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Sample records for previously identified sites

  1. HIV gene expression from intact proviruses positioned in bacterial artificial chromosomes at integration sites previously identified in latently infected T cells

    International Nuclear Information System (INIS)

    Eipers, Peter G.; Salazar-Gonzalez, Jesus F.; Morrow, Casey D.

    2011-01-01

    HIV integration predominantly occurs in introns of transcriptionally active genes. To study the impact of the integration site on HIV gene expression, a complete HIV-1 provirus (with GFP as a fusion with Nef) was inserted into bacterial artificial chromosomes (BACs) at three sites previously identified in latent T cells of patients: topoisomerase II (Top2A), DNA methyltransferase 1 (DNMT1), or basic leucine transcription factor 2 (BACH2). Transfection of BAC-HIV into 293 T cells resulted in a fourfold difference in production of infectious HIV-1. Cell lines were established that contained BAC-Top2A, BAC-DNMT1, or BAC-BACH2, but only BAC-DNMT1 spontaneously produced virus, albeit at a low level. Stimulation with TNF-α resulted in virus production from four of five BAC-Top2A and all BAC-DNMT1 cell lines, but not from the BAC-BACH2 lines. The results of these studies highlight differences between integration sites identified in latent T cells to support virus production and reactivation from latency.

  2. SitesIdentify: a protein functional site prediction tool

    Directory of Open Access Journals (Sweden)

    Doig Andrew J

    2009-11-01

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

  3. Identifying the potential wintering sites of the globally threatened ...

    African Journals Online (AJOL)

    The Aquatic Warbler is a threatened Afro-Palaearctic migrant with a largely unknown distribution in the winter (non-breeding) season. Protection of wintering sites may be crucial for the conservation of the species. Previous studies have identified extensive areas of north-western sub-Saharan Africa that could potentially be ...

  4. Change in knee flexor torque after fatiguing exercise identifies previous hamstring injury in football players.

    Science.gov (United States)

    Lord, C; Ma'ayah, F; Blazevich, A J

    2018-03-01

    Muscular fatigue and interlimb strength asymmetry are factors known to influence hamstring injury risk; however, limb-specific exacerbation of knee flexor (hamstrings) torque production after fatiguing exercise has previously been ignored. To investigate changes in muscular force production before and after sport-specific (repeated-sprint) and non-specific (knee extension-flexion) fatiguing exercise, and explore the sensitivity and specificity of isokinetic endurance (ie, muscle-specific) and single-leg vertical jump (ie, whole limb) tests to identify previous hamstring injury. Twenty Western Australia State League footballers with previous unilateral hamstring injury and 20 players without participated. Peak concentric knee extensor and flexor (180°∙s -1 ) torques were assessed throughout an isokinetic endurance test, which was then repeated alongside a single-leg vertical jump test before and after maximal repeated-sprint exercise. Greater reductions in isokinetic knee flexor torque (-16%) and the concentric hamstring:quadriceps peak torque ratio (-15%) were observed after repeated-sprint running only in the injured (kicking) leg and only in the previously injured subjects. Changes in (1) peak knee flexor torque after repeated-sprint exercise, and (2) the decline in knee flexor torque during the isokinetic endurance test measured after repeated-sprint exercise, correctly identified the injured legs (N = 20) within the cohort (N = 80) with 100% specificity and sensitivity. Decreases in peak knee flexor torque and the knee flexor torque during an isokinetic endurance test after repeated-sprint exercise identified previous hamstring injury with 100% accuracy. Changes in knee flexor torque, but not SLVJ, should be tested to determine its prospective ability to predict hamstring injury in competitive football players. © 2017 The Authors. Scandinavian Journal of Medicine & Science In Sports Published by John Wiley & Sons Ltd.

  5. Thyroid disease awareness is associated with high rates of identifying subjects with previously undiagnosed thyroid dysfunction.

    Science.gov (United States)

    Canaris, Gay J; Tape, Thomas G; Wigton, Robert S

    2013-04-16

    Conventional screening for hypothyroidism is controversial. Although hypothyroidism is underdiagnosed, many organizations do not recommend screening, citing low disease prevalence in unselected populations. We studied attendees at a thyroid health fair, hypothesizing that certain patient characteristics would enhance the yield of testing. We carried out an observational study of participants at a Michigan health fair that focused on thyroid disease. We collected patient-reported symptoms and demographics by questionnaire, and correlated these with the TSH values obtained through the health fair. 794 of 858 health fair attendees participated. Most were women, and over 40% reported a family history of thyroid disease. We identified 97 (12.2%) participants with previously unknown thyroid dysfunction. No symptom or combination of symptoms discriminated between hypothyroid and euthyroid individuals. Hypothyroid and euthyroid participants in the health fair reported each symptom with a similar prevalence (p > 0.01), a prevalence which was very high. In fact, when compared with a previously published case-control study that reported symptoms, the euthyroid health fair participants reported a higher symptom prevalence (range 3.9% to 66.3%, mean 31.5%), than the euthyroid individuals from the case-control study (range 2% to 54%, mean 17.4%). A high proportion of previously undiagnosed thyroid disease was identified at this health fair. We initially hypothesized symptoms would distinguish between thyroid function states. However, this was not the case in this health fair screening population. The prevalence of reported symptoms was similar and high in both euthyroid and hypothyroid participants. Because attendees were self-selected, it is possible that this health fair that focused on thyroid disease attracted participants specifically concerned about thyroid health. Despite the lack of symptom discrimination, the much higher prevalence of hypothyroidism in this study

  6. Streptococcus oralis previously identified as uncommon 'Streptococcus sanguis' in Behçet's disease.

    Science.gov (United States)

    Narikawa, S; Suzuki, Y; Takahashi, M; Furukawa, A; Sakane, T; Mizushima, Y

    1995-08-01

    The relation between the biochemical and serological properties of 'Streptococcus sanguis' was studied to characterize the strains isolated from dental plaque of patients with Behçet's disease and controls. Seven reference and 100 clinical strains preserved by the Behçet's Disease Research Committee of Japan were identified using established criteria and differentiated with antisera against Strep. oralis ATCC 10557, Strep. sanguis ATCC 10556 and 'Strep. sanguis' ST7, compatible with the criteria. Uncommon serovars (serotypes) KTH-1 (= ATCC 49298), KTH-2 (= ATCC 49296), KTH-3 (= ATCC KTH-4 (= ATCC 49297) and B220 (serovar KTH-1) with both IgA1 protease and neuraminidase (sialidase) were identified as Strep. oralis, whereas common serovars ST3 with IgA1 protease alone and ST7 without both enzymes were identified as Strep. sanguis and Strep. gordonii, respectively. Isolates previously ranked as uncommon serovars were identified as Strep. oralis, whereas the rest ranked as common serovars were identified as the same species as those of the grouping strains. A soft-agar technique was available for species identification except for Strep. oralis serovar KTH-1 reacting with the antiserum against Strep. gordonii ST7. The frequency of isolation of Strep. oralis was higher in Behçet's disease (52%) than in controls (38%), but no difference was observed between the properties of the two groups of isolates. Strep. oralis virulence factors may be involved in breach the mucosal barrier in patients with specific reactivity to these antigens and inducing Behçet's disease.

  7. 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

  8. 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

  9. Reproductive compatibility between mite populations previously identified as Euseius concordis (Acari: Phytoseiidae).

    Science.gov (United States)

    Noronha, Aloyséia Cristina da Silva; de Moraes, Gilberto José

    2004-01-01

    The objective of the present research is to study the reproductive compatibility between populations of predatory mites previously identified as Euseius concordis (Chant) based on morphological characteristics. Colonies of these mite populations were established in the lab with specimens collected from different localities and host plants. Reproductive compatibility was evaluated through crosses and backcrosses within and between populations and the subsequent observation of females' oviposition, over a period of 10 days. The levels of oviposition obtained in the crosses between individuals from the same population were higher than those obtained in the crosses between individuals from different populations. Results indicate the occurrence of post-mating reproductive incompatibility between the mite population from Petrolina and the other populations studied. Crosses and backcrosses between populations involving female mites from Petrolina did not produce offspring, although endospermatophores were present inside the spermathecas of those females. Oviposition was reduced, and only sons were obtained, in crosses between populations with males from Petrolina. Crosses of females from Pontes e Lacerda and males from Jaguariúna and vice versa produced only male progeny. Our results established that the populations originating from Arroio do Meio, Pontes e Lacerda, Jaguarúna and Viçosa, are reproductively compatible. However, the latter populations and the population from Petrolina are genetically isolated. Based on these results we suggest that more cytological and genetic studies are needed to establish if this reproductive isolation represents a species barrier.

  10. Targeted pathologic evaluation of bone marrow donors identifies previously undiagnosed marrow abnormalities.

    Science.gov (United States)

    Tilson, Matthew P; Jones, Richard J; Sexauer, Amy; Griffin, C A; Morsberger, Laura A; Batista, Denise A S; Small, Donald; Burns, Kathleen H; Gocke, Christopher D; Vuica-Ross, Milena; Borowitz, Michael J; Duffield, Amy S

    2013-08-01

    Potential bone marrow donors are screened to ensure the safety of both the donor and recipient. At our institution, potential donors with abnormal peripheral blood cell counts, a personal history of malignancy, or age >60 years are evaluated to ensure that they are viable candidates for donation. Evaluation of the marrow includes morphologic, flow cytometric, and cytogenetic studies. A total of 122 potential donors were screened between the years of 2001 and 2011, encompassing approximately 10% of all donors. Of the screened potential donors, the mean age was 59 years and there were 59 men and 63 women. The donors were screened because of age >60 years (n = 33), anemia (n = 22), cytopenias other than anemia (n = 27), elevated peripheral blood counts without a concurrent cytopenia (n = 20), elevated peripheral blood counts with a concurrent cytopenia (n = 10), history of malignancy (n = 4), abnormal peripheral blood differential (n = 3), prior graft failure (n = 1), history of treatment with chemotherapy (n = 1), and body habitus (n = 1). Marrow abnormalities were detected in 9% (11 of 122) of donors. These donors were screened because of anemia (5 of 22, 23%), age >60 years (2 of 33, 6%), history of malignancy (2 of 4, 50%), elevated peripheral blood counts (1 of 20, 5%), and body habitus (1 of 1, 100%). Abnormalities included plasma cell dyscrasia (n = 3), abnormal marrow cellularity (n = 3), clonal cytogenetic abnormalities (n = 2), low-grade myelodysplastic syndrome (1), a mutated JAK2 V617F allele (n = 1), and monoclonal B cell lymphocytosis (n = 1). Our experience indicates that extended screening of potential donors identifies a significant number of donors with previously undiagnosed marrow abnormalities. Copyright © 2013 American Society for Blood and Marrow Transplantation. Published by Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

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

    2017-11-01

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

  12. 76 FR 59488 - Addition to the Identifying Information for an Individual Previously Designated Pursuant to...

    Science.gov (United States)

    2011-09-26

    ... information for the following individual who was previously designated pursuant to the Order: GRAJALES PUENTES...; Cedula No. 52455790 (Colombia) (individual) [SDNT] The listing now appears as follows: GRAJALES PUENTES...

  13. 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

    on freshwater habitats throughout mainland China, straddling an area 830 km E−W and 1100 km N−S. Most wintered in discrete mountainous areas with extensive timber cover, large rivers and low human population density. Three birds tracked in more than one season returned to within 25−150 km of previous wintering...... and recaptured on nests along a 40-km stretch of the Kievka River. Mean positions for brood-rearing females during the summer were on average within 61.9 km of the nest site, suggesting reasonable device accuracy for subsequent location of winter quarters. Geolocation data showed that most birds wintered...... 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...

  14. 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....

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

    DEFF Research Database (Denmark)

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

    2012-01-01

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

  16. From The Cover: Genome-wide RNA interference screen identifies previously undescribed regulators of polyglutamine aggregation

    Science.gov (United States)

    Nollen, Ellen A. A.; Garcia, Susana M.; van Haaften, Gijs; Kim, Soojin; Chavez, Alejandro; Morimoto, Richard I.; Plasterk, Ronald H. A.

    2004-04-01

    Protein misfolding and the formation of aggregates are increasingly recognized components of the pathology of human genetic disease and hallmarks of many neurodegenerative disorders. As exemplified by polyglutamine diseases, the propensity for protein misfolding is associated with the length of polyglutamine expansions and age-dependent changes in protein-folding homeostasis, suggesting a critical role for a protein homeostatic buffer. To identify the complement of protein factors that protects cells against the formation of protein aggregates, we tested transgenic Caenorhabditis elegans strains expressing polyglutamine expansion yellow fluorescent protein fusion proteins at the threshold length associated with the age-dependent appearance of protein aggregation. We used genome-wide RNA interference to identify genes that, when suppressed, resulted in the premature appearance of protein aggregates. Our screen identified 186 genes corresponding to five principal classes of polyglutamine regulators: genes involved in RNA metabolism, protein synthesis, protein folding, and protein degradation; and those involved in protein trafficking. We propose that each of these classes represents a molecular machine collectively comprising the protein homeostatic buffer that responds to the expression of damaged proteins to prevent their misfolding and aggregation. protein misfolding | neurodegenerative diseases

  17. Intensive sampling identifies previously unknown chemotypes, population divergence and biosynthetic connections among terpenoids in Eucalyptus tricarpa.

    Science.gov (United States)

    Andrew, Rose L; Keszei, Andras; Foley, William J

    2013-10-01

    Australian members of the Myrtaceae produce large quantities of ecologically and economically important terpenes and display abundant diversity in both yield and composition of their oils. In a survey of the concentrations of leaf terpenes in Eucalyptus tricarpa (L.A.S. Johnson) L.A.S. Johnson & K.D. Hill, which were previously known from few samples, exceptional variability was found in composition. The aim was to characterize the patterns of variation and covariation among terpene components in this species and to use this information to enhance our understanding of their biosynthesis. There were marked discontinuities in the distributions of numerous compounds, including the overall proportions of mono- and sesquiterpenes, leading us to delineate three distinct chemotypes. Overall, positive covariation predominated, but negative covariation suggested competitive interactions involved in monoterpene synthesis. Two groups of covarying monoterpenes were found, each of which was positively correlated with a group of sesquiterpenes and negatively correlated with the alternate sesquiterpene group. These results imply substantial cross-talk between mono- and sesquiterpene biosynthesis pathways. However, only those compounds hypothesized to share final carbocation intermediates or post-processing steps were strongly positively correlated within chemotypes. This suggests that the broader patterns of covariation among groups of compounds may result from co-regulation of multiple biosynthetic genes, controlling the complex terpene profiles of the chemotypes of Eucalyptus. Copyright © 2013 Elsevier Ltd. All rights reserved.

  18. 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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-06-26

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

  20. 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 ...

  1. Identifying translation initiation sites in prokaryotes using support vector machine.

    Science.gov (United States)

    Gao, Tingting; Yang, Zhixia; Wang, Yong; Jing, Ling

    2010-02-21

    Gene identification in genomes has been a fundamental and long-standing task in bioinformatics and computational biology. Many computational methods have been developed to predict genes in prokaryote genomes by identifying translation initiation site (TIS) in transcript data. However, the pseudo-TISs at the genome level make these methods suffer from a high number of false positive predictions. In addition, most of the existing tools use an unsupervised learning framework, whose predictive accuracy may depend on the choice of specific organism. In this paper, we present a supervised learning method, support vector machine (SVM), to identify translation initiation site at the genome level. The features are extracted from the sequence data by modeling the sequence segment around predicted TISs as a position specific weight matrix (PSWM). We train the parameters of our SVM through well constructed positive and negative TIS datasets. Then we apply the method to recognize translation initiation sites in E. coli, B. subtilis, and validate our method on two GC-rich bacteria genomes: Pseudomonas aeruginosa and Burkholderia pseudomallei K96243. We show that translation initiation sites can be recognized accurately at the genome level by our method, irrespective of their GC content. Furthermore, we compare our method with four existing methods and demonstrate that our method outperform these methods by obtaining better performance in all the four organisms. (c) 2009. Published by Elsevier Ltd.

