentives have emphasized mitigation mechanisms only. This paper also identifies compensation, incentives, and criteria by which compensation or an incentive system can be evaluated. The study provides the means by which incentives can be identified, assessed, negotiated, and implemented by affected parties and attempts to show where incentives fit into an overall siting strategy by developing a classification scheme and an analytical framework that capture: (1) the preconditions that must exist before any incentive system can be considered; (2) the objective features of an incentive; such as adequacy and ease of administration; (3) community perceptions of an incentive, such as interpretability and relevance; and (4) the consequences of implementing an incentive, such as distributional effects and conflict and consensus. 38 references, 1 figure, 2 tables

Site-level progression of periodontal disease during a follow-up period

Science.gov (United States)

Morozumi, Toshiya; Nakagawa, Taneaki; Sugaya, Tsutomu; Kawanami, Masamitsu; Suzuki, Fumihiko; Takahashi, Keiso; Abe, Yuzo; Sato, Soh; Makino-Oi, Asako; Saito, Atsushi; Takano, Satomi; Minabe, Masato; Nakayama, Yohei; Ogata, Yorimasa; Kobayashi, Hiroaki; Izumi, Yuichi; Sugano, Naoyuki; Ito, Koichi; Sekino, Satoshi; Numabe, Yukihiro; Fukaya, Chie; Yoshinari, Nobuo; Fukuda, Mitsuo; Noguchi, Toshihide; Kono, Tomoo; Umeda, Makoto; Fujise, Osamu; Nishimura, Fusanori; Yoshimura, Atsutoshi; Hara, Yoshitaka; Nakamura, Toshiaki; Noguchi, Kazuyuki; Kakuta, Erika; Hanada, Nobuhiro; Takashiba, Shogo; Amitani, Yasuharu; Yoshie, Hiromasa

2017-01-01

Periodontal disease is assessed and its progression is determined via observations on a site-by-site basis. Periodontal data are complex and structured in multiple levels; thus, applying a summary statistical approach (i.e., the mean) for site-level evaluations results in loss of information. Previous studies have shown the availability of mixed effects modeling. However, clinically beneficial information on the progression of periodontal disease during the follow-up period is not available. We conducted a multicenter prospective cohort study. Using mixed effects modeling, we analyzed 18,834 sites distributed on 3,139 teeth in 124 patients, and data were collected 5 times over a 24-month follow-up period. The change in the clinical attachment level (CAL) was used as the outcome variable. The CAL at baseline was an important determinant of the CAL changes, which varied widely according to the tooth surface. The salivary levels of periodontal pathogens, such as Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans, were affected by CAL progression. “Linear”- and “burst”-type patterns of CAL progression occurred simultaneously within the same patient. More than half of the teeth that presented burst-type progression sites also presented linear-type progression sites, and most of the progressions were of the linear type. Maxillary premolars and anterior teeth tended to show burst-type progression. The parameters identified in this study may guide practitioners in determining the type and extent of treatment needed at the site and patient levels. In addition, these results show that prior hypotheses concerning "burst" and "linear" theories are not valid. PMID:29206238

Does Infection Site Matter? A Systematic Review of Infection Site Mortality in Sepsis.

Science.gov (United States)

Motzkus, Christine A; Luckmann, Roger

2017-09-01

Sepsis treatment protocols emphasize source control with empiric antibiotics and fluid resuscitation. Previous reviews have examined the impact of infection site and specific pathogens on mortality from sepsis; however, no recent review has addressed the infection site. This review focuses on the impact of infection site on hospital mortality among patients with sepsis. The PubMed database was searched for articles from 2001 to 2014. Studies were eligible if they included (1) one or more statistical models with hospital mortality as the outcome and considered infection site for inclusion in the model and (2) adult patients with sepsis, severe sepsis, or septic shock. Data abstracted included stage of sepsis, infection site, and raw and adjusted effect estimates. Nineteen studies were included. Infection sites most studied included respiratory (n = 19), abdominal (n = 19), genitourinary (n = 18), and skin and soft tissue infections (n = 11). Several studies found a statistically significant lower mortality risk for genitourinary infections on hospital mortality when compared to respiratory infections. Based on studies included in this review, the impact of infection site in patients with sepsis on hospital mortality could not be reliably estimated. Misclassification among infections and disease states remains a serious possibility in studies on this topic.

Site locality identification study: Hanford Site. Volume I. Methodology, guidelines, and screening

International Nuclear Information System (INIS)

1980-07-01

Presented in this report are the results of the site locality identification study for the Hanford Site using a screening process. To enable evaluation of the entire Hanford Site, the screening process was applied to a somewhat larger area; i.e., the Pasco Basin. The study consisted of a series of screening steps that progressively focused on smaller areas which are within the Hanford Site and which had a higher potential for containing suitable repository sites for nuclear waste than the areas not included for further study. Five site localities, designated H-1, H-2, H-3, H-4, H-5 (Figure A), varying in size from approximately 10 to 50 square miles, were identified on the Hanford Site. It is anticipated that each site locality may contain one or more candidate sites suitable for a nuclear waste repository. The site locality identification study began with definition of objectives and the development of guidelines for screening. Three objectives were defined: (1) maximize public health and safety; (2) minimize adverse environmental and socioeconomic impacts; and (3) minimize system costs. The screening guidelines have numerical values that provided the basis for the successive reduction of the area under study and to focus on smaller areas that had a higher likelihood of containing suitable sites

Nevada Test Site Environmental Report 2008 Summary

Energy Technology Data Exchange (ETDEWEB)

Cathy A. Wills

2009-09-01

The Nevada Test Site Environmental Report (NTSER) 2008 was prepared to meet the information needs of the public and the requirements and guidelines of the U.S. Department of Energy (DOE) for annual site environmental reports. It was prepared by National Security Technologies, LLC (NSTec), for the U.S. Department of Energy, National Nuclear Security Administration Nevada Site Office (NNSA/NSO). This and previous years’ NTSERs are posted on the NNSA/NSO website at http://www.nv.doe.gov/library/publications/aser.aspx.

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.

An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins.

Directory of Open Access Journals (Sweden)

Angela F Harper

2017-02-01

Full Text Available Peroxiredoxins (Prxs or Prdxs are a large protein superfamily of antioxidant enzymes that rapidly detoxify damaging peroxides and/or affect signal transduction and, thus, have roles in proliferation, differentiation, and apoptosis. Prx superfamily members are widespread across phylogeny and multiple methods have been developed to classify them. Here we present an updated atlas of the Prx superfamily identified using a novel method called MISST (Multi-level Iterative Sequence Searching Technique. MISST is an iterative search process developed to be both agglomerative, to add sequences containing similar functional site features, and divisive, to split groups when functional site features suggest distinct functionally-relevant clusters. Superfamily members need not be identified initially-MISST begins with a minimal representative set of known structures and searches GenBank iteratively. Further, the method's novelty lies in the manner in which isofunctional groups are selected; rather than use a single or shifting threshold to identify clusters, the groups are deemed isofunctional when they pass a self-identification criterion, such that the group identifies itself and nothing else in a search of GenBank. The method was preliminarily validated on the Prxs, as the Prxs presented challenges of both agglomeration and division. For example, previous sequence analysis clustered the Prx functional families Prx1 and Prx6 into one group. Subsequent expert analysis clearly identified Prx6 as a distinct functionally relevant group. The MISST process distinguishes these two closely related, though functionally distinct, families. Through MISST search iterations, over 38,000 Prx sequences were identified, which the method divided into six isofunctional clusters, consistent with previous expert analysis. The results represent the most complete computational functional analysis of proteins comprising the Prx superfamily. The feasibility of this novel method is

High-frequency acoustic imaging of L Lake Phase 4 [Savannah River Site, South Carolina

International Nuclear Information System (INIS)

Dunn, D.L.; Sjostrom, Keith J.; Leist, Rodney L.; Harmon, Thomas S. Jr.

1997-01-01

The objective of the seismic reflection and side scan sonar survey is to determine the location, aerial extent, and depth of burial pits situated along the reservoir bottom of L Lake, Savannah River Site, SC. The results will be used in the overall characterization of L Lake by providing continuous profile line coverage of the bottom and subbottom sediment structure along the entire length of the project area. The results are also intended to supplement previous scientific information obtained from soil samples, aerial photography, and radiometric studies. Resultant information will be used as input for an Environmental Impact Statement of the site. Overall, the seismic reflection data will provide better descriptions of variations in the actual subbottom conditions and help identify the differing sediment layers. The side scan sonar will help identify the location of the burial pits and any other features on the bottom of the reservoir. A 3.5 kiloHertz (kHz), high resolution subbottom profiling system and an EG and G Model 260 side scan sonar system were used to meet the primary objectives of the investigation

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.

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

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...

Multiple ETS family proteins regulate PF4 gene expression by binding to the same ETS binding site.

Directory of Open Access Journals (Sweden)

Yoshiaki Okada

Full Text Available In previous studies on the mechanism underlying megakaryocyte-specific gene expression, several ETS motifs were found in each megakaryocyte-specific gene promoter. Although these studies suggested that several ETS family proteins regulate megakaryocyte-specific gene expression, only a few ETS family proteins have been identified. Platelet factor 4 (PF4 is a megakaryocyte-specific gene and its promoter includes multiple ETS motifs. We had previously shown that ETS-1 binds to an ETS motif in the PF4 promoter. However, the functions of the other ETS motifs are still unclear. The goal of this study was to investigate a novel functional ETS motif in the PF4 promoter and identify proteins binding to the motif. In electrophoretic mobility shift assays and a chromatin immunoprecipitation assay, FLI-1, ELF-1, and GABP bound to the -51 ETS site. Expression of FLI-1, ELF-1, and GABP activated the PF4 promoter in HepG2 cells. Mutation of a -51 ETS site attenuated FLI-1-, ELF-1-, and GABP-mediated transactivation of the promoter. siRNA analysis demonstrated that FLI-1, ELF-1, and GABP regulate PF4 gene expression in HEL cells. Among these three proteins, only FLI-1 synergistically activated the promoter with GATA-1. In addition, only FLI-1 expression was increased during megakaryocytic differentiation. Finally, the importance of the -51 ETS site for the activation of the PF4 promoter during physiological megakaryocytic differentiation was confirmed by a novel reporter gene assay using in vitro ES cell differentiation system. Together, these data suggest that FLI-1, ELF-1, and GABP regulate PF4 gene expression through the -51 ETS site in megakaryocytes and implicate the differentiation stage-specific regulation of PF4 gene expression by multiple ETS factors.

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

New Reactor Siting in Finland, Hanhikivi Site in Pyhaejoki - STUK preliminary safety assessment

International Nuclear Information System (INIS)

Nevalainen, Janne

2013-01-01

STUK has performed a preliminary assessment of the Decision-in-Principle on the Fennovoima application. A variety of factors must be considered in the selection of a site, including effects of the site on the plant design and the effects of the plant on the site environment. These include external hazards, both natural and human-induced. Since this is a new site, an extensive siting process is followed, that can include an EIA. A site survey is performed to identify candidate sites, after investigating a large region and rejecting unsuitable sites. The remaining sites are then screened and compared on the basis of safety and other considerations to select one or more preferred sites. Natural hazards include geology, seismology, hydrology and meteorology. Offshore ice will be a particular hazard for this plant, since the site is on average only 1.5 m above sea level. The design basis earthquake corresponds to a return frequency of 100,000 years, with 50 % confidence. The existing sites in southern Finland used a design peak ground acceleration of 0.1 g with the ground response spectrum maximum at 10 Hz. The candidate sites in northern Finland will require a peak ground acceleration of 0.2 g with the ground response spectrum maximum at 25 Hz

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

Site description of Forsmark at completion of the site investigation phase. SDM-Site Forsmark

Energy Technology Data Exchange (ETDEWEB)

2008-12-15

The Swedish Nuclear Fuel and Waste Management Co., SKB, has undertaken site characterisation in two different areas, Forsmark and Laxemar-Simpevarp, in order to identify a suitable location for a geological repository of spent nuclear fuel according to the KBS-3 method. The site investigations have been conducted in campaigns, punctuated by data freezes. After each data freeze, the site data have been analysed and modelling has been carried out with the overall purpose to develop a site descriptive model (SDM). The site descriptive model is used by repository engineering to design the underground facility and to develop a repository layout adapted to the site. It is also essential for safety assessment, since the model is the only source for site-specific input. Another important use of the site descriptive model is in the environmental impact assessment. An SDM is an integrated model for geology, thermal properties, rock mechanics, hydrogeology, hydrogeochemistry, bedrock transport properties and a description of the surface system. The site descriptive model compiled in the current report, SDM-Site, presents an integrated understanding of the Forsmark area at the completion of the surface-based investigations, which were conducted at Forsmark during the period 2002 to 2007. It also provides a summary of the abundant underlying data and the discipline-specific models that support the site understanding. The description relies heavily on background reports that address, in particular, details in data analyses and modelling in the different disciplines. The Forsmark area is located in northern Uppland within the municipality of Oesthammar, about 120 km north of Stockholm. The candidate area for site investigation is located along the shoreline of Oeregrundsgrepen, within the north-western part of a major tectonic lens that formed between 1.87 and 1.85 billion years ago during the Svecokarelian orogeny. The candidate area is approximately 6 km long and 2 km wide. The