  2. 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...

  3. Identifying sites for catheter ablation of ventricular tachycardia.

    Science.gov (United States)

    Stevenson, W G; Sager, P; Nademanee, K; Hassan, H; Middlekauff, H R; Saxon, L A; Wiener, I

    1992-06-01

    reentry circuit. Catheter ablation will probably be most effective at central slow conduction zone sites. When VT originates from a small focus surrounded by normal myocardium, such as is likely for idiopathic RV outflow tract and some idiopathic left ventricular tachycardias, presystolic electrical activity and pacemapping are likely to identify the tachycardia focus. For macroreentry involving the bundle branches, the right bundle branch can be easily targeted.

  4. Patellar tendon re-rupture on the opposite end of the previous site of surgical repair.

    Science.gov (United States)

    Koh, Bryan Thean Howe; Sayampanathan, Andrew A; Lee, Keng Thiam

    2017-01-01

    We describe a rare case of a patellar tendon "re-rupture" at the opposite end of a previous proximal tendon repair. A 32-year-old male with a history of surgically repaired right proximal patellar tendon rupture presented with an acute non-traumatic right knee pain and instability during sports. Magnetic resonance imaging confirmed a complete rupture of his distal patellar tendon at the tibial tuberosity. The patellar tendon was repaired using two 5.5 mm BioCorkscrews (Arthrex) inserted into the tibial tuberosity; the tendon was stitched with the No. 2 fiberwires using Krackow technique. As the patellar tendon was degenerative, the repair was augmented with a semitendinosus tendon harvested using an open tendon stripper, leaving the distal attachment intact. At 2.6 years followup he had mild anterior knee pain, range of motion 0-130° and was able to squat. MRI scan done at followup revealed good healing of repaired patellar tendon.

  5. Activation of two forms of locomotion by a previously identified trigger interneuron for swimming in the medicinal leech.

    Science.gov (United States)

    Brodfuehrer, Peter D; McCormick, Kathryn; Tapyrik, Lauren; Albano, Alfonso M; Graybeal, Carolyn

    2008-03-01

    Higher-order projection interneurons that function in more than one behavior have been identified in a number of preparations. In this study, we document that stimulation of cell Tr1, a previously identified trigger interneuron for swimming in the medicinal leech, can also elicit the motor program for crawling in isolated nerve cords. We also show that motor choice is independent of the firing frequency of Tr1 and amount of spiking activity recorded extracellularly at three locations along the ventral nerve cord prior to Tr1 stimulation. On the other hand, during Tr1 stimulation there is a significant difference in the amount of activity elicited in the ventral nerve cord that correlates with the motor program activated. On average, Tr1 stimulation trials that lead to crawling elicit greater amounts of activity than in trials that lead to swimming.

  6. Patellar tendon re-rupture on the opposite end of the previous site of surgical repair

    Directory of Open Access Journals (Sweden)

    Bryan Thean Howe KOH

    2017-01-01

    Full Text Available We describe a rare case of a patellar tendon “re-rupture” at the opposite end of a previous proximal tendon repair. A 32-year-old male with a history of surgically repaired right proximal patellar tendon rupture presented with an acute non-traumatic right knee pain and instability during sports. Magnetic resonance imaging confirmed a complete rupture of his distal patellar tendon at the tibial tuberosity. The patellar tendon was repaired using two 5.5 mm BioCorkscrews (Arthrex inserted into the tibial tuberosity; the tendon was stitched with the No. 2 fiberwires using Krackow technique. As the patellar tendon was degenerative, the repair was augmented with a semitendinosus tendon harvested using an open tendon stripper, leaving the distal attachment intact. At 2.6 years followup he had mild anterior knee pain, range of motion 0-130[0] and was able to squat. MRI scan done at followup revealed good healing of repaired patellar tendon.

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

    Directory of Open Access Journals (Sweden)

    Ding H

    2014-05-01

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

  8. 2-methyl butyramide, a previously identified urine biomarker for Ascaris lumbricoides, is not present in infected Indonesian individuals.

    Science.gov (United States)

    Lagatie, Ole; Njumbe Ediage, Emmanuel; Pikkemaat, Jeroen A; Djuardi, Yenny; Stuyver, Lieven J

    2017-12-29

    ᅟ: Previous reports suggest that the 2-methyl butyramide and 2-methyl valeramide metabolites of Ascaris lumbricoides in urine of infected individuals could be considered as urinary biomarkers for active infection. We have developed an LC-MS method with a detection limit of 10 ng/mL using synthetic chemicals as reference material. Urine samples (n = 21) of infected individuals were analyzed for the presence of these metabolites, but they were not detected in any of the samples. Furthermore, the recorded 1 H-NMR spectrum for reference 2-methyl butyramide did not match with the spectrum that was described for the Ascaris metabolite. Based on these two observations, we concluded that the urinary biomarkers that were detected for A. lumbricoides infection are not 2-methyl butyramide nor 2-methylvaleramide. New discovery efforts will be required to identify the structure of these metabolite biomarkers in urine of infected individuals. Urine samples used in this study were collected as part of a clinical trial with trial number ISRCTN75636394 (12 November 2013).

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

    Directory of Open Access Journals (Sweden)

    Priyanka eSingh

    2011-03-01

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

  10. Use of thallium to identify monovalent cation binding sites in GroEL

    Science.gov (United States)

    Kiser, Philip D.; Lorimer, George H.; Palczewski, Krzysztof

    2009-01-01

    GroEL is a bacterial chaperone protein that assembles into a homotetra­decameric complex exhibiting D 7 symmetry and utilizes the co-chaperone protein GroES and ATP hydrolysis to assist in the proper folding of a variety of cytosolic proteins. GroEL utilizes two metal cofactors, Mg2+ and K+, to bind and hydrolyze ATP. A K+-binding site has been proposed to be located next to the nucleotide-binding site, but the available structural data do not firmly support this conclusion. Moreover, more than one functionally significant K+-binding site may exist within GroEL. Because K+ has important and complex effects on GroEL activity and is involved in both positive (intra-ring) and negative (inter-ring) cooperativity for ATP hydrolysis, it is important to determine the exact location of these cation-binding site(s) within GroEL. In this study, the K+ mimetic Tl+ was incorporated into GroEL crystals, a moderately redundant 3.94 Å resolution X-ray diffraction data set was collected from a single crystal and the strong anomalous scattering signal from the thallium ion was used to identify monovalent cation-binding sites. The results confirmed the previously proposed placement of K+ next to the nucleotide-binding site and also identified additional binding sites that may be important for GroEL function and cooperativity. These findings also demonstrate the general usefulness of Tl+ for the identification of monovalent cation-binding sites in protein crystal structures, even when the quality and resolution of the diffraction data are relatively low. PMID:19851000

  11. Using site-selection model to identify suitable sites for seagrass transplantation in the west coast of South Sulawesi

    Science.gov (United States)

    Lanuru, Mahatma; Mashoreng, S.; Amri, K.

    2018-03-01

    The success of seagrass transplantation is very much depending on the site selection and suitable transplantation methods. The main objective of this study is to develop and use a site-selection model to identify the suitability of sites for seagrass (Enhalus acoroides) transplantation. Model development was based on the physical and biological characteristics of the transplantation site. The site-selection process is divided into 3 phases: Phase I identifies potential seagrass habitat using available knowledge, removes unnecessary sites before the transplantation test is performed. Phase II involves field assessment and transplantation test of the best scoring areas identified in Phase I. Phase III is the final calculation of the TSI (Transplant Suitability Index), based on results from Phases I and II. The model was used to identify the suitability of sites for seagrass transplantation in the West coast of South Sulawesi (3 sites at Labakkang Coast, 3 sites at Awerange Bay, and 3 sites at Lale-Lae Island). Of the 9 sites, two sites were predicted by the site-selection model to be the most suitable sites for seagrass transplantation: Site II at Labakkang Coast and Site III at Lale-Lae Island.

  12. Geological heritage: Identifying, valuing and managing geological sites

    Directory of Open Access Journals (Sweden)

    Omar R. Martínez

    2008-01-01

    Full Text Available Little development has research in Geological Sciences, in our country and particularly in the province of Buenos Aires, had in connection with the sites which require special preservation and protection. However, there are many sites named by geological bibliography which should be valued and ,preserved as Geological Heritage. The Geological Heritage is just one more element of the natural heritage, and is a big part of our natural inheritance. At the 1972 UNESCO Conference in Paris on the protection of the world cultural and natural heritage, some countries began doing research to get to know, protect and value geological sites, which is undoubtedly a significant resource as well as a key tool for the tourist development of a territory. Making inventories, filing all the information necessary for description, and collecting data of interest so as to keep the inventories updated, all become indispensable to have a thorough knowledge of the geological wealth of an area. The files' designs bear some problems, in some cases, in connection with being too subjective and synthetic, and, in others, too detailed and rigorous.

  13. 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.

  14. 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.

  15. 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

  16. Fine-mapping of lipid regions in global populations discovers ethnic-specific signals and refines previously identified lipid loci

    Science.gov (United States)

    Zubair, Niha; Luis Ambite, Jose; Bush, William S.; Kichaev, Gleb; Lu, Yingchang; Manichaikul, Ani; Sheu, Wayne H-H.; Absher, Devin; Assimes, Themistocles L.; Bielinski, Suzette J.; Bottinger, Erwin P.; Buzkova, Petra; Chuang, Lee-Ming; Chung, Ren-Hua; Cochran, Barbara; Dumitrescu, Logan; Gottesman, Omri; Haessler, Jeffrey W.; Haiman, Christopher; Heiss, Gerardo; Hsiung, Chao A.; Hung, Yi-Jen; Hwu, Chii-Min; Juang, Jyh-Ming J.; Le Marchand, Loic; Lee, I-Te; Lee, Wen-Jane; Lin, Li-An; Lin, Danyu; Lin, Shih-Yi; Mackey, Rachel H.; Martin, Lisa W.; Pasaniuc, Bogdan; Peters, Ulrike; Predazzi, Irene; Quertermous, Thomas; Reiner, Alex P.; Robinson, Jennifer; Rotter, Jerome I.; Ryckman, Kelli K.; Schreiner, Pamela J.; Stahl, Eli; Tao, Ran; Tsai, Michael Y.; Waite, Lindsay L.; Wang, Tzung-Dau; Buyske, Steven; Ida Chen, Yii-Der; Cheng, Iona; Crawford, Dana C.; Loos, Ruth J.F.; Rich, Stephen S.; Fornage, Myriam; North, Kari E.; Kooperberg, Charles; Carty, Cara L.

    2016-01-01

    Abstract Genome-wide association studies have identified over 150 loci associated with lipid traits, however, no large-scale studies exist for Hispanics and other minority populations. Additionally, the genetic architecture of lipid-influencing loci remains largely unknown. We performed one of the most racially/ethnically diverse fine-mapping genetic studies of HDL-C, LDL-C, and triglycerides to-date using SNPs on the MetaboChip array on 54,119 individuals: 21,304 African Americans, 19,829 Hispanic Americans, 12,456 Asians, and 530 American Indians. The majority of signals found in these groups generalize to European Americans. While we uncovered signals unique to racial/ethnic populations, we also observed systematically consistent lipid associations across these groups. In African Americans, we identified three novel signals associated with HDL-C (LPL, APOA5, LCAT) and two associated with LDL-C (ABCG8, DHODH). In addition, using this population, we refined the location for 16 out of the 58 known MetaboChip lipid loci. These results can guide tailored screening efforts, reveal population-specific responses to lipid-lowering medications, and aid in the development of new targeted drug therapies. PMID:28426890

  17. Examination of Previously Published Data to Identify Patterns in the Social Representation of 'Hearing Aids' Across Countries.

    Science.gov (United States)

    Manchaiah, Vinaya; Ratinaud, Pierre; Tympas, Aristotle; Danermark, Berth; Germundsson, Per

    2018-04-01

    Societal factors seem to exercise a strong influence on hearing aid uptake, use, and satisfaction. In particular, knowledge, perception, and attitude of people will have bearing towards their and others health behavior and decisions. The current study aimed at understanding the perception of hearing aids by adults belonging to the general population in different countries. The study employed a crosssectional design. A sample of 404 adults from India, Iran, Portugal, and the United Kingdom were recruited by relying on a convenience sampling. Previously published data was re-analyzed but it was applied for different approach. Free association task was used to collect the data. They were asked to provide up to five words or phrases that come to mind when thinking about "hearing aids." The data was initially analyzed based on qualitative content analysis. This was followed by quantitative cluster analysis and chi square analysis. The content analysis suggested 39 main categories of responses related to hearing aids. The cluster analysis resulted in five main clusters, namely: 1) positive attitude, 2) external factors, 3) hearing aid use and satisfaction, 4) etiology, and 5) benefits and limitations of technology. A few demographic factors (i.e., education, occupation type, country) showed association with different clusters, although country of origin seemed to be associated with most clusters. The study provides us with unique insights into the perception of hearing aids by the general public, and additionally, the way demographic variables may influence these perceptions.

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

    Science.gov (United States)

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

    2017-10-31

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

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

    Science.gov (United States)

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

    2014-04-01

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

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

    Directory of Open Access Journals (Sweden)

    Tzong-Yi Lee

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

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

    Directory of Open Access Journals (Sweden)

    Yi-Ju Chen

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

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

    International Nuclear Information System (INIS)

    1990-04-01

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

  3. Criteria for identifying and evaluating candidate sites for open-field trials of genetically engineered mosquitoes.

    Science.gov (United States)

    Brown, David M; Alphey, Luke S; McKemey, Andrew; Beech, Camilla; James, Anthony A

    2014-04-01

    Recent laboratory successes in the development of genetically engineered mosquitoes for controlling pathogen transmission have fostered the need for standardized procedures for advancing the technical achievements to practical tools. It is incumbent in many cases for the same scientists doing the in-laboratory discovery research to also take on the initial challenges of developing the pathway that will move the technologies to the field. One of these challenges is having a set of criteria for selecting collaborators and sites for efficacy and safety field trials that combine rigorous science with good ethical and legal practices. Specific site-selection criteria were developed in four categories-Scientific, Regulatory, Community Engagement, and Resources-in anticipation of open-field releases of a transgenic mosquito strain designed to suppress populations of the dengue vector mosquito, Aedes aegypti. The criteria are derived from previous published material, discussions, and personal experiences with the expectation of providing guidance to laboratory scientists for addressing the conceptual and operational considerations for identifying partner researchers and countries with whom to collaborate. These criteria are not intended to be prescriptive nor can they be applied to every circumstance where genetic approaches are proposed for deployment. However, we encourage those involved in the discovery phase of research to consider each criterion during project planning activities, and where appropriate, incorporate them into a "go/no-go" decision-making process for further development and testing of the technologies.

  4. [Application of double created restriction site PCR-RFLP to identify MGMT gene polymorphisms].