Site description of Laxemar at completion of the site investigation phase. SDM-Site Laxemar

Energy Technology Data Exchange (ETDEWEB)

2009-12-15

The Swedish Nuclear Fuel and Waste Management Company (SKB) has undertaken site characterisation in two different areas, Forsmark and Laxemar-Simpevarp, in order to identify a suitable location for a geological repository of spent nuclear fuel according to the KBS-3 method. The site investigations have been conducted in campaigns, punctuated by data freezes. After each data freeze, the site data have been analysed and modelling has been carried out with the overall purpose to develop a site descriptive model (SDM). The site descriptive model is used by repository engineering to design the underground facility and to develop a repository layout adapted to the site. It is also essential for safety assessment, since the SDM is the only source for site-specific input. Another important use of the site descriptive model is in the environmental impact assessment. An SDM is an integrated model of geology, thermal properties, rock mechanics, hydrogeology, hydrogeochemistry, bedrock transport properties and a description of the surface system. The site descriptive model compiled in the current report, SDM-Site Laxemar, presents an integrated understanding of the Laxemar-Simpevarp area (with special emphasis on the Laxemar subarea) at the completion of the surface-based investigations, which were conducted during the period 2002 to 2007. A summary is also provided of the abundant underlying data and the discipline specific models that support the site understanding. The description relies heavily on background reports that address, in particular, details of the data analyses and modelling of the different disciplines. The Laxemar-Simpevarp area is located in the province of Smaaland within the municipality of Oskarshamn, about 230 km south of Stockholm. The candidate area for site investigation is located along the shoreline of the strait of Kalmarsund, within a 1.8 billion year old suite of well preserved bedrock belonging to the Transscandinavian Igneous Belt formed during

Site description of Laxemar at completion of the site investigation phase. SDM-Site Laxemar

International Nuclear Information System (INIS)

2009-12-01

The Swedish Nuclear Fuel and Waste Management Company (SKB) has undertaken site characterisation in two different areas, Forsmark and Laxemar-Simpevarp, in order to identify a suitable location for a geological repository of spent nuclear fuel according to the KBS-3 method. The site investigations have been conducted in campaigns, punctuated by data freezes. After each data freeze, the site data have been analysed and modelling has been carried out with the overall purpose to develop a site descriptive model (SDM). The site descriptive model is used by repository engineering to design the underground facility and to develop a repository layout adapted to the site. It is also essential for safety assessment, since the SDM is the only source for site-specific input. Another important use of the site descriptive model is in the environmental impact assessment. An SDM is an integrated model of geology, thermal properties, rock mechanics, hydrogeology, hydrogeochemistry, bedrock transport properties and a description of the surface system. The site descriptive model compiled in the current report, SDM-Site Laxemar, presents an integrated understanding of the Laxemar-Simpevarp area (with special emphasis on the Laxemar subarea) at the completion of the surface-based investigations, which were conducted during the period 2002 to 2007. A summary is also provided of the abundant underlying data and the discipline specific models that support the site understanding. The description relies heavily on background reports that address, in particular, details of the data analyses and modelling of the different disciplines. The Laxemar-Simpevarp area is located in the province of Smaaland within the municipality of Oskarshamn, about 230 km south of Stockholm. The candidate area for site investigation is located along the shoreline of the strait of Kalmarsund, within a 1.8 billion year old suite of well preserved bedrock belonging to the Transscandinavian Igneous Belt formed during

Site description of Forsmark at completion of the site investigation phase. SDM-Site Forsmark

International Nuclear Information System (INIS)

2008-12-01

The Swedish Nuclear Fuel and Waste Management Co., SKB, has undertaken site characterisation in two different areas, Forsmark and Laxemar-Simpevarp, in order to identify a suitable location for a geological repository of spent nuclear fuel according to the KBS-3 method. The site investigations have been conducted in campaigns, punctuated by data freezes. After each data freeze, the site data have been analysed and modelling has been carried out with the overall purpose to develop a site descriptive model (SDM). The site descriptive model is used by repository engineering to design the underground facility and to develop a repository layout adapted to the site. It is also essential for safety assessment, since the model is the only source for site-specific input. Another important use of the site descriptive model is in the environmental impact assessment. An SDM is an integrated model for geology, thermal properties, rock mechanics, hydrogeology, hydrogeochemistry, bedrock transport properties and a description of the surface system. The site descriptive model compiled in the current report, SDM-Site, presents an integrated understanding of the Forsmark area at the completion of the surface-based investigations, which were conducted at Forsmark during the period 2002 to 2007. It also provides a summary of the abundant underlying data and the discipline-specific models that support the site understanding. The description relies heavily on background reports that address, in particular, details in data analyses and modelling in the different disciplines. The Forsmark area is located in northern Uppland within the municipality of Oesthammar, about 120 km north of Stockholm. The candidate area for site investigation is located along the shoreline of Oeregrundsgrepen, within the north-western part of a major tectonic lens that formed between 1.87 and 1.85 billion years ago during the Svecokarelian orogeny. The candidate area is approximately 6 km long and 2 km wide. The

California LLW disposal site development update: Ahead of milestone schedule

International Nuclear Information System (INIS)

Romano, S.A.; Gaynor, R.K.

1987-01-01

US Ecology has been designated by the State of California to locate, develop and operate a low-level radioactive waste disposal facility. In early 1986, the firm identified eighteen desert basins in southeastern California for siting consideration. Three candidate sites were selected for detailed field characterization work in February, 1987. A preferred site for licensing purposes will be identified in early 1988. California is currently ahead of the siting milestone schedule mandated by the Low-Level Radioactive Waste Policy Amendments Act. It is likely that a license application will be filed before the 1990 milestone date. This paper describes the process undertaken by US Ecology to identify three candidates sites for characterization, and the public involvement program supporting this decision. Future activities leading to final site development are also described

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.

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

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.``

The GridSite Web/Grid security system

International Nuclear Information System (INIS)

McNab, Andrew; Li Yibiao

2010-01-01

We present an overview of the current status of the GridSite toolkit, describing the security model for interactive and programmatic uses introduced in the last year. We discuss our experiences of implementing these internal changes and how they and previous rounds of improvements have been prompted by requirements from users and wider security trends in Grids (such as CSRF). Finally, we explain how these have improved the user experience of GridSite-based websites, and wider implications for portals and similar web/grid sites.

A dynamic system for ATLAS software installation on OSG grid sites

International Nuclear Information System (INIS)

Zhao, X; Maeno, T; Wenaus, T; Leuhring, F; Youssef, S; Brunelle, J; De Salvo, A; Thompson, A S

2010-01-01

A dynamic and reliable system for installing the ATLAS software releases on Grid sites is crucial to guarantee the timely and smooth start of ATLAS production and reduce its failure rate. In this paper, we discuss the issues encountered in the previous software installation system, and introduce the new approach, which is built upon the new development in the areas of the ATLAS workload management system (PanDA), and software package management system (pacman). It is also designed to integrate with the EGEE ATLAS software installation framework. In the new system, ATLAS software releases are packaged as pacball, a uniquely identifiable and reproducible self-installing data file. The distribution of pacballs to remote sites is managed by ATLAS data management system (DQ2) and PanDA server. The installation on remote sites is automatically triggered by the PanDA pilot jobs. The installation job payload connects to a central ATLAS software installation portal, making the information of installation status easily accessible across OSG and EGEE Grids. The issues encountered in running the new system in production, and our future plan for improvement, will also be discussed.

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.

Construction of Site Risk Model using Individual Unit Risk Model in a NPP Site

Energy Technology Data Exchange (ETDEWEB)

Lim, Ho Gon; Han, Sang Hoon [KAERI, Daejeon (Korea, Republic of)

2016-05-15

Since Fukushima accident, strong needs to estimate site risk has been increased to identify the possibility of re-occurrence of such a tremendous disaster and prevent such a disaster. Especially, in a site which has large fleet of nuclear power plants, reliable site risk assessment is very emergent to confirm the safety. In Korea, there are several nuclear power plant site which have more than 6 NPPs. In general, risk model of a NPP in terms of PSA is very complicated and furthermore, it is expected that the site risk model is more complex than that. In this paper, the method for constructing site risk model is proposed by using individual unit risk model. Procedure for the development of site damage (risk) model was proposed in the present paper. Since the site damage model is complicated in the sense of the scale of the system and dependency of the components of the system, conventional method may not be applicable in many side of the problem.

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.

Robotics and Automation Activities at the Savannah River Site: A Site Report for SUBWOG 39F

International Nuclear Information System (INIS)

Teese, G.D.

1995-01-01

The Savannah River Site has successfully used robots, teleoperators, and remote video to reduce exposure to ionizing radiation, improve worker safety, and improve the quality of operations. Previous reports have described the use of mobile teleoperators in coping with a high level liquid waste spill, the removal of highly contaminated equipment, and the inspection of nuclear reactor vessels. This report will cover recent applications at the Savannah River, as well as systems which SRS has delivered to other DOE site customers

Non-Invasive Seismic Methods for Earthquake Site Classification Applied to Ontario Bridge Sites

Science.gov (United States)

Bilson Darko, A.; Molnar, S.; Sadrekarimi, A.

2017-12-01

How a site responds to earthquake shaking and its corresponding damage is largely influenced by the underlying ground conditions through which it propagates. The effects of site conditions on propagating seismic waves can be predicted from measurements of the shear wave velocity (Vs) of the soil layer(s) and the impedance ratio between bedrock and soil. Currently the seismic design of new buildings and bridges (2015 Canadian building and bridge codes) requires determination of the time-averaged shear-wave velocity of the upper 30 metres (Vs30) of a given site. In this study, two in situ Vs profiling methods; Multichannel Analysis of Surface Waves (MASW) and Ambient Vibration Array (AVA) methods are used to determine Vs30 at chosen bridge sites in Ontario, Canada. Both active-source (MASW) and passive-source (AVA) surface wave methods are used at each bridge site to obtain Rayleigh-wave phase velocities over a wide frequency bandwidth. The dispersion curve is jointly inverted with each site's amplification function (microtremor horizontal-to-vertical spectral ratio) to obtain shear-wave velocity profile(s). We apply our non-invasive testing at three major infrastructure projects, e.g., five bridge sites along the Rt. Hon. Herb Gray Parkway in Windsor, Ontario. Our non-invasive testing is co-located with previous invasive testing, including Standard Penetration Test (SPT), Cone Penetration Test and downhole Vs data. Correlations between SPT blowcount and Vs are developed for the different soil types sampled at our Ontario bridge sites. A robust earthquake site classification procedure (reliable Vs30 estimates) for bridge sites across Ontario is evaluated from available combinations of invasive and non-invasive site characterization methods.

Hanford Site Waste Management Units Report

Energy Technology Data Exchange (ETDEWEB)

Shearer, Jeffrey P. [Hanford Site (HNF), Richland, WA (United States)

2012-02-29

The Hanford Site Waste Management Units Report (HSWMUR) has been created to meet the requirements of the Tri-Party Agreement (TPA) Action Plan, Section 3.5, which states: “The Hanford Site Waste Management Units Report shall be generated, in a format agreed upon by the Parties, as a calendar year report and issued annually by the DOE by the end of February of each year, and posted electronically for regulator and public access. This report shall reflect all changes made in waste management unit status during the previous year.” This February 2012 version of the HSWMUR contains a comprehensive inventory of the 3389 sites and 540 subsites in the Waste Information Data System (WIDS). The information for each site contains a description of each unit and the waste it contains, where applicable. The WIDS database provides additional information concerning the sites contained in this report and is maintained with daily changes to these sites.

Hanford Site Waste Management Units Report

Energy Technology Data Exchange (ETDEWEB)

Shearer, Jeffrey P. [Hanford Site (HNF), Richland, WA (United States)

2013-02-13

The Hanford Site Waste Management Units Report (HSWMUR) has been created to meet the requirements of the Tri-Party Agreement (TPA) Action Plan, Section 3.5, which states: “The Hanford Site Waste Management Units Report shall be generated, in a format agreed upon by the Parties, as a calendar year report and issued annually by the DOE by the end of February of each year, and posted electronically for regulator and public access. This report shall reflect all changes made in waste management unit status during the previous year.” This February 2013 version of the HSWMUR contains a comprehensive inventory of the 3427 sites and 564 subsites in the Waste Information Data System (WIDS). The information for each site contains a description of each unit and the waste it contains, where applicable. The WIDS database provides additional information concerning the sites contained in this report and is maintained with daily changes to these sites.