    Science.gov (United States)

    Wang, Wei; Miao, Wenbin; Qiu, Yulan; Xia, Zhaolin

    2008-01-01

    To develop a proper assay for identifying single nucleotide polymorphisms( SNPs) of the MGMT gene. PCR primers were designed by create restriction site (CRS) method, then polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was adopted to identify four SNPs in MGMT gene. By PCR, one primer pair yielded target products containing MGMT84 SNP site, and the other primer pair yielded target products containing MGMT143, 160, 178 SNP sites. Four restriction enzymes were adopted to identify the four SNPs, respectively. The effects of PCR and RFLP were good. The methods for four SNPs of MGMT determinated by CRS-PCR-RFLP theory could be facility, economy, and rapidness.

  5. [Application of created restriction site PCR-RFLP to identify alcohol dehydrogenase 2 gene polymorphism].

    Science.gov (United States)

    Jiao, Jie; Wang, Wei; Liu, Jing; Xia, Zhaolin

    2009-01-01

    To develop a appropriate assay for identifying single nucleotide polymorphism (SNP) of alcohol dehydrogenase 2 (ADH2) gene. According to base substitution situation of one single base mutational site, we designed the present study primers. One of the primers was designed on the basis of neighbourhood sequence of the mutational site, that is, we made one mismatch base to let product a new enzyme site between the 3' end of the primer and the single base mutation type after the PCR amplification. Then PCR-RFLP was adopted to identify the SNP in ADH2 gene. One primer pair can get target products containing ADH2 SNP site by PCR, restriction enzymes Bsh1236I were adopted to identify the SNP site. The expected results were reached. It suggested that the method of detecting the SNP of ADH2 based on CRS-PCR-RFLP theory is facilitated, economic, and rapid.

  6. Identifying Service Delivery Strategies for Ethnically Diverse Users of a Wildland-Urban Recreation Site

    Science.gov (United States)

    John M. Baas

    1992-01-01

    Service delivery has become an increasingly important part of managing public lands for recreation. The range of preferences held by ethnically diverse users of recreation sites may warrant the development of more than one service delivery strategy. Two questions were examined: (1) Are there differences in site perceptions that can be identified on the basis on...

  7. 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.

  8. A screening system to identify transcription factors that induce binding site-directed DNA demethylation.

    Science.gov (United States)

    Suzuki, Takahiro; Maeda, Shiori; Furuhata, Erina; Shimizu, Yuri; Nishimura, Hajime; Kishima, Mami; Suzuki, Harukazu

    2017-12-08

    DNA methylation is a fundamental epigenetic modification that is involved in many biological systems such as differentiation and disease. We and others recently showed that some transcription factors (TFs) are involved in the site-specific determination of DNA demethylation in a binding site-directed manner, although the reports of such TFs are limited. Here, we develop a screening system to identify TFs that induce binding site-directed DNA methylation changes. The system involves the ectopic expression of target TFs in model cells followed by DNA methylome analysis and overrepresentation analysis of the corresponding TF binding motif at differentially methylated regions. It successfully identified binding site-directed demethylation of SPI1, which is known to promote DNA demethylation in a binding site-directed manner. We extended our screening system to 15 master TFs involved in cellular differentiation and identified eight novel binding site-directed DNA demethylation-inducing TFs (RUNX3, GATA2, CEBPB, MAFB, NR4A2, MYOD1, CEBPA, and TBX5). Gene ontology and tissue enrichment analysis revealed that these TFs demethylate genomic regions associated with corresponding biological roles. We also describe the characteristics of binding site-directed DNA demethylation induced by these TFs, including the targeting of highly methylated CpGs, local DNA demethylation, and the overlap of demethylated regions between TFs of the same family. Our results show the usefulness of the developed screening system for the identification of TFs that induce DNA demethylation in a site-directed manner.

  9. On site disposal of ex situ solidified contaminated soils. Previous tests of trazability; Reemplantacion en el emplazamiento de suelos estabilizados Ex-Situ. Ensayos previos de tratabilidad

    Energy Technology Data Exchange (ETDEWEB)

    Cordellat, F.; Dickhoff, K.

    2000-07-01

    On Site Disposal of Ex Situ Solidified contaminated soils. Feasibility tests: within site remediation technologies, Stabilization/solidification is among the flew ones that not only survived but also increased its importance in the last years. We will focus our attention in the case of leaving the ex-situ on-site stabilization/solidification. This possibility of ex-situ but on-site has many advantages and is getting increasing importance, so that for many cases, it has been established as proffered alternative by the Ministry of the Environment of Baden-Wuttemberg (Germany). In this paper we will deal mainly with pollution caused by metals. In this paper we will also focus the attention on the most important step in the previous feasibility study: the lixiviation tests and its application to the risk assessment of stabilized soils. (Author) 16 refs.

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

    Science.gov (United States)

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

    2016-01-01

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

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

    DEFF Research Database (Denmark)

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

    2009-01-01

    ; underestimating residual symptoms, negative symptoms, and side effects; or being to open for individual interpretation. The aim of this study was to present and evaluate a new method of classification according to treatment response and, thus, to identify patients in functional remission. METHOD: A naturalistic......, 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. RESULTS: In the patient population (n = 123), the patients in functional remission, as defined by CANSEPT, had higher quality of life, fewer hospitalizations...

  12. Grouping Parturients by Parity, Previous-Cesarean, and Mode of Delivery (P-C-MoD Classification) Better Identifies Groups at Risk for Postpartum Hemorrhage.

    Science.gov (United States)

    Reichman, Orna; Gal, Micahel; Sela, Hen Y; Khayyat, Izzat; Emanuel, Michael; Samueloff, Arnon

    2016-10-01

    Objective We aimed to create a clinical classification to better identify parturients at risk for postpartum hemorrhage (PPH). Method A retrospective cohort, including all women who delivered at a single tertiary care medical center, between 2006 and 2014. Parturients were grouped by parity and history of cesarean delivery (CD): primiparas, multipara, and multipara with previous CD. Each were further subgrouped by mode of delivery (spontaneous vaginal delivery [SVD], operative vaginal delivery [OVD], emergency or elective CD). In all, 12 subgroups, based on parity, previous cesarean, and mode of delivery, formed the P-C-MoD classification. PPH was defined as a decrease of ≥3 gram% hemoglobin from admission and/or transfusion of blood products. Univariate analysis followed by multivariate analysis was performed to assess risk for PPH, controlling for confounders. Results The crude rate of PPH among 126,693 parturients was 7%. The prevalence differed significantly among independent risk factors: primiparity, 14%; multiparity, 4%; OVD, 22%; and CD, 15%. The P-C-MoD classification, segregated better between parturients at risk for PPH. The prevalence of PPH was highest for primiparous undergoing OVD (27%) compared with multiparous with SVD (3%), odds ratio [OR] = 12.8 (95% confidence interval [CI],11.9-13.9). These finding were consistent in the multivariate analysis OR = 13.1 (95% CI,12.1-14.3). Conclusion Employing the P-C-MoD classification more readily identifies parturients at risk for PPH and is superior to estimations based on single risk factors. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

  13. Computational mapping identifies the binding sites of organic solvents on proteins

    Science.gov (United States)

    Dennis, Sheldon; Kortvelyesi, Tamas; Vajda, Sandor

    2002-01-01

    Computational mapping places molecular probes—small molecules or functional groups—on a protein surface to identify the most favorable binding positions. Although x-ray crystallography and NMR show that organic solvents bind to a limited number of sites on a protein, current mapping methods result in hundreds of energy minima and do not reveal why some sites bind molecules with different sizes and polarities. We describe a mapping algorithm that explains the origin of this phenomenon. The algorithm has been applied to hen egg-white lysozyme and to thermolysin, interacting with eight and four different ligands, respectively. In both cases the search finds the consensus site to which all molecules bind, whereas other positions that bind only certain ligands are not necessarily found. The consensus sites are pockets of the active site, lined with partially exposed hydrophobic residues and with a number of polar residues toward the edge. These sites can accommodate each ligand in a number of rotational states, some with a hydrogen bond to one of the nearby donor/acceptor groups. Specific substrates and/or inhibitors of hen egg-white lysozyme and thermolysin interact with the same side chains identified by the mapping, but form several hydrogen bonds and bind in unique orientations. PMID:11904374

  14. Diazepam-bound GABAA receptor models identify new benzodiazepine binding-site ligands

    Science.gov (United States)

    Richter, Lars; de Graaf, Chris; Sieghart, Werner; Varagic, Zdravko; Mörzinger, Martina; de Esch, Iwan J P; Ecker, Gerhard F; Ernst, Margot

    2012-01-01

    Benzodiazepines exert their anxiolytic, anticonvulsant, muscle-relaxant and sedative-hypnotic properties by allosterically enhancing the action of GABA at GABAA receptors via their benzodiazepine-binding site. Although these drugs have been used clinically since 1960, the molecular basis of this interaction is still not known. By using multiple homology models and an un biased docking protocol, we identified a binding hypothesis for the diazepam-bound structure of the benzodiazepine site, which was confirmed by experimental evidence. Moreover, two independent virtual screening approaches based on this structure identified known benzodiazepine-site ligands from different structural classes and predicted potential new ligands for this site. Receptor-binding assays and electrophysiological studies on recombinant receptors confirmed these predictions and thus identified new chemotypes for the benzodiazepine-binding site. Our results support the validity of the diazepam-bound structure of the benzodiazepine-binding pocket, demonstrate its suitability for drug discovery and pave the way for structure-based drug design. PMID:22446838

  15. Targeting the Akt1 allosteric site to identify novel scaffolds through virtual screening.

    Science.gov (United States)

    Yilmaz, Oya Gursoy; Olmez, Elif Ozkirimli; Ulgen, Kutlu O

    2014-02-01

    Preclinical data and tumor specimen studies report that AKT kinases are related to many human cancers. Therefore, identification and development of small molecule inhibitors targeting AKT and its signaling pathway can be therapeutic in treatment of cancer. Numerous studies report inhibitors that target the ATP-binding pocket in the kinase domains, but the similarity of this site, within the kinase family makes selectivity a major problem. The sequence identity amongst PH domains is significantly lower than that in kinase domains and developing more selective inhibitors is possible if PH domain is targeted. This in silico screening study is the first time report toward the identification of potential allosteric inhibitors expected to bind the cavity between kinase and PH domains of Akt1. Structural information of Akt1 was used to develop structure-based pharmacophore models comprising hydrophobic, acceptor, donor and ring features. The 3D structural information of previously identified allosteric Akt inhibitors obtained from literature was employed to develop a ligand-based pharmacophore model. Database was generated with drug like subset of ZINC and screening was performed based on 3D similarity to the selected pharmacophore hypotheses. Binding modes and affinities of the ligands were predicted by Glide software. Top scoring hits were further analyzed considering 2D similarity between the compounds, interactions with Akt1, fitness to pharmacophore models, ADME, druglikeness criteria and Induced-Fit docking. Using virtual screening methodologies, derivatives of 3-methyl-xanthine, quinoline-4-carboxamide and 2-[4-(cyclohexa-1,3-dien-1-yl)-1H-pyrazol-3-yl]phenol were proposed as potential leads for allosteric inhibition of Akt1. Copyright © 2013 Elsevier Ltd. All rights reserved.

  16. 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.

  17. 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.

  18. Identifying candidate sites for crop biofortification in Latin America: case studies in Colombia, Nicaragua and Bolivia.

    Science.gov (United States)

    Zapata-Caldas, Emmanuel; Hyman, Glenn; Pachón, Helena; Monserrate, Fredy Alexander; Varela, Liliana Vesga

    2009-05-19

    Agricultural science can address a population's vitamin, amino acid and mineral malnutrition through biofortification - agronomy, plant breeding and biotechnology to develop crops with high nutrient contents. Biofortified crop varieties should be grown in areas with populations at risk of nutrient deficiency and in areas where the same crop is already grown and consumed. Information on the population at risk of nutrient deficiency is rarely available for sub-national administrative units, such as provinces, districts, and municipalities. Nor is this type of information commonly analyzed with data on agricultural production. This project developed a method to identify populations at risk of nutrient deficiency in zones with high crop production, places where biofortification interventions could be targeted. Nutrient deficiency risk data were combined with crop production and socioeconomic data to assess the suitability of establishing an intervention. Our analysis developed maps of candidate sites for biofortification interventions for nine countries in Latin America and the Caribbean. Results for Colombia, Nicaragua, and Bolivia are presented in this paper. Interventions in northern Colombia appear promising for all crops, while sites for bean biofortification are widely scattered throughout the country. The most promising sites in Nicaragua are found in the center-north region. Candidate sites for biofortification in Bolivia are found in the central part of the country, in the Andes Mountains. The availability and resolution of data limits the analysis. Some areas show opportunities for biofortification of several crops, taking advantage of their spatial coincidence. Results from this analysis should be confirmed by experts or through field visits. This study demonstrates a method for identifying candidate sites for biofortification interventions. The method evaluates populations at risk of nutrient deficiencies for sub-national administrative regions, and

  19. 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

  20. 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

  1. Evaluation of different approaches for identifying optimal sites to predict mean hillslope soil moisture content

    Science.gov (United States)

    Liao, Kaihua; Zhou, Zhiwen; Lai, Xiaoming; Zhu, Qing; Feng, Huihui

    2017-04-01

    The identification of representative soil moisture sampling sites is important for the validation of remotely sensed mean soil moisture in a certain area and ground-based soil moisture measurements in catchment or hillslope hydrological studies. Numerous approaches have been developed to identify optimal sites for predicting mean soil moisture. Each method has certain advantages and disadvantages, but they have rarely been evaluated and compared. In our study, surface (0-20 cm) soil moisture data from January 2013 to March 2016 (a total of 43 sampling days) were collected at 77 sampling sites on a mixed land-use (tea and bamboo) hillslope in the hilly area of Taihu Lake Basin, China. A total of 10 methods (temporal stability (TS) analyses based on 2 indices, K-means clustering based on 6 kinds of inputs and 2 random sampling strategies) were evaluated for determining optimal sampling sites for mean soil moisture estimation. They were TS analyses based on the smallest index of temporal stability (ITS, a combination of the mean relative difference and standard deviation of relative difference (SDRD)) and based on the smallest SDRD, K-means clustering based on soil properties and terrain indices (EFs), repeated soil moisture measurements (Theta), EFs plus one-time soil moisture data (EFsTheta), and the principal components derived from EFs (EFs-PCA), Theta (Theta-PCA), and EFsTheta (EFsTheta-PCA), and global and stratified random sampling strategies. Results showed that the TS based on the smallest ITS was better (RMSE = 0.023 m3 m-3) than that based on the smallest SDRD (RMSE = 0.034 m3 m-3). The K-means clustering based on EFsTheta (-PCA) was better (RMSE land use was more efficient than the global random method. Forty and 60 sampling sites are needed for stratified sampling and global sampling respectively to make their performances comparable to the best K-means method (EFsTheta-PCA). Overall, TS required only one site, but its accuracy was limited. The best K

  2. 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

  3. 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.

  4. A Python analytical pipeline to identify prohormone precursors and predict prohormone cleavage sites

    Directory of Open Access Journals (Sweden)

    Bruce Southey

    2008-12-01

    Full Text Available Neuropeptides and hormones are signaling molecules that support cell-cell communication in the central nervous system. Experimentally characterizing neuropeptides requires significant efforts because of the complex and variable processing of prohormone precursor proteins into neuropeptides and hormones. We demonstrate the power and flexibility of the Python language to develop components of an bioinformatic analytical pipeline to identify precursors from genomic data and to predict cleavage as these precursors are en route to the final bioactive peptides. We identified 75 precursors in the rhesus genome, predicted cleavage sites using support vector machines and compared the rhesus predictions to putative assignments based on homology to human sequences. The correct classification rate of cleavage using the support vector machines was over 97% for both human and rhesus data sets. The functionality of Python has been important to develop and maintain NeuroPred (http://neuroproteomics.scs.uiuc.edu/neuropred.html, a user-centered web application for the neuroscience community that provides cleavage site prediction from a wide range of models, precision and accuracy statistics, post-translational modifications, and the molecular mass of potential peptides. The combined results illustrate the suitability of the Python language to implement an all-inclusive bioinformatics approach to predict neuropeptides that encompasses a large number of interdependent steps, from scanning genomes for precursor genes to identification of potential bioactive neuropeptides.

  5. A python analytical pipeline to identify prohormone precursors and predict prohormone cleavage sites.

    Science.gov (United States)

    Southey, Bruce R; Sweedler, Jonathan V; Rodriguez-Zas, Sandra L

    2008-01-01

    Neuropeptides and hormones are signaling molecules that support cell-cell communication in the central nervous system. Experimentally characterizing neuropeptides requires significant efforts because of the complex and variable processing of prohormone precursor proteins into neuropeptides and hormones. We demonstrate the power and flexibility of the Python language to develop components of an bioinformatic analytical pipeline to identify precursors from genomic data and to predict cleavage as these precursors are en route to the final bioactive peptides. We identified 75 precursors in the rhesus genome, predicted cleavage sites using support vector machines and compared the rhesus predictions to putative assignments based on homology to human sequences. The correct classification rate of cleavage using the support vector machines was over 97% for both human and rhesus data sets. The functionality of Python has been important to develop and maintain NeuroPred (http://neuroproteomics.scs.uiuc.edu/neuropred.html), a user-centered web application for the neuroscience community that provides cleavage site prediction from a wide range of models, precision and accuracy statistics, post-translational modifications, and the molecular mass of potential peptides. The combined results illustrate the suitability of the Python language to implement an all-inclusive bioinformatics approach to predict neuropeptides that encompasses a large number of interdependent steps, from scanning genomes for precursor genes to identification of potential bioactive neuropeptides.

  6. 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...... 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......-specific patterns in HCV disease and control....

  7. MONKEY: Identifying conserved transcription-factor binding sitesin multiple alignments using a binding site-specific evolutionarymodel

    Energy Technology Data Exchange (ETDEWEB)

    Moses, Alan M.; Chiang, Derek Y.; Pollard, Daniel A.; Iyer, VenkyN.; Eisen, Michael B.

    2004-10-28

    We introduce a method (MONKEY) to identify conserved transcription-factor binding sites in multispecies alignments. MONKEY employs probabilistic models of factor specificity and binding site evolution, on which basis we compute the likelihood that putative sites are conserved and assign statistical significance to each hit. Using genomes from the genus Saccharomyces, we illustrate how the significance of real sites increases with evolutionary distance and explore the relationship between conservation and function.

  8. 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.

  9. GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments.

    Science.gov (United States)

    Yevshin, Ivan; Sharipov, Ruslan; Valeev, Tagir; Kel, Alexander; Kolpakov, Fedor

    2017-01-04

    GTRD-Gene Transcription Regulation Database (http://gtrd.biouml.org)-is a database of transcription factor binding sites (TFBSs) identified by ChIP-seq experiments for human and mouse. Raw ChIP-seq data were obtained from ENCODE and SRA and uniformly processed: (i) reads were aligned using Bowtie2; (ii) ChIP-seq peaks were called using peak callers MACS, SISSRs, GEM and PICS; (iii) peaks for the same factor and peak callers, but different experiment conditions (cell line, treatment, etc.), were merged into clusters; (iv) such clusters for different peak callers were merged into metaclusters that were considered as non-redundant sets of TFBSs. In addition to information on location in genome, the sets contain structured information about cell lines and experimental conditions extracted from descriptions of corresponding ChIP-seq experiments. A web interface to access GTRD was developed using the BioUML platform. It provides: (i) browsing and displaying information; (ii) advanced search possibilities, e.g. search of TFBSs near the specified gene or search of all genes potentially regulated by a specified transcription factor; (iii) integrated genome browser that provides visualization of the GTRD data: read alignments, peaks, clusters, metaclusters and information about gene structures from the Ensembl database and binding sites predicted using position weight matrices from the HOCOMOCO database. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  10. Quantitative analysis of previously identified propionate-oxidizing bacteria and methanogens at different temperatures in an UASB reactor containing propionate as a sole carbon source.

    Science.gov (United States)

    Ban, Qiaoying; Li, Jianzheng; Zhang, Liguo; Jha, Ajay Kumar; Zhang, Yupeng

    2013-12-01

    Propionate degradation is crucial for maintaining the efficiency and stability of an anaerobic reactor. However, there was little information about the effects of ecological factor on propionate-oxidizing bacteria (POB). In current research, quantitative real-time fluorescence polymerase chain reaction (QPCR) of some identified POB and methanogens with a decrease in temperature in an upflow anaerobic sludge bed (UASB) reactor containing propionate as sole carbon source was investigated. The results showed that there were at least four identified POB, including Pelotomaculum schinkii, Pelotomaculum propionicum, Syntrophobacter fumaroxidans, and Syntrophobacter sulfatireducens, observed in this UASB reactor. Among them, P. schinkii was dominated during the whole operational period. Its quantity was 1.2 × 10(4) 16S rRNA gene copies per nanogram of DNA at 35 °C. A decrease in temperature from 35 to 30 °C led to P. schinkii to be increased by 1.8 times and then it was gradually reduced with a decrease in temperature from 30 to 25, 20, and 18 °C stepwise. A decrease in temperature from 35 to 20 °C did not make the amount of methanogens markedly changed, but hydrogenotrophic methanogens (Methanospirillum) and acetotrophic methanogens (Methanosaeta) at 18 °C were increased by an order of magnitude and 1.0 time, respectively, compared with other experimental conditions.

  11. 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

  12. Circulating levels of endocannabinoids and oxylipins altered by dietary lipids in older women are likely associated with previously identified gene targets.

    Science.gov (United States)

    Watkins, Bruce A; Kim, Jeffrey; Kenny, Anne; Pedersen, Theresa L; Pappan, Kirk L; Newman, John W

    2016-11-01

    Postmenopausal women (PMW) report marginal n-3 PUFA intakes and are at risk of chronic diseases associated with the skeletal, muscular, neuroendocrine, and cardiovascular systems. How n-3 PUFA affect the amounts of endocannabinoids (ECs) and oxylipins (OLs) of metabolic and physiologic importance in PMW is not clear. Based on our recent findings that dietary n-3 PUFA alter gene targets of the EC system and lower pro-inflammatory OL we proceeded to characterize these actions in blood of PMW. Our aim was to determine levels of the ECs, OLs, and global metabolites (GM) in white PMW (75±7y), randomized in a double-masked manner, from baseline to 6mo after receiving a fish oil supplement of n-3 PUFA (720mg 20:5n3+480mg 22:6n3/d, n=20) or placebo (1.8g oleic acid/d, n=20). ECs and OLs in serum were determined by UPLC-MS/MS and GM by GC-MS and LC-MS/MS. Plasma 20:5n3 and 22:6n3 levels increased in PMW given fish oil. EC n-6 acyl-ethanolamides, arachidonate-derived diols were decreased and 20:5n3 and 22:6n3 diols, epoxides, and alcohols were increased in PMW given fish oil. GM analysis revealed that n-3 PUFA supplementation increased renal steroid hormone and proteolytic metabolite levels in PMW. Herein, we confirm that gene targets of the EC system, previously found as modifiable by n-3 PUFA result in changes in the levels of ECs and OLs in PMW. This study shows phenotypic responses (in levels) to n-3 PUFA supplementation in PMW and increases of n-3 acyl-ethanolamide and n-3-derived OL of clinical considerations in aging. Copyright © 2016 Elsevier B.V. All rights reserved.

  13. Updated canine infection rates for Dirofilaria immitis in areas of Brazil previously identified as having a high incidence of heartworm-infected dogs.

    Science.gov (United States)

    Labarthe, Norma Vollmer; Paiva, Jonimar Pereira; Reifur, Larissa; Mendes-de-Almeida, Flavya; Merlo, Alexandre; Carvalho Pinto, Carlos Jose; Juliani, Paulo Sérgio; de Almeida, Maria Angela Ornelas; Alves, Leucio Câmara

    2014-11-07

    Canine heartworm infections were frequently diagnosed in Brazil before the new millennium. After the year 2000, the frequency of diagnosis showed a sharp decline; however, a few years later, new evidence indicated that the parasite was still present and that canine infection rates seemed to be increasing. Therefore, an updated survey of canine heartworm prevalence was conducted in several locations in south, southeast, and northeast Brazil. Dogs from 15 locations having previously reported a high prevalence of heartworm infection were included in the survey according to defined criteria, including the absence of treatment with a macrocyclic lactone for at least 1 year. Blood samples from 1531 dogs were evaluated by an in-clinic immunochromatography test kit (Witness® Heartworm, Zoetis, USA) for detection of Dirofilaria immitis antigen. At each location, epidemiologic data, including physical characteristics and clinical signs reported by owners or observed by veterinarians, were recorded on prepared forms for tabulation of results by location, clinical signs, and physical characteristics. The overall prevalence of canine heartworm infection was 23.1%, with evidence of heartworm-infected dogs detected in all 15 locations studied. There was a tendency for higher prevalence rates in environmentally protected areas, despite some locations having less-than-ideal environmental temperatures for survival of vector mosquitoes. Among physical characteristics, it was noted that dogs with predominantly white hair coats and residing in areas with a high (≥20%) prevalence of heartworm were less likely to have heartworm infection detected by a commercial heartworm antigen test kit than were dogs with other coat colors. In general, dogs older than 2 years were more frequently positive for D. immitis antigen than were younger dogs. Clinical signs of heartworm infections were rare or owners were unable to detect them, and could not be used for reliable prediction of the

  14. Delta-like ligand 4 identifies a previously uncharacterized population of inflammatory dendritic cells that plays important roles in eliciting allogeneic T cell responses in mice.

    Science.gov (United States)

    Mochizuki, Kazuhiro; Xie, Fang; He, Shan; Tong, Qing; Liu, Yongnian; Mochizuki, Izumi; Guo, Yajun; Kato, Koji; Yagita, Hideo; Mineishi, Shin; Zhang, Yi

    2013-04-01

    Graft-versus-host disease (GVHD) reflects an exaggerated inflammatory allogeneic T cell response in hosts receiving allogeneic hematopoietic stem cell transplantation (HSCT). Inhibition of pan-Notch receptor signaling in donor T cells causes reduction of GVHD. However, which Notch ligand(s) in what APCs is important for priming graft-versus-host reaction remains unknown. We demonstrate that δ-like ligand-4 (Dll4) and Dll4-positive (Dll4(high)) inflammatory dendritic cells (i-DCs) play important roles in eliciting allogeneic T cell responses. Host-type Dll4(high) i-DCs occurred in the spleen and intestine of HSCT mice during GVHD induction phase. These Dll4(high) i-DCs were CD11c(+)B220(+)PDCA-1(+), resembling plasmacytoid dentritic cells (pDCs) of naive mice. However, as compared with unstimulated pDCs, Dll4(high) i-DCs expressed higher levels of costimulatory molecules, Notch ligands Jagged1 and Jagged2, and CD11b, and produced more Ifnb and Il23 but less Il12. In contrast, Dll4-negative (Dll4(low)) i-DCs were CD11c(+)B220(-)PDCA-1(-), and had low levels of Jagged1. In vitro assays showed that Dll4(high) i-DCs induced significantly more IFN-γ- and IL-17-producing effector T cells (3- and 10-fold, respectively) than Dll4(low) i-DCs. This effect could be blocked by anti-Dll4 Ab. In vivo administration of Dll4 Ab reduced donor-alloreactive effector T cells producing IFN-γ and IL-17 in GVHD target organs, leading to reduction of GVHD and improved survival of mice after allogeneic HSCT. Our findings indicate that Dll4(high) i-DCs represent a previously uncharacterized i-DC population distinctive from steady state DCs and Dll4(low) i-DCs. Furthermore, Dll4 and Dll4(high) i-DCs may be beneficial targets for modulating allogeneic T cell responses, and could facilitate the discovery of human counterparts of mouse Dll4(high) i-DCs.

  15. Delta-like Ligand 4 Identifies a Previously Uncharacterized Population of Inflammatory Dendritic Cells That Plays Important Roles in Eliciting Allogeneic T-cell Responses in Mice1

    Science.gov (United States)

    Mochizuki, Kazuhiro; Xie, Fang; He, Shan; Tong, Qing; Liu, Yongnian; Mochizuki, Izumi; Guo, Yajun; Kato, Koji; Yagita, Hideo; Mineishi, Shin; Zhang, Yi

    2013-01-01

    Graft-versus-host disease (GVHD) reflects an exaggerated inflammatory allogeneic T-cell response in hosts receiving allogeneic hematopoietic stem cell transplantation (HSCT). Inhibition of pan-Notch receptor signaling in donor T cells causes reduction of GVHD. However, which Notch ligand(s) in what antigen-presenting cells are important for priming GVH reaction remains unknown. We demonstrate that δ-like ligand-4 (Dll4) and Dll4-positive (Dll4hi) inflammatory dendritic cells (i-DCs) play important roles in eliciting allogeneic T-cell responses. Host-type Dll4hi i-DCs occurred in the spleen and intestine of HSCT mice during GVHD induction phase. These Dll4hi i-DCs were CD11c+B220+PDCA-1+, resembling plasmacytoid DCs (pDCs) of naïve mice. However, as compared to unstimulated pDCs, Dll4hi i-DCs expressed higher levels of costimulatory molecules, Notch ligands Jagged1 and Jagged2 and CD11b and, produced more Ifnb and Il23 but less Il12. In contrast, Dll4-negative (Dll4lo) i-DCs were CD11c+B220−PDCA-1−, and had low levels of Jagged1. In vitro assays showed that Dll4hi i-DCs induced significantly more IFN-γ- and IL-17-producing effector T cells (3- and 10-fold, respectively) than Dll4lo i-DCs. This effect could be blocked by anti-Dll4 antibody. In vivo administration of Dll4 antibody reduced donor alloreactive effector T cells producing IFN-γ and IL-17 in GVHD target organs, leading to reduction of GVHD and improved survival of mice after allogeneic HSCT. Our findings indicate that Dll4hi i-DCs represent a previously uncharacterized i-DC population distinctive from steady state DCs and Dll4lo i-DCs. Furthermore, Dll4 and Dll4hi i-DCs may be beneficial targets for modulating allogeneic T-cell responses, and could facilitate the discovery of human counterparts of mouse Dll4hi i-DCs. PMID:23440416

  16. Identifying Patients Who May Be Candidates for a Clinical Trial of Salvage Accelerated Partial Breast Irradiation after Previous Whole Breast Irradiation

    Directory of Open Access Journals (Sweden)

    Linna Li

    2012-01-01

    Full Text Available Background and Objectives. Accelerated partial breast irradiation (APBI has been proposed as an alternative to salvage mastectomy for patients with ipsilateral breast tumor recurrence (IBTR after prior breast conservation. We studied factors that are associated with a more favorable local recurrence profile that could make certain patients eligible for APBI. Methods. Between 1980 and 2005, 157 Stage 0–II breast cancer patients had an IBTR treated by mastectomy. Clinical and pathological features were analyzed to identify factors associated with favorable IBTR defined as unifocal DCIS or T1 ≤ 2 cm, without skin involvement, and >2 year interval from initial treatment. Results. Median followup was 140 months and time to recurrence was 73 months. Clinical stage distribution at recurrence was DCIS in 32 pts (20%, T1 in 90 pts (57%, T2 in 14 pts (9%, T3 in 4 pts (3%, and T4 in 9 pts (6%. IBTR was classified as favorable in 71%. Clinical stage of IBTR predicted for pathologic stage –95% of patients with clinical T1 IBTR had pathologic T1 disease at salvage mastectomy . Conclusions. Clinical stage at presentation strongly correlated with pathologic stage at mastectomy. More than 70% of recurrences were favorable and may be appropriate candidates for salvage APBI trials.