Hanford Site Waste Management Units Report

Energy Technology Data Exchange (ETDEWEB)

Shearer, Jeffrey P. [Hanford Site (HNF), Richland, WA (United States)

2014-02-19

The Hanford Site Waste Management Units Report (HSWMUR) has been created to meet the requirements of the Tri-Party Agreement (TPA) Action Plan, Section 3.5, which states: “The Hanford Site Waste Management Units Report shall be generated, in a format agreed upon by the Parties, as a calendar year report and issued annually by the DOE by the end of February of each year, and posted electronically for regulator and public access. This report shall reflect all changes made in waste management unit status during the previous year.” This February 2013 version of the HSWMUR contains a comprehensive inventory of the 3438 sites and 569 subsites in the Waste Information Data System (WIDS). The information for each site contains a description of each unit and the waste it contains, where applicable. The WIDS database provides additional information concerning the sites contained in this report and is maintained with daily changes to these sites.

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.

Structural geology report: Spent Fuel Test - Climax Nevada Test Site

International Nuclear Information System (INIS)

Wilder, D.G.; Yow, J.L. Jr.

1984-10-01

We performed underground mapping and core logging in the Climax Stock, a granitic intrusive at the Nevada Test Site, as part of a major field test to determine the feasibility of using granitic or crystalline rock for the underground storage of spent fuel from a nuclear reactor. This mapping and logging identified more than 2500 fractures, over 1500 of which were described in enough detail to allow statistical analyses and orientation studies to be performed. We identified eight joint sets, three major shear sets, and a fault zone within the Spent Fuel Test - Climax (SFT-C) portion of the Stock. Joint sets identified within the SFT-C and elsewhere in the Stock correlated well. The orientations of joint sets identified by other investigators were consistent with our findings, indicating that the joint sets are persistent and have a relatively uniform orientation throughout a major portion of the Stock. The one joint set not seen elsewhere in the Stock is healed and the wall rock is altered, implying that healed joints were not included in the mapping criteria used by other investigators. The shear sets were distinguished from the joint sets by virtue of crushed minerals, continuous clay infilling, and other evidences of shearing, and from faults by the lack of offsetting. Previous investigators working mainly in the Pile Driver Drifts identified two of the shear sets. The third set, being nearly parallel to these Drifts had not been identified previously. The fault zone identified at the far (Receiving Room) end of the project is oriented approximately N45 0 E-75 0 SE, similar to both the Boundary and Shaft Station Faults. We have, therefore, concluded that the Receiving Room Fault is one of a series of normal faults that occur within the Climax Stock and that are possibly related, in both age and genesis, to the Boundary Fault. 52 refs., 26 figs., 11 tabs

Waste site grouping for 200 Areas soil investigations

International Nuclear Information System (INIS)

1997-01-01

The purpose of this document is to identify logical waste site groups for characterization based on criteria established in the 200 Areas Soil Remediation Strategy (DOE-RL 1996a). Specific objectives of the document include the following: finalize waste site groups based on the approach and preliminary groupings identified in the 200 Areas Soil Remediation Strategy; prioritize the waste site groups based on criteria developed in the 200 Areas Soil Remediation Strategy; select representative site(s) that best represents typical and worse-case conditions for each waste group; develop conceptual models for each waste group. This document will serve as a technical baseline for implementing the 200 Areas Soil Remediation Strategy. The intent of the document is to provide a framework, based on waste site groups, for organizing soil characterization efforts in the 200 Areas and to present initial conceptual models

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

Microgravity survey of the Oak Ridge K-25 Site, Oak Ridge, Tennessee

International Nuclear Information System (INIS)

Kaufmann, R.D.

1996-05-01

Karst features are known to exist within the carbonate bedrock of the Oak Ridge K-25 Site and may play an important role in groundwater flow and contaminant migration. This report discusses the results of a microgravity survey of the Oak Ridge K-25 Site. The main objective of the survey is to identify areas containing bedrock cavities. Secondary objectives included correlating the observed gravity to the geology and to variations in overburden thickness. The analysis includes 11 profile lines that are oriented perpendicular to the geologic strike and major structures throughout the K-25 Site. The profile lines are modeled in an effort to relate gravity anomalies to karst features such as concentrations of mud-filled cavities. Regolith thickness and density data provided by boreholes constrain the models. Areally distributed points are added to the profile lines to produce a gravity contour map of the site. In addition, data from the K-901 area are combined with data from previous surveys to produce a high resolution map of that site. The K-25 Site is located in an area of folded and faulted sedimentary rocks within the Appalachian Valley and Ridge physiographic province. Paleozoic age rocks of the Rome Formation, Knox Group, and Chickamauga Supergroup underlie the K-25 Site and contain structures that include the Whiteoak Mountain Fault, the K-25 Fault, a syncline, and an anticline. The mapped locations of the rock units and complex structures are currently derived from outcrop and well log analysis

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....

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.

Identifying mechanisms that structure ecological communities by snapping model parameters to empirically observed tradeoffs.

Science.gov (United States)

Thomas Clark, Adam; Lehman, Clarence; Tilman, David

2018-04-01

Theory predicts that interspecific tradeoffs are primary determinants of coexistence and community composition. Using information from empirically observed tradeoffs to augment the parametrisation of mechanism-based models should therefore improve model predictions, provided that tradeoffs and mechanisms are chosen correctly. We developed and tested such a model for 35 grassland plant species using monoculture measurements of three species characteristics related to nitrogen uptake and retention, which previous experiments indicate as important at our site. Matching classical theoretical expectations, these characteristics defined a distinct tradeoff surface, and models parameterised with these characteristics closely matched observations from experimental multi-species mixtures. Importantly, predictions improved significantly when we incorporated information from tradeoffs by 'snapping' characteristics to the nearest location on the tradeoff surface, suggesting that the tradeoffs and mechanisms we identify are important determinants of local community structure. This 'snapping' method could therefore constitute a broadly applicable test for identifying influential tradeoffs and mechanisms. © 2018 The Authors. Ecology Letters published by CNRS and John Wiley & Sons Ltd.

Current net ecosystem exchange of CO2 in a young mixed forest: any heritage from the previous ecosystem?

Science.gov (United States)

Violette, Aurélie; Heinesch, Bernard; Erpicum, Michel; Carnol, Monique; Aubinet, Marc; François, Louis

2013-04-01

For 15 years, networks of flux towers have been developed to determine accurate carbon balance with the eddy-covariance method and determine if forests are sink or source of carbon. However, for prediction of the evolution of carbon cycle and climate, major uncertainties remain on the ecosystem respiration (Reco, which includes the respiration of above ground part of trees, roots respiration and mineralization of the soil organic matter), the gross primary productivity (GPP) and their difference, the net ecosystem exchange (NEE) of forests. These uncertainties are consequences of spatial and inter-annual variability, driven by previous and current climatic conditions, as well as by the particular history of the site (management, diseases, etc.). In this study we focus on the carbon cycle in two mixed forests in the Belgian Ardennes. The first site, Vielsalm, is a mature stand mostly composed of beeches (Fagus sylvatica) and douglas fir (Pseudotsuga menziesii) from 80 to 100 years old. The second site, La Robinette, was covered before 1995 with spruces. After an important windfall and a clear cutting, the site was replanted, between 1995 and 2000, with spruces (Piceas abies) and deciduous species (mostly Betula pendula, Aulnus glutinosa and Salix aurita). The challenge here is to highlight how initial conditions can influence the current behavior of the carbon cycle in a growing stand compared to a mature one, where initial conditions are supposed to be forgotten. A modeling approach suits particularly well for sensitivity tests and estimation of the temporal lag between an event and the ecosystem response. We use the forest ecosystem model ASPECTS (Rasse et al., Ecological Modelling 141, 35-52, 2001). This model predicts long-term forest growth by calculating, over time, hourly NEE. It was developed and already validated on the Vielsalm forest. Modelling results are confronted to eddy-covariance data on both sites from 2006 to 2011. The main difference between both

Environmental Assessment for the off-site commercial cleaning of lead and asbestos contaminated laundry from the Savannah River Site

International Nuclear Information System (INIS)

1995-12-01

This Environmental Assessment (EA) has been prepared by the Department of Energy (DOE) to assess the potential environmental impacts of off-site commercial cleaning of lead and asbestos contaminated laundry generated at the Savannah River Site (SRS), located near Aiken, South Carolina. The proposed action constitutes an addition to the already-implemented action of sending controlled and routine SRS laundry to an off-site commercial facility for cleaning. This already-implemented action was evaluated in a previous EA (i.e., DOE/EA-0990; DOE, 1994) prepared under the National Environmental Policy Act of 1969 (NEPA)

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...

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...

The Effect of Top-Level Domains and Advertisements on Health Web Site Credibility

Science.gov (United States)

Wang, Zuoming; Loh, Tracy

2004-01-01

Background Concerns over health information on the Internet have generated efforts to enhance credibility markers; yet how users actually assess the credibility of online health information is largely unknown. Objective This study set out to (1) establish a parsimonious and valid questionnaire instrument to measure credibility of Internet health information by drawing on various previous measures of source, news, and other credibility scales; and (2) to identify the effects of Web-site domains and advertising on credibility perceptions. Methods Respondents (N = 156) examined one of 12 Web-site mock-ups and completed credibility scales in a 3 x 2 x 2 between-subjects experimental design. Factor analysis and validity checks were used for item reduction, and analysis of variance was employed for hypothesis testing of Web-site features' effects. Results In an attempt to construct a credibility instrument, three dimensions of credibility (safety, trustworthiness, and dynamism) were retained, reflecting traditional credibility sub-themes, but composed of items from disparate sources. When testing the effect of the presence or absence of advertising on a Web site on credibility, we found that this depends on the site's domain, with a trend for advertisements having deleterious effects on the credibility of sites with .org domain, but positive effects on sites with .com or .edu domains. Conclusions Health-information Web-site providers should select domains purposefully when they can, especially if they must accept on-site advertising. Credibility perceptions may not be invariant or stable, but rather are sensitive to topic and context. Future research may employ these findings in order to compare other forms of health-information delivery to optimal Web-site features. PMID:15471750

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.

A Conserved Target Site in HIV-1 Gag RNA is Accessible to Inhibition by Both an HDV Ribozyme and a Short Hairpin RNA

Directory of Open Access Journals (Sweden)

Robert J Scarborough

2014-01-01

Full Text Available Antisense-based molecules targeting HIV-1 RNA have the potential to be used as part of gene or drug therapy to treat HIV-1 infection. In this study, HIV-1 RNA was screened to identify more conserved and accessible target sites for ribozymes based on the hepatitis delta virus motif. Using a quantitative screen for effects on HIV-1 production, we identified a ribozyme targeting a highly conserved site in the Gag coding sequence with improved inhibitory potential compared to our previously described candidates targeting the overlapping Tat/Rev coding sequence. We also demonstrate that this target site is highly accessible to short hairpin directed RNA interference, suggesting that it may be available for the binding of antisense RNAs with different modes of action. We provide evidence that this target site is structurally conserved in diverse viral strains and that it is sufficiently different from the human transcriptome to limit off-target effects from antisense therapies. We also show that the modified hepatitis delta virus ribozyme is more sensitive to a mismatch in its target site compared to the short hairpin RNA. Overall, our results validate the potential of a new target site in HIV-1 RNA to be used for the development of antisense therapies.

Human Splice-Site Prediction with Deep Neural Networks.

Science.gov (United States)

Naito, Tatsuhiko

2018-04-18

Accurate splice-site prediction is essential to delineate gene structures from sequence data. Several computational techniques have been applied to create a system to predict canonical splice sites. For classification tasks, deep neural networks (DNNs) have achieved record-breaking results and often outperformed other supervised learning techniques. In this study, a new method of splice-site prediction using DNNs was proposed. The proposed system receives an input sequence data and returns an answer as to whether it is splice site. The length of input is 140 nucleotides, with the consensus sequence (i.e., "GT" and "AG" for the donor and acceptor sites, respectively) in the middle. Each input sequence model is applied to the pretrained DNN model that determines the probability that an input is a splice site. The model consists of convolutional layers and bidirectional long short-term memory network layers. The pretraining and validation were conducted using the data set tested in previously reported methods. The performance evaluation results showed that the proposed method can outperform the previous methods. In addition, the pattern learned by the DNNs was visualized as position frequency matrices (PFMs). Some of PFMs were very similar to the consensus sequence. The trained DNN model and the brief source code for the prediction system are uploaded. Further improvement will be achieved following the further development of DNNs.

Multi-criteria ranking and receptor modelling of airborne fine particles at three sites in the Pearl River Delta region of China.