  17. 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/.

  18. A Multi-Site Assessment of the ACSCOT Field Triage Decision Scheme for Identifying Seriously Injured Children and Adults

    Science.gov (United States)

    Newgard, Craig D; Zive, Dana; Holmes, James F; Bulger, Eileen M; Staudenmayer, Kristan; Liao, Michael; Rea, Thomas; Hsia, Renee Y; Wang, N Ewen; Fleischman, Ross; Jui, Jonathan; Mann, N Clay; Haukoos, Jason S; Sporer, Karl A; Gubler, K Dean; Hedges, Jerris R

    2011-01-01

    Background ACSCOT has developed and updated field trauma triage protocols for decades, yet the ability to identify major trauma patients remains unclear. We estimate the diagnostic value of the Field Triage Decision Scheme for identifying major trauma patients (Injury Severity Score [ISS] ≥ 16) in a large and diverse multi-site cohort. Study Design This was a retrospective cohort study of injured children and adults transported by 94 EMS agencies to 122 hospitals in 7 regions of the Western U.S. from 2006 through 2008. Patients who met any of the field trauma triage criteria (per EMS personnel) were considered triage positive. Hospital outcome measures were probabilistically linked to EMS records through trauma registries, state discharge data and emergency department data. The primary outcome defining a “major trauma patient” was ISS ≥ 16. Results 122,345 injured patients were evaluated and transported by EMS over the 3-year period, of who 34.5% met at least one triage criterion and 5.8% had ISS ≥ 16. The overall sensitivity and specificity of the criteria for identifying major trauma patients were 85.8% (95% CI 85.0 – 86.6%) and 68.7% (95% CI 68.4 – 68.9%). Triage sensitivity and specificity differed by age: 84.1% and 66.4% (0 – 17 years); 89.5% and 64.3% (18 – 54 years); and 79.9% and 75.4% (≥ 55 years). Evaluating the diagnostic value of triage by hospital destination (transport to Level I/II trauma centers) did not substantially improve these findings. Conclusions The sensitivity of the Field Triage Decision Scheme for identifying major trauma patients is lower and specificity higher than previously described, particularly among elders. PMID:22107917

  19. 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.

  20. 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.

  1. The utility of atrial pacing for identifying the electrical breakthrough sites between the left atrium and pulmonary veins

    Directory of Open Access Journals (Sweden)

    Shinya Sugiura, MD

    2017-04-01

    Conclusions: This pacing method may help to identify whether EBSs are located in the anterior Lt.PVs. Improved recognition of EBSs through pacing from different sites would be helpful for achieving PV isolation.

  2. A whole-genome approach to identifying protein binding sites: promoters in Methanocaldococcus (Methanococcus) jannaschii.

    Science.gov (United States)

    Li, Enhu; Reich, Claudia I; Olsen, Gary J

    2008-12-01

    We have adapted an electrophoretic mobility shift assay (EMSA) to isolate genomic DNA fragments that bind the archaeal transcription initiation factors TATA-binding protein (TBP) and transcription factor B (TFB) to perform a genome-wide search for promoters. Mobility-shifted fragments were cloned, tested for their ability to compete with known promoter-containing fragments for a limited concentration of transcription factors, and sequenced. We applied the method to search for promoters in the genome of Methanocaldococcus jannaschii. Selection was most efficient for promoters of tRNA genes and genes for several presumed small non-coding RNAs (ncRNA). Protein-coding gene promoters were dramatically underrepresented relative to their frequency in the genome. The repeated isolation of these genomic regions was partially rectified by including a hybridization-based screening. Sequence alignment of the affinity-selected promoters revealed previously identified TATA box, BRE, and the putative initiator element. In addition, the conserved bases immediately upstream and downstream of the BRE and TATA box suggest that the composition and structure of archaeal natural promoters are more complicated.

  3. GISMOWA: Geospatial Risk-Based Analysis Identifying Water Quality Monitoring Sites in Distribution Systems

    DEFF Research Database (Denmark)

    Larsen, Sille Lyster; Christensen, Sarah Christine Boesgaard; Albrechtsen, Hans-Jørgen

    2017-01-01

    threats, e.g., contaminated sites; and (3) sensitive consumers, e.g., hospitals, in a GIS environment. The tool used a multicriteria decision analysis to evaluate multiple monitoring site parameters and map zones particularly suitable for water quality monitoring. GISMOWA was applied to Danish water......Monitoring water quality in drinking water distribution systems is the basis for proactive approaches to prevent or manage emerging water quality issues, and such a monitoring requires a strategic selection of relevant and representative monitoring sites. GISMOWA is a new GIS and risk...

  4. Multiple antibiotic resistance indexing of coliforms to identify high risk contamination sites in aquatic environment.

    Science.gov (United States)

    Chitanand, M P; Kadam, T A; Gyananath, G; Totewad, N D; Balhal, D K

    2010-06-01

    Bacteriological analysis of the water samples collected from upstream, midstream and downstream points along the bank of the river revealed high populations of Escherichia coli, Citrobacter freundii, Citrobacter diversus, Enterobacter aerogens and Klebsiella species. All these isolates were screened against eight antibiotics to determine the prevalence of multiple antibiotic resistance among isolates at different sites of the river. The study revealed that multiple antibiotic resistance was prominently seen in coliforms at downstream sites (Average multiple antibiotic resistance index, MAR Index = 0.43) while it was low in coliforms at upstream sites (MAR Index = 0.15). These differences in MAR indices provide a method for distinguishing high risk contamination sites in aquatic environment.

  5. 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.

  6. Application of Created Restriction Site PCR-RFLP to Identify POT1 Gene Polymorphism.

    Science.gov (United States)

    Wang, Tuanwei; Wang, Sihua; Duan, Xiaoran; Feng, Xiaolei; Wang, Pengpeng; Yao, Wu; Wu, Yongjun; Feng, Feifei; Yu, Songcheng; Wu, Yiming; Wang, Wei

    2016-06-01

    Protection of telomeres protein 1 (POT1) plays pivotal roles in protection of chromosome ends and regulation of telomere length with other telomere binding proteins; its genetic polymorphisms are associated with many diseases. In this study, we explored a novel PCR-RFLP method for typing the single nucleotide polymorphism (SNP) rs1034794 of the human POT1 gene. A new restriction enzyme site was introduced into a POT1 gene amplification product by created restriction site PCR (CRS-PCR). One primer was designed based on changed sequence; after PCR amplification, a new restriction enzyme site for AluI was introduced into the PCR products. One hundred and seventy eight samples from Han Chinese individuals were tested to evaluate this new method. The 3'-end of the forward primer was next to the polymorphic site, and the third base from the 3'-end was the mismatched base A. The final PCR product contained the AGCT sequence (AluI recognition site) when the ancestral POT1 alleles were amplified. The data obtained with the new method perfectly matched those obtained with the sequencing method. Thus, CRS-PCR is a new low-cost and high-efficiency alternative for rs1034794 typing.

  7. 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

  8. 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.

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

    Science.gov (United States)

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

  10. 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 <15 kg) comprised the majority (52%) of the jaguar kill sites. From prey found at kill sites, jaguars killed calves (Bos taurus) at a lower frequency than previously reported, whereas pumas preyed on calves at a higher frequency than previously reported in the same area. In our study area, jaguars preyed on calves at approximately the same rate as pumas (jaguars 3.7 calves per year, pumas 4.9 calves per year). Calculated predation rates were limited only to collared animals within our study area and therefore should not be considered applicable to all pumas and jaguars in Sonora.

  11. 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.

  12. Derivation of Effective Resuspension Factors in Scenarios for Inhalation Exposure Involving Resuspension of Previously Deposited Fallout by Nuclear Detonations at Nevada Test Site

    Science.gov (United States)

    2009-11-30

    total activities in smallest size fractions of fallout samples from tower shots in Operation TEAPOT at NTS...Trabalka and Kocher, 2007). 2 Dancz and Chehata (2006) identified nine shots in Operations TUMBLER-SNAPPER (1952), UPSHOT-KNOTHOLE (1953), and TEAPOT ...SNAPPER, Shot MET in Operation TEAPOT , and Shots BOLTZMANN and PRISCILLA in Operation PLUMBBOB. 7 Calculations represented in Figure 2-2 apply under

  13. 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

  14. Identifying N6-methyladenosine sites using multi-interval nucleotide pair position specificity and support vector machine

    Science.gov (United States)

    Xing, Pengwei; Su, Ran; Guo, Fei; Wei, Leyi

    2017-04-01

    N6-methyladenosine (m6A) refers to methylation of the adenosine nucleotide acid at the nitrogen-6 position. It plays an important role in a series of biological processes, such as splicing events, mRNA exporting, nascent mRNA synthesis, nuclear translocation and translation process. Numerous experiments have been done to successfully characterize m6A sites within sequences since high-resolution mapping of m6A sites was established. However, as the explosive growth of genomic sequences, using experimental methods to identify m6A sites are time-consuming and expensive. Thus, it is highly desirable to develop fast and accurate computational identification methods. In this study, we propose a sequence-based predictor called RAM-NPPS for identifying m6A sites within RNA sequences, in which we present a novel feature representation algorithm based on multi-interval nucleotide pair position specificity, and use support vector machine classifier to construct the prediction model. Comparison results show that our proposed method outperforms the state-of-the-art predictors on three benchmark datasets across the three species, indicating the effectiveness and robustness of our method. Moreover, an online webserver implementing the proposed predictor has been established at http://server.malab.cn/RAM-NPPS/. It is anticipated to be a useful prediction tool to assist biologists to reveal the mechanisms of m6A site functions.

  15. Mobile and Fixed-Site Measurements To Identify Spatial Distributions of Traffic-Related Pollution Sources in Los Angeles.

    Science.gov (United States)

    Tessum, Mei W; Larson, Timothy; Gould, Timothy R; Simpson, Christopher D; Yost, Michael G; Vedal, Sverre

    2018-03-06

    Mobile monitoring and fixed-site monitoring using passive sampling devices (PSD) are popular air pollutant measurement techniques with complementary strengths and weaknesses. This study investigates the utility of combining data from concurrent 2-week mobile monitoring and fixed-site PSD campaigns in Los Angeles in the summer and early spring to identify sources of traffic-related air pollutants (TRAP) and their spatial distributions. There were strong to moderate correlations between mobile and fixed-site PSD measurements of both NO 2 and NO x in the summer and spring (Pearson's r between 0.43 and 0.79), suggesting that the two data sets can be reliably combined for source apportionment. PCA identified the major TRAP sources as light-duty vehicle emissions, diesel exhaust, crankcase vent emissions, and an independent source of combustion-derived ultrafine particle emissions. The component scores of those four sources at each site were significantly correlated across the two seasons (Pearson's r between 0.58 and 0.79). Spatial maps of absolute principal component scores showed all sources to be most prominent near major roadways and the central business district and the ultrafine particle source being, in addition, more prominent near the airport. Mobile monitoring combined with fixed-site PSD sampling can provide high spatial resolution estimates of TRAP and can reveal underlying sources of exposure variability.

  16. Phosphorus status of diverse soils in Finland as influenced by long-term P fertilisation I.Native and previously applied P at 24 experimental sites

    Directory of Open Access Journals (Sweden)

    I. SAARELA

    2008-12-01

    Full Text Available The native reserves of phosphorus (P in Finnish soils are sizeable but poorly available to plants. The P status has been generally poor, but large rates of P applied since the 1940s have substantially enhanced the supply of P from the soil. As a means of optimising P fertilisation of crops grown in the improved soils and promoting agro-environmental sustainability of agriculture, long-term field experiments were established in 1977-1981 on various soil types around Finland, between the latitudes of 60 and 65 N. The experimental sites (8 Cambisols, 9 Regosols, 6 Histosols, 1 Podsol were moderately acidic (pH w 5.6, range 4.6-6.6 and contained 1.6-31.2% organic C, and (mineral soils 3-74% clay. The concentration of total P was 1.22 (0.66-1.87 g kg -1 , and the inorganic fraction separated with fluoride and hydroxide extractions (Al,Fe-P was 8.2% (4.5-12.4% of oxalate extractable Al+Fe (P saturation index. In mineral topsoil the pool of Al,Fe-P was 850 kg ha -1 , which is 300 kg ha -1 larger than was obtained in the early 1960s and 600 kg ha -1 larger than found in virgin soils. The soil test P value was 13.1 (3.7-60 mg dm -3 by the acid ammonium acetate method, 11.5 (1.6-42 mg dm -3 by a water extraction method (1:60 v/v and 61 (23-131 mg kg -1 with a modified Olsen method. The intensity factor of soil P status has remained at a relatively low level in a major part of the cultivated area.;

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

    Directory of Open Access Journals (Sweden)

    Brian Spencer Hoyt

    2014-01-01

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

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

    Science.gov (United States)

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

    2014-06-01

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

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

    Science.gov (United States)

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

    2014-07-01

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

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

    Science.gov (United States)

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

    1998-06-01

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

  1. A combinatorial approach to identify calpain cleavage sites in the Machado-Joseph disease protein ataxin-3.

    Science.gov (United States)

    Weber, Jonasz J; Golla, Matthias; Guaitoli, Giambattista; Wanichawan, Pimthanya; Hayer, Stefanie N; Hauser, Stefan; Krahl, Ann-Christin; Nagel, Maike; Samer, Sebastian; Aronica, Eleonora; Carlson, Cathrine R; Schöls, Ludger; Riess, Olaf; Gloeckner, Christian J; Nguyen, Huu P; Hübener-Schmid, Jeannette

    2017-05-01

    Ataxin-3, the disease protein in Machado-Joseph disease, is known to be proteolytically modified by various enzymes including two major families of proteases, caspases and calpains. This processing results in the generation of toxic fragments of the polyglutamine-expanded protein. Although various approaches were undertaken to identify cleavage sites within ataxin-3 and to evaluate the impact of fragments on the molecular pathogenesis of Machado-Joseph disease, calpain-mediated cleavage of the disease protein and the localization of cleavage sites remained unclear. Here, we report on the first precise localization of calpain cleavage sites in ataxin-3 and on the characterization of the resulting breakdown products. After confirming the occurrence of calpain-derived fragmentation of ataxin-3 in patient-derived cell lines and post-mortem brain tissue, we combined in silico prediction tools, western blot analysis, mass spectrometry, and peptide overlay assays to identify calpain cleavage sites. We found that ataxin-3 is primarily cleaved at two sites, namely at amino acid positions D208 and S256 and mutating amino acids at both cleavage sites to tryptophan nearly abolished ataxin-3 fragmentation. Furthermore, analysis of calpain cleavage-derived fragments showed distinct aggregation propensities and toxicities of C-terminal polyglutamine-containing breakdown products. Our data elucidate the important role of ataxin-3 proteolysis in the pathogenesis of Machado-Joseph disease and further emphasize the relevance of targeting this disease pathway as a treatment strategy in neurodegenerative disorders. © The Author (2017). Published by Oxford University Press on behalf of the Guarantors of Brain. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  2. Biological Characterization of an Improved Pyrrole-Based Colchicine Site Agent Identified through Structure-Based Design.