Science.gov (United States)

Friend, Adrian J; Ayoko, Godwin A; Guo, Hai

2011-01-15

The multi-criteria decision making methods, Preference Ranking Organization METHods for Enrichment Evaluation (PROMETHEE) and Graphical Analysis for Interactive Assistance (GAIA), and the two-way Positive Matrix Factorization (PMF) receptor model were applied to airborne fine particle compositional data collected at three sites in Hong Kong during two monitoring campaigns held from November 2000 to October 2001 and November 2004 to October 2005. PROMETHEE/GAIA indicated that the three sites were worse during the later monitoring campaign, and that the order of the air quality at the sites during each campaign was: rural site>urban site>roadside site. The PMF analysis on the other hand, identified 6 common sources at all of the sites (diesel vehicle, fresh sea salt, secondary sulphate, soil, aged sea salt and oil combustion) which accounted for approximately 68.8±8.7% of the fine particle mass at the sites. In addition, road dust, gasoline vehicle, biomass burning, secondary nitrate, and metal processing were identified at some of the sites. Secondary sulphate was found to be the highest contributor to the fine particle mass at the rural and urban sites with vehicle emission as a high contributor to the roadside site. The PMF results are broadly similar to those obtained in a previous analysis by PCA/APCS. However, the PMF analysis resolved more factors at each site than the PCA/APCS. In addition, the study demonstrated that combined results from multi-criteria decision making analysis and receptor modelling can provide more detailed information that can be used to formulate the scientific basis for mitigating air pollution in the region. Copyright © 2010 Elsevier B.V. All rights reserved.

Surgical site infection rates following laparoscopic urological procedures.

Science.gov (United States)

George, Arvin K; Srinivasan, Arun K; Cho, Jane; Sadek, Mostafa A; Kavoussi, Louis R

2011-04-01

Surgical site infections have been categorized by the Centers for Medicare and Medicaid Services as "never events". The incidence of surgical site infection following laparoscopic urological surgery and its risk factors are poorly defined. We evaluated surgical site infection following urological laparoscopic surgery and identified possible factors that may influence occurrence. Patients who underwent transperitoneal laparoscopic procedures during a 4-year period by a single laparoscopic surgeon were retrospectively reviewed. Surgical site infections were identified postoperatively and defined using the Centers for Disease Control criteria. Clinical parameters, comorbidities, smoking history, preoperative urinalysis and culture results as well as operative data were analyzed. Nonparametric testing using the Mann-Whitney U test, multivariable logistic regression and Spearman's rank correlation coefficient were used for data analysis. In 556 patients undergoing urological laparoscopic procedures 14 surgical site infections (2.5%) were identified at mean postoperative day 21.5. Of the 14 surgical site infections 10 (71.4%) were located at a specimen extraction site. Operative time, procedure type and increasing body mass index were significantly associated with the occurrence of surgical site infections (p = 0.007, p = 0.019, p = 0.038, respectively), whereas history of diabetes mellitus (p = 0.071) and intraoperative transfusion (p = 0.053) were found to trend toward significance. Age, gender, positive urine culture, steroid use, procedure type and smoking history were not significantly associated with surgical site infection. Body mass index and operative time remained significant predictors of surgical site infection on multivariate logistic regression analysis. Surgical site infection is an infrequent complication following laparoscopic surgery with the majority occurring at the specimen extraction site. Infection is associated with prolonged operative time and

Comparison of the Radionuclides Dispersion at the UAE Barakah Site with that at the ROK Shin-Kori Site - Comparison of the radionuclides dispersion in Barakah site with that in Shin-Kori site

Energy Technology Data Exchange (ETDEWEB)

Kim, Sung-yeop; Lee, Kun Jai; Chang, Soon Heung [Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 305-701 (Korea, Republic of); Beeley, Philip A. [Khalifa University of Science, Technology and Research, P.O. Box 127788, Abu Dhabi (United Arab Emirates)

2014-07-01

In order to understand the characteristics of atmospheric dispersion of radionuclides in the desert environment of Barakah site in UAE, comparison research with the results of other environments could be an appropriate way to facilitate it. Shin-Kori site is the proper comparison target because same reactor type of APR1400 with that in Barakah site is under construction. Hypothetical accident scenario was considered and accident source term which had been developed in previous research has been applied as releasing source. After reviewing several computation codes, ADMS5 has been selected as an atmospheric dispersion modeling tool which is installing advanced Gaussian plum model and plentiful options. The climate data of both Barakah and Shin-Kori were acquired and the environments of both sites have been simulated considering wind speed, wind direction, temperature, humidity, ground surface roughness and etc. Near field final human doses on the maps have been schematised regarding statistical meteorological data of both sites and dose conversion factors from the publications of ICRP and federal guidance report of EPA. The results of this research are expected to enhance the understanding about differences between two environments which have same reactor type and to improve the comprehension of desert environment of Barakah site as well. Applying different dose conversion factors to Barakah site considering the desert biosphere could be further study to obtain more accurate results. (authors)

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.

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

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

Differences of Perceived Image Generated through the Web Site: Empirical Evidence Obtained in Spanish Destinations

Science.gov (United States)

Blazquez-Resino, Juan J.; Muro-Rodriguez, Ana I.; Perez-Jimenez, Israel R.

2016-01-01

In this paper, a study of the perceived destination image created by promotional Web Pages is expounded in an attempt to identify their differences as generators of destination image in the consumers' mind. Specifically, it seeks to analyse whether the web sites of different Spanish regions improve the image that consumers have of the destination, identifying their main dimensions and analysing its effect on satisfaction and intentions of the future behavior of potential visitors. To achieve these objectives and verify the hypotheses, a laboratory experiment was performed, where it was determined what changes are produced in the tourist's previous image after browsing the tourist webs of three different regions. Moreover, it analyses the differences in the effect of the perceived image on satisfaction and potential visitors' future behavioral intentions. The results obtained enable us to identify differences in the composition of the perceived image according to the destination, while confirming the significant effect of different perceived image dimensions regarding satisfaction. The results allow managers to gain a better understanding of the effectiveness of their sites from a consumer perspective as well as suggestions to follow in order to achieve greater efficiency in their communication actions in order to improve the motivation of visitors to go to the destination. PMID:27933027

Differences of perceived image generated through the Web site: Empirical Evidence Obtained in Spanish Destinations

Directory of Open Access Journals (Sweden)

Juan Jose Blazquez-Resino

2016-11-01

Full Text Available In this paper, a study of the perceived destination image created by promotional Web Pages is expounded in an attempt to identify their differences as generators of destination image in the consumers’ mind. Specifically, it seeks to analyse whether the web sites of different Spanish regions improve the image that consumers have of the destination, identifying their main dimensions and analysing its effect on satisfaction and intentions of the future behaviour of potential visitors. To achieve these objectives and verify the hypotheses, a laboratory experiment was performed, where it was determined what changes are produced in the tourist´s previous image after browsing the tourist webs of three different regions. Moreover, it analyses the differences in the effect of the perceived image on satisfaction and potential visitors´ future behavioural intentions. The results obtained enable us to identify differences in the composition of the perceived image according to the destination, while confirming the significant effect of different perceived image dimensions regarding satisfaction. The results allow managers to gain a better understanding of the effectiveness of their sites from a consumer perspective as well as suggestions to follow in order to achieve greater efficiency in their communication actions in order to improve the motivation of visitors to go to the destination.

Nevada National Security Site Environmental Report 2013

Energy Technology Data Exchange (ETDEWEB)

Wills, C.

2014-09-09

This report was prepared to meet the information needs of the public and the requirements and guidelines of the U.S. Department of Energy (DOE) for annual site environmental reports. It was prepared by National Security Technologies, LLC (NSTec), for the U.S. Department of Energy, National Nuclear Security Administration Nevada Field Office (NNSA/NFO) (formerly designated as the Nevada Site Office [NNSA/NSO]). The new field office designation occurred in March 2013. Published reports cited in this 2013 report, therefore, may bear the name or authorship of NNSA/NSO. This and previous years’ reports, called Annual Site Environmental Reports (ASERs), Nevada Test Site Environmental Reports (NTSERs), and, beginning in 2010, Nevada National Security Site Environmental Reports (NNSSERs), are posted on the NNSA/NFO website at http://www.nv.energy.gov/library/publications/aser.aspx.

Exploiting protein flexibility to predict the location of allosteric sites

Directory of Open Access Journals (Sweden)

Panjkovich Alejandro

2012-10-01

Full Text Available Abstract Background Allostery is one of the most powerful and common ways of regulation of protein activity. However, for most allosteric proteins identified to date the mechanistic details of allosteric modulation are not yet well understood. Uncovering common mechanistic patterns underlying allostery would allow not only a better academic understanding of the phenomena, but it would also streamline the design of novel therapeutic solutions. This relatively unexplored therapeutic potential and the putative advantages of allosteric drugs over classical active-site inhibitors fuel the attention allosteric-drug research is receiving at present. A first step to harness the regulatory potential and versatility of allosteric sites, in the context of drug-discovery and design, would be to detect or predict their presence and location. In this article, we describe a simple computational approach, based on the effect allosteric ligands exert on protein flexibility upon binding, to predict the existence and position of allosteric sites on a given protein structure. Results By querying the literature and a recently available database of allosteric sites, we gathered 213 allosteric proteins with structural information that we further filtered into a non-redundant set of 91 proteins. We performed normal-mode analysis and observed significant changes in protein flexibility upon allosteric-ligand binding in 70% of the cases. These results agree with the current view that allosteric mechanisms are in many cases governed by changes in protein dynamics caused by ligand binding. Furthermore, we implemented an approach that achieves 65% positive predictive value in identifying allosteric sites within the set of predicted cavities of a protein (stricter parameters set, 0.22 sensitivity, by combining the current analysis on dynamics with previous results on structural conservation of allosteric sites. We also analyzed four biological examples in detail, revealing

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.

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

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.

Savannah River Site Approved Site Treatment Plan, 1998 Annual Update

Energy Technology Data Exchange (ETDEWEB)

Lawrence, B. [Westinghouse Savannah River Company, AIKEN, SC (United States); Berry, M.

1998-03-01

The U.S. Department of Energy, Savannah River Operations Office (DOE- SR),has prepared the Site Treatment Plan (STP) for Savannah River Site (SRS) mixed wastes in accordance with RCRA Section 3021(b), and SCDHEC has approved the STP (except for certain offsite wastes) and issued an order enforcing the STP commitments in Volume I. DOE-SR and SCDHEC agree that this STP fulfills the requirements contained in the FFCAct, RCRA Section 3021, and therefore,pursuant to Section 105(a) of the FFCAct (RCRA Section 3021(b)(5)), DOE`s requirements are to implement the plan for the development of treatment capacities and technologies pursuant to RCRA Section 3021.Emerging and new technologies not yet considered may be identified to manage waste more safely, effectively, and at lower cost than technologies currently identified in the plan. DOE will continue to evaluate and develop technologies that offer potential advantages in public acceptance, privatization, consolidation, risk abatement, performance, and life-cycle cost. Should technologies that offer such advantages be identified, DOE may request a revision/modification of the STP in accordance with the provisions of Consent Order 95-22-HW.The Compliance Plan Volume (Volume I) identifies project activity schedule milestones for achieving compliance with Land Disposal Restrictions (LDR). Information regarding the technical evaluation of treatment options for SRS mixed wastes is contained in the Background Volume (Volume II) and is provided for information.

Site characterization report for the basalt waste isolation project. Volume III

International Nuclear Information System (INIS)

1982-11-01

The reference location for a repository in basalt for the terminal storage of nuclear wastes on the Hanford Site and the candidate horizons within this reference repository location have been identified and the preliminary characterization work in support of the site screening process has been completed. Fifteen technical questions regarding the qualification of the site were identified to be addressed during the detailed site characterization phase of the US Department of Energy-National Waste Terminal Storage Program site selection process. Resolution of these questions will be provided in the final site characterization progress report, currently planned to be issued in 1987, and in the safety analysis report to be submitted with the License Application. The additional information needed to resolve these questions and the plans for obtaining the information have been identified. This Site Characterization Report documents the results of the site screening process, the preliminary site characterization data, the technical issues that need to be addressed, and the plans for resolving these issues. Volume 3 contains chapters 13 through 19: site issues and plans; geoengineering and repository design issues and plans; waste package and site geochemistry issues and plans; performance-assessment issues and plans; site characterization program; quality assurance; and identification of alternate sites

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

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...