    Science.gov (United States)

    Rohena, Cristina C; Telang, Nakul S; Da, Chenxiao; Risinger, April L; Sikorski, James A; Kellogg, Glen E; Gupton, John T; Mooberry, Susan L

    2016-02-01

    A refined model of the colchicine site on tubulin was used to design an improved analog of the pyrrole parent compound, JG-03-14. The optimized compound, NT-7-16, was evaluated in biological assays that confirm that it has potent activities as a new colchicine site microtubule depolymerizer. NT-7-16 exhibits antiproliferative and cytotoxic activities against multiple cancer cell lines, with IC(50) values of 10-16 nM, and it is able to overcome drug resistance mediated by the expression of P-glycoprotein and the βIII isotype of tubulin. NT-7-16 initiated the concentration-dependent loss of cellular microtubules and caused the formation of abnormal mitotic spindles, leading to mitotic accumulation. The direct interaction of NT-7-16 with purified tubulin was confirmed, and it was more potent than combretastatin A-4 in these assays. Binding studies verified that NT-7-16 binds to tubulin within the colchicine site. The antitumor effects of NT-7-16 were evaluated in an MDA-MB-435 xenograft model and it had excellent activity at concentrations that were not toxic. A second compound, NT-9-21, which contains dichloro moieties in place of the 3,5-dibromo substituents of NT-7-16, had a poorer fit within the colchicine site as predicted by modeling and the Hydropathic INTeractions score. Biological evaluations showed that NT-9-21 has 10-fold lower potency than NT-7-16, confirming the modeling predictions. These studies highlight the value of the refined colchicine-site model and identify a new pyrrole-based colchicine-site agent with potent in vitro activities and promising in vivo antitumor actions. Copyright © 2016 by The American Society for Pharmacology and Experimental Therapeutics.

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

    DEFF Research Database (Denmark)

    Lindhard, Søren Munch

    2014-01-01

    In on-site production, mass-customized subproducts are assembled through standardized processes. The production is pushing mass customization to the edge by producing unique and complex products. Due to the project structure, it has proven difficult to avoid repetitions of problems and to learn...... from mistakes. A central part of the control framework Last Planner System is to identify not completed activities to identify root causes and to learn. One tool to investigate root causes is the 5 WHYs approach. The 5 WHYs approach has been applied in a case study research to analysis the root cause...... to not completed activities. In total, 17 non-completed activities were registered and analyzed. To reduce non-completions, the risks each activity is carrying should be analyzed and understood, the product should be followed to identify problems early and to reveal time for intervention, and finally...

  4. Longitudinal Antigenic Sequences and Sites from Intra-Host Evolution (LASSIE Identifies Immune-Selected HIV Variants

    Directory of Open Access Journals (Sweden)

    Peter Hraber

    2015-10-01

    Full Text Available Within-host genetic sequencing from samples collected over time provides a dynamic view of how viruses evade host immunity. Immune-driven mutations might stimulate neutralization breadth by selecting antibodies adapted to cycles of immune escape that generate within-subject epitope diversity. Comprehensive identification of immune-escape mutations is experimentally and computationally challenging. With current technology, many more viral sequences can readily be obtained than can be tested for binding and neutralization, making down-selection necessary. Typically, this is done manually, by picking variants that represent different time-points and branches on a phylogenetic tree. Such strategies are likely to miss many relevant mutations and combinations of mutations, and to be redundant for other mutations. Longitudinal Antigenic Sequences and Sites from Intrahost Evolution (LASSIE uses transmitted founder loss to identify virus “hot-spots” under putative immune selection and chooses sequences that represent recurrent mutations in selected sites. LASSIE favors earliest sequences in which mutations arise. With well-characterized longitudinal Env sequences, we confirmed selected sites were concentrated in antibody contacts and selected sequences represented diverse antigenic phenotypes. Practical applications include rapidly identifying immune targets under selective pressure within a subject, selecting minimal sets of reagents for immunological assays that characterize evolving antibody responses, and for immunogens in polyvalent “cocktail” vaccines.

  5. Strategy for identifying natural analogs of the long-term performance of low-level waste disposal sites

    Energy Technology Data Exchange (ETDEWEB)

    Chatters, J.C.; Waugh, W.J.; Foley, M.G.; Kincaid, C.T.

    1990-07-01

    The US Department of Energy's Low-Level Waste (LLW) Management Program has asked Pacific Northwest Laboratory (PNL) to explore the feasibility of using natural analogs of anticipated waste site and conditions to help validate predictions of the performance of LLW disposal sites. Current regulations require LLW facilities to control the spread of hazardous substances into the environment for at least the next 500 years. Natural analog studies can provide information about processes affecting waste containment that cannot be fully explored through laboratory experimentation and modeling because of the extended period of required performance. For LLW applications, natural analogs include geochemical systems, pedogenic (soil formation) indicators, proxy climate data, and ecological and archaeological settings that portray long-term changes in disposal site environments and the survivability of proposed waste containment materials and structures. Analog data consist of estimates of performance assessment (PA) model input parameters that define possible future environmental states of waste sites, validation parameters that can be predicted by PA models, and descriptive information that can build public confidence in waste disposal practices. This document describes PNL's overall stategy for identifying analogs for LLW disposal systems, reviews lessons learned from past analogs work, outlines the findings of the workshop, and presents examples of analog studies that workshop participants found to be applicable to LLW performance assessment. The lessons from the high-level waste analogs experience and workshop discussions will be used to develop detailed study plans during FY 1990. 39 refs.

  6. PolyA_DB 3 catalogs cleavage and polyadenylation sites identified by deep sequencing in multiple genomes.

    Science.gov (United States)

    Wang, Ruijia; Nambiar, Ram; Zheng, Dinghai; Tian, Bin

    2018-01-04

    PolyA_DB is a database cataloging cleavage and polyadenylation sites (PASs) in several genomes. Previous versions were based mainly on expressed sequence tags (ESTs), which had a limited amount and could lead to inaccurate PAS identification due to the presence of internal A-rich sequences in transcripts. Here, we present an updated version of the database based solely on deep sequencing data. First, PASs are mapped by the 3' region extraction and deep sequencing (3'READS) method, ensuring unequivocal PAS identification. Second, a large volume of data based on diverse biological samples increases PAS coverage by 3.5-fold over the EST-based version and provides PAS usage information. Third, strand-specific RNA-seq data are used to extend annotated 3' ends of genes to obtain more thorough annotations of alternative polyadenylation (APA) sites. Fourth, conservation information of PAS across mammals sheds light on significance of APA sites. The database (URL: http://www.polya-db.org/v3) currently holds PASs in human, mouse, rat and chicken, and has links to the UCSC genome browser for further visualization and for integration with other genomic data. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  7. 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.

  8. Quantitative Phosphoproteomics after Auxin-stimulated Lateral Root Induction Identifies an SNX1 Protein Phosphorylation Site Required for Growth*

    Science.gov (United States)

    Zhang, Hongtao; Zhou, Houjiang; Berke, Lidija; Heck, Albert J. R.; Mohammed, Shabaz; Scheres, Ben; Menke, Frank L. H.

    2013-01-01

    Protein phosphorylation is instrumental to early signaling events. Studying system-wide phosphorylation in relation to processes under investigation requires a quantitative proteomics approach. In Arabidopsis, auxin application can induce pericycle cell divisions and lateral root formation. Initiation of lateral root formation requires transcriptional reprogramming following auxin-mediated degradation of transcriptional repressors. The immediate early signaling events prior to this derepression are virtually uncharacterized. To identify the signal molecules responding to auxin application, we used a lateral root-inducible system that was previously developed to trigger synchronous division of pericycle cells. To identify and quantify the early signaling events following this induction, we combined 15N-based metabolic labeling and phosphopeptide enrichment and applied a mass spectrometry-based approach. In total, 3068 phosphopeptides were identified from auxin-treated root tissue. This root proteome dataset contains largely phosphopeptides not previously reported and represents one of the largest quantitative phosphoprotein datasets from Arabidopsis to date. Key proteins responding to auxin treatment included the multidrug resistance-like and PIN2 auxin carriers, AUXIN RESPONSE FACTOR2 (ARF2), SUPPRESSOR OF AUXIN RESISTANCE 3 (SAR3), and SORTING NEXIN1 (SNX1). Mutational analysis of serine 16 of SNX1 showed that overexpression of the mutated forms of SNX1 led to retarded growth and reduction of lateral root formation due to the reduced outgrowth of the primordium, showing proof of principle for our approach. PMID:23328941

  9. Quantitative phosphoproteomics after auxin-stimulated lateral root induction identifies an SNX1 protein phosphorylation site required for growth.

    Science.gov (United States)

    Zhang, Hongtao; Zhou, Houjiang; Berke, Lidija; Heck, Albert J R; Mohammed, Shabaz; Scheres, Ben; Menke, Frank L H

    2013-05-01

    Protein phosphorylation is instrumental to early signaling events. Studying system-wide phosphorylation in relation to processes under investigation requires a quantitative proteomics approach. In Arabidopsis, auxin application can induce pericycle cell divisions and lateral root formation. Initiation of lateral root formation requires transcriptional reprogramming following auxin-mediated degradation of transcriptional repressors. The immediate early signaling events prior to this derepression are virtually uncharacterized. To identify the signal molecules responding to auxin application, we used a lateral root-inducible system that was previously developed to trigger synchronous division of pericycle cells. To identify and quantify the early signaling events following this induction, we combined (15)N-based metabolic labeling and phosphopeptide enrichment and applied a mass spectrometry-based approach. In total, 3068 phosphopeptides were identified from auxin-treated root tissue. This root proteome dataset contains largely phosphopeptides not previously reported and represents one of the largest quantitative phosphoprotein datasets from Arabidopsis to date. Key proteins responding to auxin treatment included the multidrug resistance-like and PIN2 auxin carriers, auxin response factor2 (ARF2), suppressor of auxin resistance 3 (SAR3), and sorting nexin1 (SNX1). Mutational analysis of serine 16 of SNX1 showed that overexpression of the mutated forms of SNX1 led to retarded growth and reduction of lateral root formation due to the reduced outgrowth of the primordium, showing proof of principle for our approach.

  10. 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.

  11. 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

  12. A pseudo-full mutation identified in fragile X assay reveals a novel base change abolishing an EcoRI restriction site.

    Science.gov (United States)

    Liang, Shujian; Bass, Harold N; Gao, Hanlin; Astbury, Caroline; Jamehdor, Mehdi R; Qu, Yong

    2008-09-01

    Diagnostic testing for the fragile X syndrome is designed to detect the most common mutation, a CGG expansion in the 5'-untranslated region of the fragile X mental retardation (FMRI) gene. PCR can determine the number of CGG repeats less than 100, whereas Southern analysis can detect large premutations, full mutations, and their methylation status. Bands larger than 5.8 kb observed via Southern analysis are usually considered a methylated full mutation, causing fragile X syndrome in males and varied clinical presentations in females. We observed a 10.9-kb band on a Southern blot assay from an autistic girl with language delay. Further investigation identified a novel G-to-A transition at an EcoRI cleavage site, upstream of the CGG repeat region of the FMRI gene. This base change abolished the EcoRI restriction site, resulting in a 10.9-kb pseudo-full mutation. This G-to-A base change has not been previously reported and was not identified in a subsequent analysis of 105 male and 30 female patient samples. The clear 10.9-kb band detected on a Southern blot assay for fragile X syndrome mimics a large, methylated full mutation, which could result in a misdiagnosis without the benefit of family studies and further testing.

  13. Genome-wide analysis of p63 binding sites identifies AP-2 factors as co-regulators of epidermal differentiation.

    Science.gov (United States)

    McDade, Simon S; Henry, Alexandra E; Pivato, Geraldine P; Kozarewa, Iwanka; Mitsopoulos, Constantinos; Fenwick, Kerry; Assiotis, Ioannis; Hakas, Jarle; Zvelebil, Marketa; Orr, Nicholas; Lord, Christopher J; Patel, Daksha; Ashworth, Alan; McCance, Dennis J

    2012-08-01

    The p63 transcription factor (TP63) is critical in development, growth and differentiation of stratifying epithelia. This is highlighted by the severity of congenital abnormalities caused by TP63 mutations in humans, the dramatic phenotypes in knockout mice and de-regulation of TP63 expression in neoplasia altering the tumour suppressive roles of the TP53 family. In order to define the normal role played by TP63 and provide the basis for better understanding how this network is perturbed in disease, we used chromatin immunoprecipitation combined with massively parallel sequencing (ChIP-seq) to identify >7500 high-confidence TP63-binding regions across the entire genome, in primary human neonatal foreskin keratinocytes (HFKs). Using integrative strategies, we demonstrate that only a subset of these sites are bound by TP53 in response to DNA damage. We identify a role for TP63 in transcriptional regulation of multiple genes genetically linked to cleft palate and identify AP-2alpha (TFAP2A) as a co-regulator of a subset of these genes. We further demonstrate that AP-2gamma (TFAP2C) can bind a subset of these regions and that acute depletion of either TFAP2A or TFAP2C alone is sufficient to reduce terminal differentiation of organotypic epidermal skin equivalents, indicating overlapping physiological functions with TP63.

  14. 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

    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...

  15. Random mutagenesis MAPPIT analysis identifies binding sites for Vif and Gag in both cytidine deaminase domains of Apobec3G.

    Directory of Open Access Journals (Sweden)

    Isabel Uyttendaele

    Full Text Available The mammalian two-hybrid system MAPPIT allows the detection of protein-protein interactions in intact human cells. We developed a random mutagenesis screening strategy based on MAPPIT to detect mutations that disrupt the interaction of one protein with multiple protein interactors simultaneously. The strategy was used to detect residues of the human cytidine deaminase Apobec3G that are important for its homodimerization and its interaction with the HIV-1 Gag and Vif proteins. The strategy is able to identify the previously described head-to-head homodimerization interface in the N-terminal domain of Apobec3G. Our analysis further detects two new potential interaction surfaces in the N-and C-terminal domain of Apobec3G for interaction with Vif and Gag or for Apobec3G dimerization.

  16. Mendelian Randomization Analysis Identifies CpG Sites as Putative Mediators for Genetic Influences on Cardiovascular Disease Risk.

    Science.gov (United States)

    Richardson, Tom G; Zheng, Jie; Davey Smith, George; Timpson, Nicholas J; Gaunt, Tom R; Relton, Caroline L; Hemani, Gibran

    2017-10-05

    The extent to which genetic influences on cardiovascular disease risk are mediated by changes in DNA methylation levels has not been systematically explored. We developed an analytical framework that integrates genetic fine mapping and Mendelian randomization with epigenome-wide association studies to evaluate the causal relationships between methylation levels and 14 cardiovascular disease traits. We identified ten genetic loci known to influence proximal DNA methylation which were also associated with cardiovascular traits after multiple-testing correction. Bivariate fine mapping provided evidence that the individual variants responsible for the observed effects on cardiovascular traits at the ADCY3 and ADIPOQ loci were potentially mediated through changes in DNA methylation, although we highlight that we are unable to reliably separate causality from horizontal pleiotropy. Estimates of causal effects were replicated with results from large-scale consortia. Genetic variants and CpG sites identified in this study were enriched for histone mark peaks in relevant tissue types and gene promoter regions. Integrating our results with expression quantitative trait loci data, we provide evidence that variation at these regulatory regions is likely to also influence gene expression levels at these loci. Copyright © 2017 American Society of Human Genetics. All rights reserved.

  17. 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.

  18. 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 pumas preyed on calves at a higher frequency than previously reported in the same area. In our study area, jaguars preyed on calves at approximately the same rate as pumas (jaguars 3.7 calves per year, pumas 4.9 calves per year). Calculated predation rates were limited only to collared animals within our study area and therefore should not be considered applicable to all pumas and jaguars in Sonora.

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

    Science.gov (United States)

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

    2015-01-01

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

  20. 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

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

    Science.gov (United States)

    Sharp, G.; Mount, G.

    2017-12-01

    Acid mine drainage pollutes over 3000 miles of streams and ground water in Pennsylvania alone, and in response many solutions have been developed to counteract the effects of acidic mine drainage. It is estimated by USGS that restoring these watersheds would cost 5 billion-15 billion in total. As economic conditions place limits on expenditures, cost effective means of remediation will be of critical importance. One such method is passive bioremediation, and in the case of metal contamination, self-sustaining oxygenation. Our location of interest is the Tanoma Acid Mine Drainage engineered wetland near Tanoma, Pennsylvania. It is estimated that up to 5,000 gallons per minute is currently being discharged into the site. While most local remediation sites are acidic (pH <4), the Tanoma wetland allows for the study of bioremediation in more neutral pH setting (pH of 5.5-7.5). In this study, we look to further understand biologic, chemical, and hydrologic controls that contribute to the efficiency of the wetland. Our research will focus on the spatial and temporal distribution of biomass through the wetland system as well as changes in water and soil chemistry. Local biofilm (Leptothrix discophora ) are an important part of the remediation process, using iron from the water as an energy source. The bacteria reduce the iron content of the water, precipitating it onto the pond bed as Terraced Iron Formations (TIF). Terraces iron formations (TIF's) are correlated with localized biofilm-archaea densities where archaea thrive in iron rich sediments. By determining bacteria densities in the wetland through gram stain analysis, we can further understand their role in terraced iron formation creation, find localized TIF's that occur, and correlate methane production due to archaea in that location. Mapping TIF locations and identifying bacteria densities will help determine the bioremediation effects on the overall efficiency of iron reduction throughout the Tanoma AMD passive

  2. 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.

  3. 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/.

  4. 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.

  5. PREVIOUS SECOND TRIMESTER ABORTION

    African Journals Online (AJOL)

    PNLC

    PREVIOUS SECOND TRIMESTER ABORTION: A risk factor for third trimester uterine rupture in three ... for accurate diagnosis of uterine rupture. KEY WORDS: Induced second trimester abortion - Previous uterine surgery - Uterine rupture. ..... scarred uterus during second trimester misoprostol- induced labour for a missed ...

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

    KAUST Repository

    Pham, Tony

    2014-01-01

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

  7. 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.

  8. Identifying the binding site(s) for antidepressants on the Torpedo nicotinic acetylcholine receptor: [3H]2-azidoimipramine photolabeling and molecular dynamics studies.

    Science.gov (United States)

    Sanghvi, Mitesh; Hamouda, Ayman K; Jozwiak, Krzysztof; Blanton, Michael P; Trudell, James R; Arias, Hugo R

    2008-12-01

    Radioligand binding, photoaffinity labeling, and docking and molecular dynamics were used to characterize the tricyclic antidepressant (TCA) binding sites in the nicotinic acetylcholine receptor (nAChR). Competition experiments indicate that the noncompetitive antagonist phencyclidine (PCP) inhibits [3H]imipramine binding to resting (closed) and desensitized nAChRs. [3H]2-azidoimipramine photoincorporates into each subunit from the desensitized nAChR with approximately 25% of the labeling specifically inhibited by TCP (a PCP analog), whereas no TCP-inhibitable labeling was observed in the resting (closed) state. For the desensitized nAChR and within the alpha subunit, the majority of specific [3H]2-azidoimipramine labeling mapped to a approximately 20 kDa Staphylococcus aureus V8 protease fragment (alphaV8-20; Ser173-Glu338). To further map the labeling site, the alphaV8-20 fragment was further digested with endoproteinase Lys-C and resolved by Tricine SDS-PAGE. The principal labeled fragment (11 kDa) was further purified by rpHPLC and subjected to N-terminal sequencing. Based on the amino terminus (alphaMet243) and apparent molecular weight, the 11 kDa fragment contains the channel lining M2 segment. Finally, docking and molecular dynamics results indicate that imipramine and PCP interact preferably with the M2 transmembrane segments in the middle of the ion channel. Collectively, these results are consistent with a model where PCP and TCA bind to overlapping sites within the lumen of the Torpedo nAChR ion channel.

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

    DEFF Research Database (Denmark)

    Farajzadeh, Leila; Hornshøj, Henrik; Momeni, Jamal

    2013-01-01

    expression level, together with an analysis of variation in transcription start sites, promoter usage, and splicing. Totally, 223 million RNA fragments were sequenced leading to the identification of 59,930 transcribed gene locations and 290,936 transcript variants using Cufflinks with similarity......The transcriptome is the absolute set of transcripts in a tissue or cell at the time of sampling. In this study RNA-Seq is employed to enable the differential analysis of the transcriptome profile for ten porcine tissues in order to evaluate differences between the tissues at the gene and isoform...... of differential transcription start sites showed that the number of these sites is generally increased in comparisons including hypothalamus in contrast to other pairwise assessments. A comprehensive analysis of one of the tissue contrasts, i.e. cerebellum versus heart for differential variation at the gene...

  10. 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.

  11. Identifying and overcoming the constraints that prevent the full implementation of decommissioning and remediation programs in uranium mining sites.

    Science.gov (United States)

    Franklin, Mariza Ramalho; Fernandes, Horst Monken

    2013-05-01

    Environmental remediation of radioactive contamination is about achieving appropriate reduction of exposures to ionizing radiation. This goal can be achieved by means of isolation or removal of the contamination source(s) or by breaking the exposure pathways. Ideally, environmental remediation is part of the planning phase of any industrial operation with the potential to cause environmental contamination. This concept is even more important in mining operations due to the significant impacts produced. This approach has not been considered in several operations developed in the past. Therefore many legacy sites face the challenge to implement appropriate remediation plans. One of the first barriers to remediation works is the lack of financial resources as environmental issues used to be taken in the past as marginal costs and were not included in the overall budget of the company. This paper analyses the situation of the former uranium production site of Poços de Caldas in Brazil. It is demonstrated that in addition to the lack of resources, other barriers such as the lack of information on site characteristics, appropriate regulatory framework, funding mechanisms, stakeholder involvement, policy and strategy, technical experience and mechanism for the appropriation of adequate technical expertise will play key roles in preventing the implementation of remediation programs. All these barriers are discussed and some solutions are suggested. It is expected that lessons learned from the Poços de Caldas legacy site may stimulate advancement of more sustainable options in the development of future uranium production centers. Copyright © 2011 Elsevier Ltd. All rights reserved.

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

    Energy Technology Data Exchange (ETDEWEB)

    Farajzadeh, Leila; Hornshøj, Henrik; Momeni, Jamal; Thomsen, Bo; Larsen, Knud; Hedegaard, Jakob; Bendixen, Christian; Madsen, Lone Bruhn, E-mail: LoneB.Madsen@agrsci.dk

    2013-08-23

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

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

    International Nuclear Information System (INIS)

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

    2013-01-01

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

  14. 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.

  15. An analysis approach to identify specific functional sites in orthologous proteins using sequence and structural information: application to neuroserpin reveals regions that differentially regulate inhibitory activity.

    Science.gov (United States)

    Lee, Tet Woo; Yang, Annie Shu-Ping; Brittain, Thomas; Birch, Nigel P

    2015-01-01

    The analysis of sequence conservation is commonly used to predict functionally important sites in proteins. We have developed an approach that first identifies highly conserved sites in a set of orthologous sequences using a weighted substitution-matrix-based conservation score and then filters these conserved sites based on the pattern of conservation present in a wider alignment of sequences from the same family and structural information to identify surface-exposed sites. This allows us to detect specific functional sites in the target protein and exclude regions that are likely to be generally important for the structure or function of the wider protein family. We applied our method to two members of the serpin family of serine protease inhibitors. We first confirmed that our method successfully detected the known heparin binding site in antithrombin while excluding residues known to be generally important in the serpin family. We next applied our sequence analysis approach to neuroserpin and used our results to guide site-directed polyalanine mutagenesis experiments. The majority of the mutant neuroserpin proteins were found to fold correctly and could still form inhibitory complexes with tissue plasminogen activator (tPA). Kinetic analysis of tPA inhibition, however, revealed altered inhibitory kinetics in several of the mutant proteins, with some mutants showing decreased association with tPA and others showing more rapid dissociation of the covalent complex. Altogether, these results confirm that our sequence analysis approach is a useful tool that can be used to guide mutagenesis experiments for the detection of specific functional sites in proteins. © 2014 Wiley Periodicals, Inc.

  16. American Bird conservancy's approach to the U.S. Important Bird Area Program - identifying the top 500 global sites

    Science.gov (United States)

    Robert M. Chipley

    2005-01-01

    The idea for the Important Bird Area Program originated in a series of studies in the early 1980s conducted by BirdLife International. Recognizing that these studies could become a powerful tool for conservation, BirdLife International began an effort to identify and gather data regarding the most important areas for birds in Europe and to make this information...

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

    International Nuclear Information System (INIS)

    Nobile, C.; Romeo, G.

    1988-01-01

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

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

    DEFF Research Database (Denmark)

    Fleskens, Luuk; Irvine, Brian; Kirkby, Mike

    2012-01-01

    -explicit cost-benefit analysis to calculate the financial viability of technologies. After setting up the PESERA-DESMICE modelling system, a series of scenarios were designed to assess land degradation and land (biomass) productivity under different circumstances. A scenario typology including baseline...... scenarios, technology scenarios, policy scenarios, adoption scenarios and global scenarios was used for this purpose. A total of 65 different scenario simulations were performed for 22 different technologies in 12 study sites. The report first explains how the models were calibrated and how the scenarios...... and increase food production. A major bottleneck for adoption is financial viability. Low (zero) cost agronomic measures and other options that deliver important benefits in the short term are the preferred technologies. Stakeholder evaluation and model output mostly concur on this. There are important design...

  19. Combining bulk sediment OSL and meteoric 10 Be fingerprinting techniques to identify gully initiation sites and erosion depths

    OpenAIRE

    Portenga, E.W.; Bishop, P.; Rood, D.H.; Bierman, P.R.

    2017-01-01

    Deep erosional gullies dissect landscapes around the world. Existing erosion models focus on predicting where gullies might begin to erode, but identifying where existing gullies were initiated and under what conditions is difficult, especially when historical records are unavailable. Here we outline a new approach for fingerprinting alluvium and tracing it back to its source by combining bulk sediment optically stimulated luminescence (bulk OSL) and meteoric 10Be (10Bem) measurements made on...

  20. The Min system and nucleoid occlusion are not required for identifying the division site in Bacillus subtilis but ensure its efficient utilization.

    Directory of Open Access Journals (Sweden)

    Christopher D A Rodrigues

    Full Text Available Precise temporal and spatial control of cell division is essential for progeny survival. The current general view is that precise positioning of the division site at midcell in rod-shaped bacteria is a result of the combined action of the Min system and nucleoid (chromosome occlusion. Both systems prevent assembly of the cytokinetic Z ring at inappropriate places in the cell, restricting Z rings to the correct site at midcell. Here we show that in the bacterium Bacillus subtilis Z rings are positioned precisely at midcell in the complete absence of both these systems, revealing the existence of a mechanism independent of Min and nucleoid occlusion that identifies midcell in this organism. We further show that Z ring assembly at midcell is delayed in the absence of Min and Noc proteins, while at the same time FtsZ accumulates at other potential division sites. This suggests that a major role for Min and Noc is to ensure efficient utilization of the midcell division site by preventing Z ring assembly at potential division sites, including the cell poles. Our data lead us to propose a model in which spatial regulation of division in B. subtilis involves identification of the division site at midcell that requires Min and nucleoid occlusion to ensure efficient Z ring assembly there and only there, at the right time in the cell cycle.

  1. Randomized proof of concept trial of GLYX-13, an N-methyl-D-aspartate receptor glycine site partial agonist, in major depressive disorder nonresponsive to a previous antidepressant agent.

    Science.gov (United States)

    Preskorn, Sheldon; Macaluso, Matthew; Mehra, D O Vishaal; Zammit, Gary; Moskal, Joseph R; Burch, Ronald M

    2015-03-01

    Approximately 45% of patients with major depressive disorder (MDD) do not remit when treated with biogenic amine antidepressants. Consequently, there is a significant need for antidepressant agents with different mechanisms of action. Early proof of concept (POC) studies with such novel agents play a significant role in helping drug developers identify agents and mechanisms of action that merit more intensive research. Studies have demonstrated that high affinity N-methyl-Daspartate (NMDA) receptor blockers (eg, ketamine) can produce rapid antidepressant effects in patients who have not responded to currently available agents, but treatment with these agents is accompanied by psychotomimetic effects that make their use problematic. This column describes a POC study involving GLYX-13, an N-methyl-D-aspartate receptor glycine site functional partial agonist. In this double-blind, randomized, placebo-controlled study, a single intravenous (IV) dose of GLYX-13 (1, 5, 10, or 30 mg/kg) or placebo was administered to 116 subjects with MDD who had not benefitted from a trial of at least one biogenic amine antidepressant during the current episode. The primary outcome measure was score on the Hamilton Depression Rating Scale-17 (Ham-D17), which was used to rate overall depressive symptoms at baseline and at 24 hours and days 3, 7, 14, and, in some arms, days 21 and 28 after administration. GLYX-13, 5 or 10 mg/kg IV, reduced depressive symptoms as assessed by the Ham-D17 at days 1 through 7. Onset of action as assessed using the Bech-6 occurred within 2 hours. GLYX-13 did not elicit psychotomimetic or other significant side effects. In this early POC study, GLYX-13 reduced depressive symptoms within 2 hours and this effect was maintained for 7 days on average in subjects with MDD who had not responded to another antidepressant agent during the current depressive episode. The findings of this study support the hypothesis that modulation of the NMDA receptor is a valid target

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

    Science.gov (United States)

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

    2010-12-01

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

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

    Science.gov (United States)

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

    2010-01-01

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

  4. Using Rare Earth Element (REE) tracers to identify preferential micro-sites of post-fire aeolian erosion

    Science.gov (United States)

    Van Pelt, R.; Zobeck, T. M.; Barnes, M. A.; Baddock, M.; D'Odorico, P.