A GIS methodology to identify potential corn stover collection locations

Energy Technology Data Exchange (ETDEWEB)

Haddad, Monica A. [Department of Community and Regional Planning, 583 College of Design, Iowa State University, Ames, IA 50011-3095 (United States); Anderson, Paul F. [Department of Landscape Architecture, 481 College of Design, Iowa State University, Ames, IA 50011 (United States); Department of Agronomy, 481 College of Design, Iowa State University, Ames, IA 50011 (United States)

2008-12-15

In this study, we use geographic information systems technology to identify potential locations in a Midwestern region for collection and storage of corn stover for use as biomass feedstock. Spatial location models are developed to identify potential collection sites along an existing railroad. Site suitability analysis is developed based on two main models: agronomic productivity potential and environmental costs. The analysis includes the following steps: (1) elaboration of site selection criteria; (2) identification of the study region and service area based on transportation network analysis; (3) reclassification of input spatial layers based on common scales; (4) overlaying the reclassified spatial layers with equal weights to generate the two main models; and (5) overlaying the main models using different weights. A pluralistic approach is adopted, presenting three different scenarios as alternatives for the potential locations. Our results suggest that there is a significant subset of potential sites that meet site selection criteria. Additional studies are needed to evaluate potential sites through field visits, assess economic and social costs, and estimate the proportion of corn producers willing to sell and transport corn stover to collection facilities. (author)

Site observational work plan for the UMTRA project site at Grand Junction, Colorado

International Nuclear Information System (INIS)

1996-01-01

This site observational work plan (SOWP) is one of the first Uranium Mill Tailings Remedial Action (UMTRA) Ground Water Project documents developed to select a compliance strategy that meets the UMTRA ground water standards for the Grand Junction site. This SOWP applies information about the Grand Junction site to the compliance strategy selection framework developed in the UMTRA Ground Water Project draft programmatic environmental impact statement. This risk-based, decision-making framework identifies the decision logic for selecting compliance strategies that could be used to meet the ground water standards. The US Department of Energy (DOE) goal is to implement a cost-effective site strategy that complies with the ground water standards and protects human health and the environment. Based on an evaluation of the site characterization and risk assessment data available for the preparation of this SOWP, DOE proposes that the most likely compliance strategy for the Grand Junction site is no remediation with the application of supplemental standards. This proposed strategy is based on a conceptual site model that indicates site-related contamination is confined to a limited-use aquifer as defined in the ground water standards. The conceptual model demonstrates that the uranium processing-related contamination at the site has affected the unconfined alluvial aquifer, but not the deeper confined aquifer

Site specific plan. [Environmental Restoration and Waste Management, Savannah River Site

Energy Technology Data Exchange (ETDEWEB)

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.

Savannah River Site Approved Site Treatment Plan, 1998 Annual Update (U)

International Nuclear Information System (INIS)

Lawrence, B.; Berry, M.

1998-03-01

The U.S. Department of Energy, Savannah River Operations Office (DOE- SR),has prepared the Site Treatment Plan (STP) for Savannah River Site (SRS) mixed wastes in accordance with RCRA Section 3021(b), and SCDHEC has approved the STP (except for certain offsite wastes) and issued an order enforcing the STP commitments in Volume I. DOE-SR and SCDHEC agree that this STP fulfills the requirements contained in the FFCAct, RCRA Section 3021, and therefore,pursuant to Section 105(a) of the FFCAct (RCRA Section 3021(b)(5)), DOE's requirements are to implement the plan for the development of treatment capacities and technologies pursuant to RCRA Section 3021.Emerging and new technologies not yet considered may be identified to manage waste more safely, effectively, and at lower cost than technologies currently identified in the plan. DOE will continue to evaluate and develop technologies that offer potential advantages in public acceptance, privatization, consolidation, risk abatement, performance, and life-cycle cost. Should technologies that offer such advantages be identified, DOE may request a revision/modification of the STP in accordance with the provisions of Consent Order 95-22-HW.The Compliance Plan Volume (Volume I) identifies project activity schedule milestones for achieving compliance with Land Disposal Restrictions (LDR). Information regarding the technical evaluation of treatment options for SRS mixed wastes is contained in the Background Volume (Volume II) and is provided for information

Promoter proximal polyadenylation sites reduce transcription activity

DEFF Research Database (Denmark)

Andersen, Pia Kjølhede; Lykke-Andersen, Søren; Jensen, Torben Heick

2012-01-01

Gene expression relies on the functional communication between mRNA processing and transcription. We previously described the negative impact of a point-mutated splice donor (SD) site on transcription. Here we demonstrate that this mutation activates an upstream cryptic polyadenylation (CpA) site......, which in turn causes reduced transcription. Functional depletion of U1 snRNP in the context of the wild-type SD triggers the same CpA event accompanied by decreased RNA levels. Thus, in accordance with recent findings, U1 snRNP can shield premature pA sites. The negative impact of unshielded pA sites...... on transcription requires promoter proximity, as demonstrated using artificial constructs and supported by a genome-wide data set. Importantly, transcription down-regulation can be recapitulated in a gene context devoid of splice sites by placing a functional bona fide pA site/transcription terminator within ∼500...

Zeta potentials of the rare earth element fluorcarbonate minerals focusing on bastnäsite and parisite.

Science.gov (United States)

Owens, C L; Nash, G R; Hadler, K; Fitzpatrick, R S; Anderson, C G; Wall, F

2018-06-01

Rare earth elements (REE) are critical to a wide range of technologies ranging from mobile phones to wind turbines. Processing and extraction of REE minerals from ore bodies is, however, both challenging and relatively poorly understood, as the majority of deposits contain only limited enrichment of REEs. An improved understanding of the surface properties of the minerals is important in informing and optimising their processing, in particular for separation by froth flotation. The measurement of zeta potential can be used to extract information regarding the electrical double layer, and hence surface properties of these minerals. There are over 34 REE fluorcarbonate minerals currently identified, however bastnäsite, synchysite and parisite are of most economic importance. Bastnäsite-(Ce), the most common REE fluorcarbonate, supplies over 50% of the world's REE. Previous studies of bastnäsite have showed a wide range of surface behaviour, with the iso-electric point (IEP), being measured between pH values of 4.6 and 9.3. In contrast, no values of IEP have been reported for parisite or synchysite. In this work, we review previous studies of the zeta potentials of bastnäsite to investigate the effects of different methodologies and sample preparation. In addition, measurements of zeta potentials of parisite under water, collector and supernatant conditions were conducted, the first to be reported. These results showed an iso-electric point for parisite of 5.6 under water, with a shift to a more negative zeta potential with both collector (hydroxamic and fatty acids) and supernatant conditions. The IEP with collectors and supernatant was <3.5. As zeta potential measurements in the presence of reagents and supernatants are the most rigorous way of determining the efficiency of a flotation reagent, the agreement between parisite zeta potentials obtained here and previous work on bastnäsite suggests that parisite may be processed using similar reagent schemes to

Identifying transposon insertions and their effects from RNA-sequencing data.

Science.gov (United States)

de Ruiter, Julian R; Kas, Sjors M; Schut, Eva; Adams, David J; Koudijs, Marco J; Wessels, Lodewyk F A; Jonkers, Jos

2017-07-07

Insertional mutagenesis using engineered transposons is a potent forward genetic screening technique used to identify cancer genes in mouse model systems. In the analysis of these screens, transposon insertion sites are typically identified by targeted DNA-sequencing and subsequently assigned to predicted target genes using heuristics. As such, these approaches provide no direct evidence that insertions actually affect their predicted targets or how transcripts of these genes are affected. To address this, we developed IM-Fusion, an approach that identifies insertion sites from gene-transposon fusions in standard single- and paired-end RNA-sequencing data. We demonstrate IM-Fusion on two separate transposon screens of 123 mammary tumors and 20 B-cell acute lymphoblastic leukemias, respectively. We show that IM-Fusion accurately identifies transposon insertions and their true target genes. Furthermore, by combining the identified insertion sites with expression quantification, we show that we can determine the effect of a transposon insertion on its target gene(s) and prioritize insertions that have a significant effect on expression. We expect that IM-Fusion will significantly enhance the accuracy of cancer gene discovery in forward genetic screens and provide initial insight into the biological effects of insertions on candidate cancer genes. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

The development of surface barriers at the Hanford Site

International Nuclear Information System (INIS)

Wing, N.R.; Gee, G.W.

1994-03-01

Engineered barriers are being developed to isolate wastes disposed of near the earth's surface at the US Department of Energy's (DOE) Hanford Site near Richland, Washington. Much of the waste that would be disposed of by in-place stabilization currently is located in relatively shallow subsurface structures such as solid waste burial grounds, tanks, vaults, and cribs. Unless protected in some way, the wastes could be transported to the accessible environment via the following pathways: plant, animal, and human intrusion; water infiltration; erosion; and the exhalation of noxious gases. Permanent isolation surface barriers have been proposed to protect wastes disposed of ''in place'' from the transport pathways identified previously (Figure 1). The protective barrier consists of a variety of different materials (e.g., fine soil, sand, gravel, riprap, asphalt, etc.) placed in layers to form an above-grade mound directly over the waste zone. Surface markers are being considered for placement around the periphery of the waste sites to inform future generations of the nature and hazards of the buried wastes. In addition, throughout the protective barrier, subsurface markers could be placed to warn any inadvertent human intruders of the dangers of the buried wastes (Figure 2)

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.

Sigma A recognition sites in the Bacillus subtilis genome

DEFF Research Database (Denmark)

Jarmer, Hanne Østergaard; Larsen, Thomas Schou; Krogh, Anders Stærmose

2001-01-01

A hidden Markov model of sigma (A) RNA polymerase cofactor recognition sites in Bacillus subtilis, containing either the common or the extended -10 motifs, has been constructed based on experimentally verified sigma (A) recognition sites. This work suggests that more information exists...... at the initiation site of transcription in both types of promoters than previously thought. When tested on the entire B. subtilis genome, the model predicts that approximately half of the sigma (A) recognition sites are of the extended type. Some of the response-regulator aspartate phosphatases were among...

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

Geo-Proxy-Based Site Classification for Regional Zonation of Seismic Site Effects in South Korea

Directory of Open Access Journals (Sweden)

Chang-Guk Sun

2018-02-01

Full Text Available Seismic site effects and topographic effects related to ground motion occur during an earthquake due to site-specific geotechnical or geological characteristics, including the geological or geographical structure and the characteristics of near-surface sub-soil layers. Site-specific site effects due to geological conditions have been confirmed in recent earthquake events. Earthquake-induced damage has mainly occurred at accumulated soft soil layers under basins or along coasts and rivers. An alternative method has recently been proposed for evaluating regional seismic site effects and amplification factors using digital elevation models (DEM. High-quality DEMs at high resolutions may be employed to resolve finer-scale variations in topographic gradients and consequently, correlated site response parameters. Because there are many regions in South Korea lacking borehole datasets, which are insufficient for site classification only using borehole datasets, a DEM-based proxy for seismic zonation can be effective. Thus, in this study, geo-proxy-based site classification was proposed based on empirical correlations with site response parameters and conducted for regional zonation of seismic site effects to identify the amplification of characteristics in the western metropolitan areas of South Korea, depending on the site-specific geo-spatial conditions.

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.

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.

The alpha-fetoprotein (AFP) third domain: a search for AFP interaction sites of cell cycle proteins.

Science.gov (United States)

Mizejewski, G J

2016-09-01

The carboxy-terminal third domain of alpha-fetoprotein (AFP-3D) is known to harbor binding and/or interaction sites for hydrophobic ligands, receptors, and binding proteins. Such reports have established that AFP-3D consists of amino acid (AA) sequence stretches on the AFP polypeptide that engages in protein-to-protein interactions with various ligands and receptors. Using a computer software program specifically designed for such interactions, the present report identified AA sequence fragments on AFP-3D that could potentially interact with a variety of cell cycle proteins. The cell cycle proteins identified were (1) cyclins, (2) cyclin-dependent kinases, (3) cell cycle-associated proteins (inhibitors, checkpoints, initiators), and (4) ubiquitin ligases. Following detection of the AFP-3D to cell cycle protein interaction sites, the computer-derived AFP localization AA sequences were compared and aligned with previously reported hydrophobic ligand and receptor interaction sites on AFP-3D. A literature survey of the association of cell cycle proteins with AFP showed both positive relationships and correlations. Previous reports of experimental AFP-derived peptides effects on various cell cycle proteins served to confirm and verify the present computer cell cycle protein identifications. Cell cycle protein interactions with AFP-CD peptides have been reported in cultured MCF-7 breast cancer cells subjected to mRNA microarray analysis. After 7 days in culture with MCF-7 cells, the AFP-derived peptides were shown to downregulate cyclin E, SKP2, checkpoint suppressors, cyclin-dependent kinases, and ubiquitin ligases that modulate cyclin E/CdK2 transition from the G1 to the S-phase of the cell cycle. Thus, the experimental data on AFP-CD interaction with cell cycle proteins were consistent with the "in silico" findings.

Finding erotic oases: locating the sites of men's same-sex anonymous sexual encounters.

Science.gov (United States)

Tewksbury, Richard

2008-01-01

Because anonymous sexual relations between two men are widely considered deviant many men seeking such activities look to erotic oases-natural environments appropriated for covert, often furtive sexual purposes. Previous research on erotic oases has focused on characteristics of involved men and processes of locating, negotiating with, and consummating sexual relations with others. This study draws on one major Web site listing of "cruising places" in the United States to identify common locations for erotic oases. Results show that the most common locations identified as erotic oases by users are public parks, adult bookstores, health clubs, and college campuses. Locations most likely to be listed as believed to be under law enforcement surveillance are outdoor, high traffic locations. Based on these results existing research has only begun to examine the most common locations for this highly stigmatized, deviant behavior and subculture.

Sorption of trivalent lanthanides and actinides onto montmorillonite: Macroscopic, thermodynamic and structural evidence for ternary hydroxo and carbonato surface complexes on multiple sorption sites.

Science.gov (United States)

Fernandes, M Marques; Scheinost, A C; Baeyens, B

2016-08-01

The credibility of long-term safety assessments of radioactive waste repositories may be greatly enhanced by a molecular level understanding of the sorption processes onto individual minerals present in the near- and far-fields. In this study we couple macroscopic sorption experiments to surface complexation modelling and spectroscopic investigations, including extended X-ray absorption fine structure (EXAFS) and time-resolved laser fluorescence spectroscopies (TRLFS), to elucidate the uptake mechanism of trivalent lanthanides and actinides (Ln/An(III)) by montmorillonite in the absence and presence of dissolved carbonate. Based on the experimental sorption isotherms for the carbonate-free system, the previously developed 2 site protolysis non electrostatic surface complexation and cation exchange (2SPNE SC/CE) model needed to be complemented with an additional surface complexation reaction onto weak sites. The fitting of sorption isotherms in the presence of carbonate required refinement of the previously published model by reducing the strong site capacity and by adding the formation of Ln/An(III)-carbonato complexes both on strong and weak sites. EXAFS spectra of selected Am samples and TRLFS spectra of selected Cm samples corroborate the model assumptions by showing the existence of different surface complexation sites and evidencing the formation of Ln/An(III) carbonate surface complexes. In the absence of carbonate and at low loadings, Ln/An(III) form strong inner-sphere complexes through binding to three Al(O,OH)6 octahedra, most likely by occupying vacant sites in the octahedral layers of montmorillonite, which are exposed on {010} and {110} edge faces. At higher loadings, Ln/An(III) binds to only one Al octahedron, forming a weaker, edge-sharing surface complex. In the presence of carbonate, we identified a ternary mono- or dicarbonato Ln/An(III) complex binding directly to one Al(O,OH)6 octahedron, revealing that type-A ternary complexes form with the one

O-GlcNAc site-mapping of liver X receptor-α and O-GlcNAc transferase.

Science.gov (United States)

Fan, Qiong; Moen, Anders; Anonsen, Jan Haug; Bindesbøll, Christian; Sæther, Thomas; Carlson, Cathrine Rein; Grønning-Wang, Line M

2018-05-05

The Liver X Receptor α (LXRα) belongs to the nuclear receptor superfamily and plays an essential role in regulating cholesterol, lipid and glucose metabolism and inflammatory responses. We have previously shown that LXRα is post-translationally modified by O-linked β-N-acetyl-glucosamine (O-GlcNAc) with increased transcriptional activity. Moreover, we showed that LXRα associates with O-GlcNAc transferase (OGT) in vitro and in vivo in mouse liver. In this study, we report that human LXRα is O-GlcNAc modified in its N-terminal domain (NTD) by identifying a specific O-GlcNAc site S49 and a novel O-GlcNAc modified peptide 20 LWKPGAQDASSQAQGGSSCILRE 42 . However, O-GlcNAc site-mutations did not modulate LXRα transactivation of selected target gene promoters in vitro. Peptide array and co-immunoprecipitation assays demonstrate that LXRα interacts with OGT in its NTD and ligand-binding domain (LBD) in a ligand-independent fashion. Moreover, we map two new O-GlcNAc sites in the longest OGT isoform (ncOGT): S437 in the tetratricopeptide repeat (TPR) 13 domain and T1043 in the far C-terminus, and a new O-GlcNAc modified peptide (amino acids 826-832) in the intervening region (Int-D) within the catalytic domain. We also map four new O-GlcNAc sites in the short isoform sOGT: S391, T393, S399 and S437 in the TPRs 11-13 domain. Future studies will reveal the biological role of identified O-GlcNAc sites in LXRα and OGT. Copyright © 2018 Elsevier Inc. All rights reserved.

Novel immunohistochemistry-based signatures to predict metastatic site of triple-negative breast cancers.

Science.gov (United States)

Klimov, Sergey; Rida, Padmashree Cg; Aleskandarany, Mohammed A; Green, Andrew R; Ellis, Ian O; Janssen, Emiel Am; Rakha, Emad A; Aneja, Ritu

2017-09-05

Although distant metastasis (DM) in breast cancer (BC) is the most lethal form of recurrence and the most common underlying cause of cancer related deaths, the outcome following the development of DM is related to the site of metastasis. Triple negative BC (TNBC) is an aggressive form of BC characterised by early recurrences and high mortality. Athough multiple variables can be used to predict the risk of metastasis, few markers can predict the specific site of metastasis. This study aimed at identifying a biomarker signature to predict particular sites of DM in TNBC. A clinically annotated series of 322 TNBC were immunohistochemically stained with 133 biomarkers relevant to BC, to develop multibiomarker models for predicting metastasis to the bone, liver, lung and brain. Patients who experienced metastasis to each site were compared with those who did not, by gradually filtering the biomarker set via a two-tailed t-test and Cox univariate analyses. Biomarker combinations were finally ranked based on statistical significance, and evaluated in multivariable analyses. Our final models were able to stratify TNBC patients into high risk groups that showed over 5, 6, 7 and 8 times higher risk of developing metastasis to the bone, liver, lung and brain, respectively, than low-risk subgroups. These models for predicting site-specific metastasis retained significance following adjustment for tumour size, patient age and chemotherapy status. Our novel IHC-based biomarkers signatures, when assessed in primary TNBC tumours, enable prediction of specific sites of metastasis, and potentially unravel biomarkers previously unknown in site tropism.

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.

5 CFR 2604.202 - Index identifying information for the public.

Science.gov (United States)

2010-01-01

... 5 Administrative Personnel 3 2010-01-01 2010-01-01 false Index identifying information for the... DISCLOSURE REPORTS FOIA Public Reading Room Facility and Web Site; Index Identifying Information for the Public § 2604.202 Index identifying information for the public. (a) The Office of Government Ethics will...

Consumer trust to a Web site: moderating effect of attitudes toward online shopping.

Science.gov (United States)

San Martín, Sonia; Camarero, Carmen

2008-10-01

In this paper, authors suggest a model that reflects the role played by the Web site characteristics and the previous level of satisfaction as determinant factors of trust in the Web site. Also, authors consider the moderating effects of consumers' motives and inhibitors to purchase online. Results show that satisfaction with previous purchases, the Web site security and privacy policies, and service quality are the main determinants of trust. Also, the motives and inhibitors the individuals perceive when buying online determine the type of signals they consider to trust.

Small Scale Multisource Site – Hydrogeology Investigation

Science.gov (United States)

A site impacted by brackish water was evaluated using traditional hydrogeologic and geochemical site characterization techniques. No single, specific source of the brine impacted ground water was identified. However, the extent of the brine impacted ground water was found to be...

Bald eagle site management plan for the Hanford Site, south-central Washington

International Nuclear Information System (INIS)

Fitzner, R.F.; Weiss, S.G.

1994-12-01

The CERCLA remedial investigations of waste sites on the Hanford Site will involve lands containing or adjacent to a bald eagle nest, winter concentration areas, or communal night roost. Because these CERCLA investigations may affect bald eagles, the DOE has prepared this Bald Eagle Site Management Plan (BESMP). However, it is intended that this BESMP be used or updated so as to be also applicable to future activities that affect bald eagles on the Hanford Site. Bald eagles regularly use the US Department of Energy's (DOE) Hanford Site in south-central Washington State during winter months for roosting, perching, and foraging. Each of these activities requires buffer zones to protect eagles from human disturbances. Buffer zones developed in this plan follow recommended guidelines and are intended to be used in planning. If Hanford Site activities in the vicinity of identified bald eagle use areas are carried out in accordance with this plan, such actions are not likely to adversely affect the eagles or their habitat. Activities that may be exceptions will involve informal or formal (whichever is appropriate) consultation with the US Fish and Wildlife Service as required by the Endangered Species Act

Factors influencing unsafe behaviors and accidents on construction sites: a review.

Science.gov (United States)

Khosravi, Yahya; Asilian-Mahabadi, Hassan; Hajizadeh, Ebrahim; Hassanzadeh-Rangi, Narmin; Bastani, Hamid; Behzadan, Amir H

2014-01-01

Construction is a hazardous occupation due to the unique nature of activities involved and the repetitiveness of several field behaviors. The aim of this methodological and theoretical review is to explore the empirical factors influencing unsafe behaviors and accidents on construction sites. In this work, results and findings from 56 related previous studies were investigated. These studies were categorized based on their design, type, methods of data collection, analytical methods, variables, and key findings. A qualitative content analysis procedure was used to extract variables, themes, and factors. In addition, all studies were reviewed to determine the quality rating and to evaluate the strength of provided evidence. The content analysis identified 8 main categories: (a) society, (b) organization, (c) project management, (d) supervision, (e) contractor, (f) site condition, (g) work group, and (h) individual characteristics. The review highlighted the importance of more distal factors, e.g., society and organization, and project management, that may contribute to reducing the likelihood of unsafe behaviors and accidents through the promotion of site condition and individual features (as proximal factors). Further research is necessary to provide a better understanding of the links between unsafe behavior theories and empirical findings, challenge theoretical assumptions, develop new applied theories, and make stronger recommendations.

Tests for evaluating sites for disposal of low-level radioactive waste

International Nuclear Information System (INIS)

Lutton, R.J.; Butler, D.K.; Meade, R.B.; Patrick, D.M.; Strong, A.B.; Taylor, H.M. Jr.

1982-12-01

This report, the second of a series, identifies the tests and other means of evaluating or documenting the important characteristics of sites for disposal of low-level radioactive waste. The specific parameters were identified and explained in regard to their importance in characterizing disposal facilities in the previous report. More than half of the tests and procedures are standard methods recognized and used nationwide, most conspicuously the numerous chemical tests. Other tests are commonly used methods recognized widely as state of the art, e.g., geological and geophysical methods. The basis for choosing these state-of-the-art methods is discussed, and the concepts and procedures themselves are reviewed in the absence of standards for ready reference. Besides standards and state-of-the-art practices a third category of methods involves the use of existing data sources or recognized correlations in place of new testing or documentation. It is particularly important that mapping, logging, sampling, testing, interpretation, and analysis be conducted by technically qualified and professionally motivated personnel using appropriate equipment and facilities, and general guidance is provided in this direction. There will be cases where site-specific testing and measurement are indicated to be unnecessary on a technical basis. This report calls attention to the usual subordinate role of such parameters and their only infrequent need for testing

TumorTracer: a method to identify the tissue of origin from the somatic mutations of a tumor specimen

DEFF Research Database (Denmark)

Marquard, Andrea Marion; Birkbak, Nicolai Juul; Thomas, Cecilia Engel

2015-01-01

A substantial proportion of cancer cases present with a metastatic tumor and require further testing to determine the primary site; many of these are never fully diagnosed and remain cancer of unknown primary origin (CUP). It has been previously demonstrated that the somatic point mutations......-copy-number classifier on three independent data sets: 1669 newly available public tumors of various types, a cohort of 91 breast metastases, and a set of 24 specimens from 9 lung cancer patients subjected to multiregion sequencing. The cross-validation accuracy was highest when all three types of information were used...... detected in a tumor can be used to identify its site of origin with limited accuracy. We hypothesized that higher accuracy could be achieved by a classification algorithm based on the following feature sets: 1) the number of nonsynonymous point mutations in a set of 232 specific cancer-associated genes, 2...

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

Site scientific mission plan for the southern great plains CART site January-June 2000.; TOPICAL

International Nuclear Information System (INIS)

Peppler, R. A.; Sisterson, D. L.; Lamb, P.

2001-01-01

The Southern Great Plains (SGP) Cloud and Radiation Testbed (CART) site was designed to help satisfy the data needs of the Atmospheric Radiation Measurement (ARM) Program Science Team. This Site Scientific Mission Plan defines the scientific priorities for site activities during the six months beginning on January 1, 2000, and looks forward in less detail to subsequent six-month periods. The primary purpose of this document is to provide scientific guidance for the development of plans for site operations. It also provides information on current plans to the ARM functional teams (Management Team, Data and Science Integration Team[DSIT], Operations Team, and Instrument Team[IT]) and serves to disseminate the plans more generally within the ARM Program and among the members of the Science Team. This document includes a description of the operational status of the site and the primary site activities envisioned, together with information concerning approved and proposed intensive observation periods (IOPs). The primary users of this document are the site operator, the site program manager, the Site Scientist Team (SST), the Science Team through the ARM Program science director, the ARM Program Experiment Center, and the aforementioned ARM Program functional teams. This plan is a living document that is updated and reissued every six months as the observational facilities are developed, tested, and augmented and as priorities are adjusted in response to developments in scientific planning and understanding. With this issue, many aspects of earlier Site Scientific Mission Plan reports have been moved to ARM sites on the World Wide Web. This report and all previous reports are available on the SGP CART web site

Malargue site, to-day and its future

International Nuclear Information System (INIS)

Meza, Juan C.; Giordano, Norberto L.

2005-01-01

In Argentina the National Atomic Energy Commission (CNEA) has the responsibility of restoring uranium mining facilities once the operations have finished. To carry out these clean up actions CNEA created the Project for Uranium Mining Environmental Restoration (PRAMU). Malargue Site, Mendoza province, has the first restoration priority among 8 sites in the country. The approved project for restoration consists of on site relocation of tailings to an engineering repository. To isolate the tailings from the environment, a multilayer system has been designed. Several works have been made, the secondary previous works were completed and nowadays works on the button portion of the multilayer barrier are being carries out. At the present, it is quite probable that the World Bank grants a credit to finish the works on Malargue Site and in the other sites in Argentina as well. (author)

Hemoglobin cleavage site-specificity of the Plasmodium falciparum cysteine proteases falcipain-2 and falcipain-3.

Directory of Open Access Journals (Sweden)

Shoba Subramanian

Full Text Available The Plasmodium falciparum cysteine proteases falcipain-2 and falcipain-3 degrade host hemoglobin to provide free amino acids for parasite protein synthesis. Hemoglobin hydrolysis has been described as an ordered process initiated by aspartic proteases, but cysteine protease inhibitors completely block the process, suggesting that cysteine proteases can also initiate hemoglobin hydrolysis. To characterize the specific roles of falcipains, we used three approaches. First, using random P(1 - P(4 amino acid substrate libraries, falcipain-2 and falcipain-3 demonstrated strong preference for cleavage sites with Leu at the P(2 position. Second, with overlapping peptides spanning alpha and beta globin and proteolysis-dependent (18O labeling, hydrolysis was seen at many cleavage sites. Third, with intact hemoglobin, numerous cleavage products were identified. Our results suggest that hemoglobin hydrolysis by malaria parasites is not a highly ordered process, but rather proceeds with rapid cleavage by falcipains at multiple sites. However, falcipain-2 and falcipain-3 show strong specificity for P(2 Leu in small peptide substrates, in agreement with the specificity in optimized small molecule inhibitors that was identified previously. These results are consistent with a principal role of falcipain-2 and falcipain-3 in the hydrolysis of hemoglobin by P. falciparum and with the possibility of developing small molecule inhibitors with optimized specificity as antimalarial agents.

Comparative Analysis of Site-Selection Process for Power Plants in Korea: Cases of Thermal, Nuclear, and Renewable Energies

International Nuclear Information System (INIS)

Kang, M.; Lee, M.; Yoon, J. W.; Choi, H. C.; Chu, C.; Lee, H.; Park, J.

2017-01-01

There are various conflicts related to power generation facilities; however, the conflicts that arise during the process of luring facilities or site selection, as in the previous cases, can eventually influence greatly the implementation of the national energy policy or strategy. This study analyzed the conflict phenomenon that occurred in the site selection policy of the power generation facilities through the case studies. We selected the most recent conflict cases by each energy source, identified the qualitative context characteristics of the cases and tried to suggest the policy leverages. In this study, it is concluded that the cause of conflicts in decision making system for site selection of power plants is insufficient yet due to the variable circumstances such as environmental events, stakeholder range, etc. However, the conclusions obtained from the case study are difficult generalization without specific prescription books, so further studies for those areas are required.

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).

A role for the weak DnaA binding sites in bacterial replication origins

DEFF Research Database (Denmark)

Charbon, Godefroid; Løbner-Olesen, Anders

2011-01-01

DnaA initiates the chromosomal DNA replication in nearly all bacteria, and replication origins are characterized by binding sites for the DnaA protein (DnaA-boxes) along with an ‘AT-rich’ region. However, great variation in number, spatial organization and specificity of DnaA-boxes is observed...... between species. In the study by Taylor et al. (2011), new and unexpectedly weak DnaA-boxes were identified within the Caulobacter crescentus origin of replication (Cori). The position of weak and stronger DnaA-boxes follows a pattern seen in Escherichia coli oriC. This raises the possibility...... that bacterial origins might be more alike than previously thought....

Prediction of Poly(A Sites by Poly(A Read Mapping.

Directory of Open Access Journals (Sweden)

Thomas Bonfert

Full Text Available RNA-seq reads containing part of the poly(A tail of transcripts (denoted as poly(A reads provide the most direct evidence for the position of poly(A sites in the genome. However, due to reduced coverage of poly(A tails by reads, poly(A reads are not routinely identified during RNA-seq mapping. Nevertheless, recent studies for several herpesviruses successfully employed mapping of poly(A reads to identify herpesvirus poly(A sites using different strategies and customized programs. To more easily allow such analyses without requiring additional programs, we integrated poly(A read mapping and prediction of poly(A sites into our RNA-seq mapping program ContextMap 2. The implemented approach essentially generalizes previously used poly(A read mapping approaches and combines them with the context-based approach of ContextMap 2 to take into account information provided by other reads aligned to the same location. Poly(A read mapping using ContextMap 2 was evaluated on real-life data from the ENCODE project and compared against a competing approach based on transcriptome assembly (KLEAT. This showed high positive predictive value for our approach, evidenced also by the presence of poly(A signals, and considerably lower runtime than KLEAT. Although sensitivity is low for both methods, we show that this is in part due to a high extent of spurious results in the gold standard set derived from RNA-PET data. Sensitivity improves for poly(A sites of known transcripts or determined with a more specific poly(A sequencing protocol and increases with read coverage on transcript ends. Finally, we illustrate the usefulness of the approach in a high read coverage scenario by a re-analysis of published data for herpes simplex virus 1. Thus, with current trends towards increasing sequencing depth and read length, poly(A read mapping will prove to be increasingly useful and can now be performed automatically during RNA-seq mapping with ContextMap 2.

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.

Dataset of cocoa aspartic protease cleavage sites

Directory of Open Access Journals (Sweden)

Katharina Janek

2016-09-01

Full Text Available The data provide information in support of the research article, “The cleavage specificity of the aspartic protease of cocoa beans involved in the generation of the cocoa-specific aroma precursors” (Janek et al., 2016 [1]. Three different protein substrates were partially digested with the aspartic protease isolated from cocoa beans and commercial pepsin, respectively. The obtained peptide fragments were analyzed by matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/TOF-MS/MS and identified using the MASCOT server. The N- and C-terminal ends of the peptide fragments were used to identify the corresponding in-vitro cleavage sites by comparison with the amino acid sequences of the substrate proteins. The same procedure was applied to identify the cleavage sites used by the cocoa aspartic protease during cocoa fermentation starting from the published amino acid sequences of oligopeptides isolated from fermented cocoa beans. Keywords: Aspartic protease, Cleavage sites, Cocoa, In-vitro proteolysis, Mass spectrometry, Peptides

Identifying key soil cyanobacteria easy to isolate and culture for arid soil restoration

Science.gov (United States)

Roncero-Ramos, Beatriz; Ángeles Muñoz-Martín, M.; Chamizo, Sonia; Román, Raúl; Rodriguez-Caballero, Emilio; Mateo, Pilar; Cantón, Yolanda

2017-04-01

Drylands represent an important fraction of the Earth land's surface. Low cover of vascular plants characterizes these regions, and the large open areas among plants are often colonized by cyanobacteria, mosses, lichens, algae, bryophytes, bacteria and fungi, known as biocrusts. Because these communities are on or within the soil surface, they contribute to improve physicochemical properties of the uppermost soil layers and have important effects on soil fertility and stability, so they could play an important role on soil restoration. Cyanobacteria appear to be a cross component of biocrusts and they have been demonstrated to enhance water availability, soil fertility (fixing atmospheric C and N), and soil aggregation (thanks to their filamentous morphology and the exopolysaccharides they excrete), and significantly reduce water and wind erosion. Besides, they are able to tolerate high temperatures and UV radiation. All these features convert cyanobacteria in pioneer organisms capable of colonizing degraded soils and may be crucial in facilitating the succession of more developed organisms such as vascular plants. Therefore, the use of native cyanobacteria, already adapted to site environmental conditions, could guarantee a successful restoration approach of degraded soils. However, previous to their application for soil restoration, the most representative species inhabiting these soils should be identified. The objective of this study was to identify (morphologically and genetically) and isolate representative native cyanobacteria species from arid soils in SE Spain, characterized for being easily isolated and cultured with the aim of using them to inoculate degraded arid soil. We selected two study areas in Almería, SE Spain, where biocrust cover most of the open spaces between plants: El Cautivo experimental site located in the Tabernas desert and a limestone quarry located at the southeastern edge of the Gádor massif. The first site is characterized by

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

Session II-A. Site characterization

International Nuclear Information System (INIS)

McIntosh, W.

1981-01-01

Section II-A on Site Characterization consists of the following papers which describe the progress made during the past fiscal year toward identifying sites for high-level radioactive waste repositories in deep geologic formations: (1) progress in expanded studies for repository sites; (2) evaluation of geologic and hydrologic characteristics in the Basin and Range Province relative to high-level nuclear waste disposal; (3) siting progress: Permian region; (4) Paradox Basin site exploration: a progress report; (5) progress toward recommending a salt site for an exploratory shaft; (6) status of geologic investigations for nuclear waste disposal at the Nevada Test Site; (7) geohydrologic investigation of the Hanford Site, Washington: basalt waste isolation project. Highlights include: expanding studies in crystalline rocks, both in the Appalachian and Lake Superior regions; laying the ground work with the states in the Basin and Range Province to kick off a joint USGS-state province study; narrowing areas of the Permian and Paradox bedded salt regions to a few promising locations; issuing a Gulf Coast Salt Dome Evaluation report (ONWI-109) for public review and comment; narrowing the Nevada Test Site area and Hanford Site area to locations for detailed site investigations and exploratory shafts; progress in developing the subseabed and space disposals alternatives

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...

Distinct Molecular Signature of Murine Fetal Liver and Adult Hematopoietic Stem Cells Identify Novel Regulators of Hematopoietic Stem Cell Function.

Science.gov (United States)

Manesia, Javed K; Franch, Monica; Tabas-Madrid, Daniel; Nogales-Cadenas, Ruben; Vanwelden, Thomas; Van Den Bosch, Elisa; Xu, Zhuofei; Pascual-Montano, Alberto; Khurana, Satish; Verfaillie, Catherine M

2017-04-15

During ontogeny, fetal liver (FL) acts as a major site for hematopoietic stem cell (HSC) maturation and expansion, whereas HSCs in the adult bone marrow (ABM) are largely quiescent. HSCs in the FL possess faster repopulation capacity as compared with ABM HSCs. However, the molecular mechanism regulating the greater self-renewal potential of FL HSCs has not yet extensively been assessed. Recently, we published RNA sequencing-based gene expression analysis on FL HSCs from 14.5-day mouse embryo (E14.5) in comparison to the ABM HSCs. We reanalyzed these data to identify key transcriptional regulators that play important roles in the expansion of HSCs during development. The comparison of FL E14.5 with ABM HSCs identified more than 1,400 differentially expressed genes. More than 200 genes were shortlisted based on the gene ontology (GO) annotation term "transcription." By morpholino-based knockdown studies in zebrafish, we assessed the function of 18 of these regulators, previously not associated with HSC proliferation. Our studies identified a previously unknown role for tdg, uhrf1, uchl5, and ncoa1 in the emergence of definitive hematopoiesis in zebrafish. In conclusion, we demonstrate that identification of genes involved in transcriptional regulation differentially expressed between expanding FL HSCs and quiescent ABM HSCs, uncovers novel regulators of HSC function.

Site characterization report for the basalt waste isolation project. Volume II

Energy Technology Data Exchange (ETDEWEB)

None

1982-11-01

The reference location for a repository in basalt for the terminal storage of nuclear wastes on the Hanford Site and the candidate horizons within this reference repository location have been identified and the preliminary characterization work in support of the site screening process has been completed. Fifteen technical questions regarding the qualification of the site were identified to be addressed during the detailed site characterization phase of the US Department of Energy-National Waste Terminal Storage Program site selection process. Resolution of these questions will be provided in the final site characterization progress report, currently planned to be issued in 1987, and in the safety analysis report to be submitted with the License Application. The additional information needed to resolve these questions and the plans for obtaining the information have been identified. This Site Characterization Report documents the results of the site screening process, the preliminary site characterization data, the technical issues that need to be addressed, and the plans for resolving these issues. Volume 2 contains chapters 6 through 12: geochemistry; surface hydrology; climatology, meteorology, and air quality; environmental, land-use, and socioeconomic characteristics; repository design; waste package; and performance assessment.

Site characterization report for the basalt waste isolation project. Volume II

International Nuclear Information System (INIS)

1982-11-01

The reference location for a repository in basalt for the terminal storage of nuclear wastes on the Hanford Site and the candidate horizons within this reference repository location have been identified and the preliminary characterization work in support of the site screening process has been completed. Fifteen technical questions regarding the qualification of the site were identified to be addressed during the detailed site characterization phase of the US Department of Energy-National Waste Terminal Storage Program site selection process. Resolution of these questions will be provided in the final site characterization progress report, currently planned to be issued in 1987, and in the safety analysis report to be submitted with the License Application. The additional information needed to resolve these questions and the plans for obtaining the information have been identified. This Site Characterization Report documents the results of the site screening process, the preliminary site characterization data, the technical issues that need to be addressed, and the plans for resolving these issues. Volume 2 contains chapters 6 through 12: geochemistry; surface hydrology; climatology, meteorology, and air quality; environmental, land-use, and socioeconomic characteristics; repository design; waste package; and performance assessment

Site observational work plan for the UMTRA Project Site at Grand Junction, Colorado

International Nuclear Information System (INIS)

1996-03-01

The U.S. Department of Energy (DOE) has prepared this initial site observational work plan (SOWP) for the Uranium Mill Tailings Remedial Action (UMTRA) Project site in Grand Junction, Colorado. This SOWP is one of the first UMTRA Ground Water Project documents developed to select a compliance strategy that meets the UMTRA ground water standards (40 CFR Part 192, as amended by 60 FR 2854) for the Grand Junction site. This SOWP applies information about the Grand Junction site to the compliance strategy selection framework developed in the UMTRA Ground Water Project draft programmatic environmental impact statement (PEIS). This risk-based, decision-making framework identifies the decision logic for selecting compliance strategies that could be used to meet the ground water standards. The DOE goal is to use the observational method to implement a cost-effective site strategy that complies with the ground water standards and protects human health and the environment. Based on an evaluation of the site characterization and risk assessment data available for the preparation of this SOWP, DOE proposes that the most likely compliance strategy for the Grand Junction site is no remediation based on the application of supplemental standards. This proposed strategy is based on a conceptual site model that indicates site-related contamination is confined to a limited-use aquifer as defined in the ground water standards

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.

Progress in forming bottom barriers under waste sites

International Nuclear Information System (INIS)

Carter, E.E.

1997-01-01

The paper describes an new method for the construction, verification, and maintenance of underground vaults to isolate and contain radioactive burial sites without excavation or drilling in contaminated areas. The paper begins with a discussion of previous full-scale field tests of horizontal barrier tools which utilized high pressure jetting technology. This is followed by a discussion of the TECT process, which cuts with an abrasive cable instead of high pressure jets. The new method is potentially applicable to more soil types than previous methods and can form very thick barriers. Both processes are performed from the perimeter of a site and require no penetration or disturbance of the active waste area. The paper also describes long-term verification methods to monitor barrier integrity passively

Life cycle of petroleum biodegradation metabolite plumes, and implications for risk management at fuel release sites.

Science.gov (United States)

Zemo, Dawn A; O'Reilly, Kirk T; Mohler, Rachel E; Magaw, Renae I; Espino Devine, Catalina; Ahn, Sungwoo; Tiwary, Asheesh K

2017-07-01

This paper summarizes the results of a 5-y research study of the nature and toxicity of petroleum biodegradation metabolites in groundwater at fuel release sites that are quantified as diesel-range "Total Petroleum Hydrocarbons" (TPH; also known as TPHd, diesel-range organics (DRO), etc.), unless a silica gel cleanup (SGC) step is used on the sample extract prior to the TPH analysis. This issue is important for site risk management in regulatory jurisdictions that use TPH as a metric; the presence of these metabolites may preclude site closure even if all other factors can be considered "low-risk." Previous work has shown that up to 100% of the extractable organics in groundwater at petroleum release sites can be biodegradation metabolites. The metabolites can be separated from the hydrocarbons by incorporating an SGC step; however, regulatory agency acceptance of SGC has been inconsistent because of questions about the nature and toxicity of the metabolites. The present study was conducted to answer these specific questions. Groundwater samples collected from source and downgradient wells at fuel release sites were extracted and subjected to targeted gas chromatography-mass spectrometry (GC-MS) and nontargeted two-dimensional gas chromatography with time-of-flight mass spectrometry (GC×GC-MS) analyses, and the metabolites identified in each sample were classified according to molecular structural classes and assigned an oral reference dose (RfD)-based toxicity ranking. Our work demonstrates that the metabolites identified in groundwater at biodegrading fuel release sites are in classes ranked as low toxicity to humans and are not expected to pose significant risk to human health. The identified metabolites naturally attenuate in a predictable manner, with an overall trend to an increasingly higher proportion of organic acids and esters, and a lower human toxicity profile, and a life cycle that is consistent with the low-risk natural attenuation paradigm adopted

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

Environmental site characterization and remediation at Lawrence Livermore National Laboratory Site 300

International Nuclear Information System (INIS)

Lamarre, A.L.; Ferry, R.A.

1992-04-01

Lawrence Livermore National Laboratory (LLNL) is a research and development laboratory owned by the US Department of Energy (DOE) and operated by the University of California. The Laboratory operates its Site 300 test facility in support of DOE's national defense programs. In support of activities, at the 300 Site numerous industrial fluids are used and various process or rinse waters and solid wastes are produced. Some of these materials are hazardous by current standards. HE rinse waters were previously discharged to inlined lagoons; they now are discharged to a permitted Class II surface impoundment Solid wastes have been deposited in nine landfills. Waste HE compounds are destroyed by open burning at a burn pit facility. As a result of these practices, environmental contaminants have been released to the soil and ground water

Web 2.0 Sites for Collaborative Self-Access: The Learning Advisor vs. Google®

Directory of Open Access Journals (Sweden)

Craig D. Howard

2011-09-01

Full Text Available While Web 2.0 technologies provide motivated, self-access learners with unprecedented opportunities for language learning, Web 2.0 designs are not of universally equal value for learning. This article reports on research carried out at Indiana University Bloomington using an empirical method to select websites for self-access language learning. Two questions related to Web 2.0 recommendations were asked: (1 How do recommended Web 2.0 sites rank in terms of interactivity features? (2 How likely is a learner to find highly interactive sites on their own? A list of 20 sites used for supplemental and self-access activities in language programs at five universities was compiled and provided the initial data set. Purposive sampling criteria revealed 10 sites truly represented Web 2.0 design. To address the first question, a feature analysis was applied (Herring, The international handbook of internet research. Berlin: Springer, 2008. An interactivity framework was developed from previous research to identify Web 2.0 design features, and sites were ranked according to feature quantity. The method used to address the second question was an interconnectivity analysis that measured direct and indirect interconnectivity within Google results. Highly interactive Web 2.0 sites were not prominent in Google search results, nor were they often linked via third party sites. It was determined that, using typical keywords or searching via blogs and recommendation sites, self-access learners were highly unlikely to find the most promising Web 2.0 sites for language learning. A discussion of the role of the learning advisor in guiding Web 2.0 collaborative self-access, as well as some strategic short cuts to quick analysis, conclude the article.

Protective actions as a factor in power reactor siting

Energy Technology Data Exchange (ETDEWEB)

Gant, K.S.; Schweitzer, M.

1984-06-01

This report examines the relationship between a power reactor site and the ease of implementing protective actions (emergency measures a serious accident). Limiting populating density around a reactor lowers the number of people at risk but cannot assure that all protective actions are possible for those who reside near the reactor. While some protective measures can always be taken (i.e., expedient respiratory protection, sheltering) the ability to evacuate the area or find adequate shelter may depend on the characteristics of the area near the reactor site. Generic siting restrictions designed to identify and eliminate these site-specific constraints would be difficult to formulate. The authors suggest identifying possible impediments to protective actions at a proposed reactor site and addressing these problems in the emergency plans. 66 references, 6 figures, 8 tables.

Protective actions as a factor in power reactor siting

International Nuclear Information System (INIS)

Gant, K.S.; Schweitzer, M.

1984-06-01

This report examines the relationship between a power reactor site and the ease of implementing protective actions (emergency measures a serious accident). Limiting populating density around a reactor lowers the number of people at risk but cannot assure that all protective actions are possible for those who reside near the reactor. While some protective measures can always be taken (i.e., expedient respiratory protection, sheltering) the ability to evacuate the area or find adequate shelter may depend on the characteristics of the area near the reactor site. Generic siting restrictions designed to identify and eliminate these site-specific constraints would be difficult to formulate. The authors suggest identifying possible impediments to protective actions at a proposed reactor site and addressing these problems in the emergency plans. 66 references, 6 figures, 8 tables

Site observational work plan for the UMTRA Project site at Ambrosia Lake, New Mexico

International Nuclear Information System (INIS)

1994-09-01

The Ambrosia Lake Uranium Mill Tailings Remedial Action (UMTRA) Project site is within the Grants Mineral Belt and was one of numerous uranium mills supplied by many local mines. Ground water contamination at the site occurred as a result of uranium mill operations. The potential for impacts to human health and the environment from contaminated ground water currently does not exist. No domestic or livestock wells accessing ground water from the uppermost aquifer have been identified within a 5 mile radius from the site. Therefore, no current exposure pathways to humans, livestock, or wildlife exist, nor are any foreseen. The proposed ground water compliance strategy under consideration for application at the Ambrosia Lake site is to perform no remediation, based on the application of supplemental standards because the ground water has ''limited use.''

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.

Interaction of Zn(II)bleomycin-A2 and Zn(II)peplomycin with a DNA hairpin containing the 5'-GT-3' binding site in comparison with the 5'-GC-3' binding site studied by NMR spectroscopy.

Science.gov (United States)

Follett, Shelby E; Ingersoll, Azure D; Murray, Sally A; Reilly, Teresa M; Lehmann, Teresa E

2017-10-01

Bleomycins are a group of glycopeptide antibiotics synthesized by Streptomyces verticillus that are widely used for the treatment of various neoplastic diseases. These antibiotics have the ability to chelate a metal center, mainly Fe(II), and cause site-specific DNA cleavage. Bleomycins are differentiated by their C-terminal regions. Although this antibiotic family is a successful course of treatment for some types of cancers, it is known to cause pulmonary fibrosis. Previous studies have identified that bleomycin-related pulmonary toxicity is linked to the C-terminal region of these drugs. This region has been shown to closely interact with DNA. We examined the binding of Zn(II)peplomycin and Zn(II)bleomycin-A 2 to a DNA hairpin of sequence 5'-CCAGTATTTTTACTGG-3', containing the binding site 5'-GT-3', and compared the results with those obtained from our studies of the same MBLMs bound to a DNA hairpin containing the binding site 5'-GC-3'. We provide evidence that the DNA base sequence has a strong impact in the final structure of the drug-target complex.

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).

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.

Confidence assessment. Site-descriptive modelling SDM-Site Laxemar

International Nuclear Information System (INIS)

2009-06-01

The objective of this report is to assess the confidence that can be placed in the Laxemar site descriptive model, based on the information available at the conclusion of the surface-based investigations (SDM-Site Laxemar). In this exploration, an overriding question is whether remaining uncertainties are significant for repository engineering design or long-term safety assessment and could successfully be further reduced by more surface-based investigations or more usefully by explorations underground made during construction of the repository. Procedures for this assessment have been progressively refined during the course of the site descriptive modelling, and applied to all previous versions of the Forsmark and Laxemar site descriptive models. They include assessment of whether all relevant data have been considered and understood, identification of the main uncertainties and their causes, possible alternative models and their handling, and consistency between disciplines. The assessment then forms the basis for an overall confidence statement. The confidence in the Laxemar site descriptive model, based on the data available at the conclusion of the surface based site investigations, has been assessed by exploring: - Confidence in the site characterization data base, - remaining issues and their handling, - handling of alternatives, - consistency between disciplines and - main reasons for confidence and lack of confidence in the model. Generally, the site investigation database is of high quality, as assured by the quality procedures applied. It is judged that the Laxemar site descriptive model has an overall high level of confidence. Because of the relatively robust geological model that describes the site, the overall confidence in the Laxemar Site Descriptive model is judged to be high, even though details of the spatial variability remain unknown. The overall reason for this confidence is the wide spatial distribution of the data and the consistency between

Confidence assessment. Site-descriptive modelling SDM-Site Laxemar

Energy Technology Data Exchange (ETDEWEB)

2008-12-15

The objective of this report is to assess the confidence that can be placed in the Laxemar site descriptive model, based on the information available at the conclusion of the surface-based investigations (SDM-Site Laxemar). In this exploration, an overriding question is whether remaining uncertainties are significant for repository engineering design or long-term safety assessment and could successfully be further reduced by more surface-based investigations or more usefully by explorations underground made during construction of the repository. Procedures for this assessment have been progressively refined during the course of the site descriptive modelling, and applied to all previous versions of the Forsmark and Laxemar site descriptive models. They include assessment of whether all relevant data have been considered and understood, identification of the main uncertainties and their causes, possible alternative models and their handling, and consistency between disciplines. The assessment then forms the basis for an overall confidence statement. The confidence in the Laxemar site descriptive model, based on the data available at the conclusion of the surface based site investigations, has been assessed by exploring: - Confidence in the site characterization data base, - remaining issues and their handling, - handling of alternatives, - consistency between disciplines and - main reasons for confidence and lack of confidence in the model. Generally, the site investigation database is of high quality, as assured by the quality procedures applied. It is judged that the Laxemar site descriptive model has an overall high level of confidence. Because of the relatively robust geological model that describes the site, the overall confidence in the Laxemar Site Descriptive model is judged to be high, even though details of the spatial variability remain unknown. The overall reason for this confidence is the wide spatial distribution of the data and the consistency between