    2011-12-01

    Plant communities in desert environments are spatially anisotropic. Nutrient islands develop below shrub canopies and in the bases of bunch grasses that enhance plant growth and reinforce the spatial anisotropy. Catastrophic disturbance that removes the vegetation such as fire or drought can result in the release of the trapped sediment which becomes redistributed over the landscape by wind and water. We applied Rare Earth Element (REE) tracers to different landscape positions of an anisotropic Northern Chihuahua Desert ecosystem at the Sevilleta National Wildlife Refuge in central New Mexico in an effort to study this process. We delineated three 0.5 m by 6 m plots of desert grassland and three plots of desert grassland-shrubland ecotone. Nitric acid was used to dissolve the REE oxides (Eu2O3, Dy2O3, and Pr6O11) which were then diluted in distilled water to a target concentration of 1 g REE l-1 and applied to the surface at a rate of 4 l m-2. From laboratory column studies using soil collected at the site, we estimated that this would penetrate the surface to a depth of 2.5 cm resulting in a sediment REE concentration of approximately 100 mg kg-1. Eu was applied to bare surfaces between vegetation characterized as sand with a surface covering of gravel, Pr was applied under grass clumps, and Dy was applied under Creosote Bush (Larrea tridentata (DC.). Two replicate 0.25 m2 areas of each surface type were also tagged to obtain a sample of tagged surface sediment for analysis. The area containing the plots was burned by U.S. Fish and Wildlife personnel on April 14, 2010. During the next two days, two grassland plots and two grassland-shrubland ecotone plots were tested by placing a portable boundary layer field wind tunnel over the plots and blowing them with 12 m s-1 wind for 10 minutes during which time a paired set of entrained sediment samples were captured at the outlet of the wind tunnel. This period was followed by a 30 minute test in which clean quartz sand

  5. 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.

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

    Directory of Open Access Journals (Sweden)

    Praveen Kulkarni

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

  7. iRPIS-PseNNC: identifying RNA-protein interaction sites by incorporating the position-specific dinucleotide propensity into ensemble random forest approach

    Science.gov (United States)

    Li, Long; Chen, Guojin; Jin, Tingdu

    2017-06-01

    As the pile of RNA-Protein complexes sequences mounted, in order to overcome time-consuming problem of the traditional identify RNA-Protein interaction sites (RPIS) method, it is urgent need develop intelligent recognition approach for quickly and reliable recognition of the RNA-Protein interaction sites (RPIS). To settle the question, we developed a new method named iRPIS-PseNNC, in which each sample is a nineteen nucleotides segment that for positive the centre of the segments is RPIS and for negative the segments centre is non-RPIS, and the sample was obtained by sliding window. The RNA sample was formulated by combining the dipeptide position-specific propensity into random forest approach, and by using the random sampling to balance the training dataset. According the voting system, we combine eleven random forest together to construct an ensemble classifier. It is shown that via the rigorous cross validations that the new predictor “iRPIS-PseNNC” achieved very high percentage of accuracy than any other existing algorithms in this field, indicating that the iRPIS-PseNNC predictor will be an effective tool for prediction RNA-Protein interaction sites.

  8. CaMKII Phosphorylation of Na(V)1.5: Novel in Vitro Sites Identified by Mass Spectrometry and Reduced S516 Phosphorylation in Human Heart Failure.

    Science.gov (United States)

    Herren, Anthony W; Weber, Darren M; Rigor, Robert R; Margulies, Kenneth B; Phinney, Brett S; Bers, Donald M

    2015-05-01

    The cardiac voltage-gated sodium channel, Na(V)1.5, drives the upstroke of the cardiac action potential and is a critical determinant of myocyte excitability. Recently, calcium (Ca(2+))/calmodulin(CaM)-dependent protein kinase II (CaMKII) has emerged as a critical regulator of Na(V)1.5 function through phosphorylation of multiple residues including S516, T594, and S571, and these phosphorylation events may be important for the genesis of acquired arrhythmias, which occur in heart failure. However, phosphorylation of full-length human Na(V)1.5 has not been systematically analyzed and Na(V)1.5 phosphorylation in human heart failure is incompletely understood. In the present study, we used label-free mass spectrometry to assess phosphorylation of human Na(V)1.5 purified from HEK293 cells with full coverage of phosphorylatable sites and identified 23 sites that were phosphorylated by CaMKII in vitro. We confirmed phosphorylation of S516 and S571 by LC-MS/MS and found a decrease in S516 phosphorylation in human heart failure, using a novel phospho-specific antibody. This work furthers our understanding of the phosphorylation of Na(V)1.5 by CaMKII under normal and disease conditions, provides novel CaMKII target sites for functional validation, and provides the first phospho-proteomic map of full-length human Na(V)1.5.

  9. STD-NMR experiments identify a structural motif with novel second-site activity against West Nile virus NS2B-NS3 protease.

    Science.gov (United States)

    Schöne, Tobias; Grimm, Lena Lisbeth; Sakai, Naoki; Zhang, Linlin; Hilgenfeld, Rolf; Peters, Thomas

    2017-10-01

    West Nile virus (WNV) belongs to the genus Flavivirus of the family Flaviviridae. This mosquito-borne virus that is highly pathogenic to humans has been evolving into a global threat during the past two decades. Despite many efforts, neither antiviral drugs nor vaccines are available. The viral protease NS2B-NS3 pro is essential for viral replication, and therefore it is considered a prime drug target. However, success in the development of specific NS2B-NS3 pro inhibitors had been moderate so far. In the search for new structural motifs with binding affinity for NS2B-NS3 pro , we have screened a fragment library, the Maybridge Ro5 library, employing saturation transfer difference (STD) NMR experiments as readout. About 30% of 429 fragments showed binding to NS2B-NS3 pro . Subsequent STD-NMR competition experiments using the known active site fragment A as reporter ligand yielded 14 competitively binding fragments, and 22 fragments not competing with A. In a fluorophore-based protease assay, all of these fragments showed inhibition in the micromolar range. Interestingly, 10 of these 22 fragments showed a notable increase of STD intensities in the presence of compound A suggesting cooperative binding. The most promising non-competitive inhibitors 1 and 2 (IC 50 ∼ 500 μM) share a structural motif that may guide the development of novel second-site (potentially allosteric) inhibitors of NS2B-NS3 pro . To identify the matching protein binding site, chemical shift perturbation studies employing 1 H, 15 N-TROSY-HSQC experiments with uniformly 2 H, 15 N-labeled protease were performed in the presence of 1, and in the concomitant absence or presence of A. The data suggest that 1 interacts with Met 52* of NS2B, identifying a secondary site adjacent to the binding site of A. Therefore, our study paves the way for the synthesis of novel bidentate NS2B-NS3 pro inhibitors. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Whole exome sequencing identifies a novel splice-site mutation in ADAMTS17 in an Indian family with Weill-Marchesani syndrome.

    Science.gov (United States)

    Shah, Mohd Hussain; Bhat, Vishwanath; Shetty, Jyoti S; Kumar, Arun

    2014-01-01

    Weill-Marchesani syndrome (WMS) is a rare connective tissue disorder, characterized by short stature, microspherophakic lens, and stubby hands and feet (brachydactyly). WMS is caused by mutations in the FBN1, ADAMTS10, and LTBP2 genes. Mutations in the LTBP2 and ADAMTS17 genes cause a WMS-like syndrome, in which the affected individuals show major features of WMS but do not display brachydactyly and joint stiffness. The main purpose of our study was to determine the genetic cause of WMS in an Indian family. Whole exome sequencing (WES) was used to identify the genetic cause of WMS in the family. The cosegregation of the mutation was determined with Sanger sequencing. Reverse transcription (RT)-PCR analysis was used to assess the effect of a splice-site mutation on splicing of the ADAMTS17 transcript. The WES analysis identified a homozygous novel splice-site mutation c.873+1G>T in a known WMS-like syndrome gene, ADAMTS17, in the family. RT-PCR analysis in the patient showed that exon 5 was skipped, which resulted in the deletion of 28 amino acids in the ADAMTS17 protein. The mutation in the WMS-like syndrome gene ADAMTS17 also causes WMS in an Indian family. The present study will be helpful in genetic diagnosis of this family and increases the number of mutations of this gene to six.

  11. A Novel Computational Strategy to Identify A-to-I RNA Editing Sites by RNA-Seq Data: De Novo Detection in Human Spinal Cord Tissue

    Science.gov (United States)

    Picardi, Ernesto; Gallo, Angela; Galeano, Federica; Tomaselli, Sara; Pesole, Graziano

    2012-01-01

    RNA editing is a post-transcriptional process occurring in a wide range of organisms. In human brain, the A-to-I RNA editing, in which individual adenosine (A) bases in pre-mRNA are modified to yield inosine (I), is the most frequent event. Modulating gene expression, RNA editing is essential for cellular homeostasis. Indeed, its deregulation has been linked to several neurological and neurodegenerative diseases. To date, many RNA editing sites have been identified by next generation sequencing technologies employing massive transcriptome sequencing together with whole genome or exome sequencing. While genome and transcriptome reads are not always available for single individuals, RNA-Seq data are widespread through public databases and represent a relevant source of yet unexplored RNA editing sites. In this context, we propose a simple computational strategy to identify genomic positions enriched in novel hypothetical RNA editing events by means of a new two-steps mapping procedure requiring only RNA-Seq data and no a priori knowledge of RNA editing characteristics and genomic reads. We assessed the suitability of our procedure by confirming A-to-I candidates using conventional Sanger sequencing and performing RNA-Seq as well as whole exome sequencing of human spinal cord tissue from a single individual. PMID:22957051

  12. Quantitative in vivo Analyses Reveal Calcium-dependent Phosphorylation Sites and Identifies a Novel Component of the Toxoplasma Invasion Motor Complex

    Science.gov (United States)

    Nebl, Thomas; Prieto, Judith Helena; Kapp, Eugene; Smith, Brian J.; Williams, Melanie J.; Yates, John R.; Cowman, Alan F.; Tonkin, Christopher J.

    2011-01-01

    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. PMID:21980283

  13. Genome-wide mapping of estrogen receptor α binding sites by ChIP-seq to identify genes related to sexual maturity in hens.

    Science.gov (United States)

    Guo, Miao; Li, Yi; Chen, Yuxia; Guo, Xiaoli; Yuan, Zhenjie; Jiang, Yunliang

    2018-02-05

    In ovarian follicle development, estrogen acts as a regulatory molecule to mediate proliferation and differentiation of follicular cells. ERα (estrogen receptor α) exerts regulatory function classically by binding directly to the estrogen response element, recruiting co-factors and activating or repressing transcription in response to E2. In this study, we used ChIP-seq to map ERα-binding sites in ovaries of Hy-line Brown commercial hens at 45d, 90d and 160d. In total, 24,886, 21,680 and 23,348 binding sites were identified in the ovaries of hens at 45d, 90d and 160d, which are linked to 86, 83 and 74 genes, respectively. The PPI network contains 47 protein nodes and 164 interaction edges, among which, AKT1 (V-Akt Murine Thymoma Viral Oncogene Homolog 1) and ACTN2 (Actinin Alpha 2) with the highest weight in the network, followed by CREB1 (CAMP Responsive Element Binding Protein 1), and EPHA5 (EPH Receptor A5) were identified. These genes are likely related to sexual maturity in hens. This study also provides insight into the regulation of the ERα target gene networks and a reference for understanding ERα-regulated transcription. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. An ENU mutagenesis screen in zebrafish for visual system mutants identifies a novel splice-acceptor site mutation in patched2 that results in Colobomas.

    Science.gov (United States)

    Lee, Jiwoon; Cox, Ben D; Daly, Christina M S; Lee, Chanjae; Nuckels, Richard J; Tittle, Rachel K; Uribe, Rosa A; Gross, Jeffrey M

    2012-12-13

    To identify recessive mutations affecting development and/or maintenance of the zebrafish visual system. A three-generation ENU (N-Nitroso-N-ethylurea)-based forward genetic screen was performed. F3 embryos were screened visually from 1 to 5 days postfertilization (dpf) for ocular abnormalities, and 5 dpf embryos were fixed and processed for cryosectioning, after which eye sections were screened for defects in cellular organization within the retina, lens, and cornea. A combination of PCR and DNA sequencing, in situ hybridization, and pharmacological treatments were used to clone and characterize a coloboma mutant. A total of 126 F2 families were screened, and, from these, 18 recessive mutations were identified that affected eye development. Phenotypes included lens malformations and cataracts, photoreceptor defects, oculocutaneous albinism, microphthalmia, and colobomas. Analysis of one such coloboma mutant, uta(1), identified a splice-acceptor mutation in the patched2 gene that resulted in an in-frame deletion of 19 amino acids that are predicted to contribute to the first extracellular loop of Patched2. ptch2(uta1) mutants possessed elevated Hedgehog (Hh) pathway activity, and blocking the Hh pathway with cyclopamine prevented colobomas in ptch2(uta1) mutant embryos. We have identified 18 recessive mutations affecting development of the zebrafish visual system and we have characterized a novel splice-acceptor site mutation in patched2 that results in enhanced Hh pathway activity and colobomas.

  15. 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.

  16. iPreny-PseAAC: Identify C-terminal Cysteine Prenylation Sites in Proteins by Incorporating Two Tiers of Sequence Couplings into PseAAC.

    Science.gov (United States)

    Xu, Yan; Wang, Zu; Li, Chunhui; Chou, Kuo-Chen

    2017-01-01

    Occurring at the cysteine residue in the C-terminal of a protein, prenylation is a special kind of post-translational modification (PTM), which may play a key role for statin in altering immune function. Therefore, knowledge of the prenylation sites in proteins is important for drug development as well as for in-depth understanding the biological process concerned. Given a query protein whose C-terminal contains some cysteine residues, which one can be of prenylation or none of them can be prenylated? To address this problem, we have developed a new predictor, called "iPreny-PseAAC", by incorporating two tiers of sequence pair coupling effects into the general form of PseAAC (pseudo amino acid composition). It has been observed by four different cross-validation approaches that all the important indexes in reflecting its prediction quality are quite high and fully consistent to each other. It is anticipated that the iPreny-PseAAC predictor holds very high potential to become a useful high throughput tool in identifying protein C-terminal cysteine prenylation sites and the other relevant areas. To maximize the convenience for most experimental biologists, the webserver for the new predictor has been established at http://app.aporc.org/iPreny-PseAAC/, by which users can easily get their desired results without needing to go through the mathematical details involved in this paper. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  17. 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.

  18. A transposon site hybridization screen identifies galU and wecBC as important for survival of Yersinia pestis in murine macrophages.

    Science.gov (United States)

    Klein, Kathryn A; Fukuto, Hana S; Pelletier, Mark; Romanov, Galina; Grabenstein, Jens P; Palmer, Lance E; Ernst, Robert; Bliska, James B

    2012-02-01

    Yersinia pestis is able to survive and replicate within murine macrophages. However, the mechanism by which Y. pestis promotes its intracellular survival is not well understood. To identify genes that are important for Y. pestis survival in macrophages, a library comprised of ∼31,500 Y. pestis KIM6+ transposon insertion mutants (input pool) was subjected to negative selection in primary murine macrophages. Genes underrepresented in the output pool of surviving bacteria were identified by transposon site hybridization to DNA oligonucleotide microarrays. The screen identified several genes known to be important for survival of Y. pestis in macrophages, including phoPQ and members of the PhoPQ regulon (e.g., pmrF). In addition, genes predicated to encode a glucose-1-phosphate uridylyltransferase (galU), a UDP-N-acetylglucosamine 2-epimerase (wecB) and a UDP-N-acetyl-d-mannosamine dehydrogenase (wecC) were identified in the screen. Viable-count assays demonstrated that a KIM6+ galU mutant and a KIM6+ wecBC mutant were defective for survival in murine macrophages. The galU mutant was studied further because of its strong phenotype. The KIM6+ galU mutant exhibited increased susceptibility to the antimicrobial peptides polymyxin B and cathelicidin-related antimicrobial peptide (CRAMP). Polyacrylamide gel electrophoresis demonstrated that the lipooligosaccharide (LOS) of the galU mutant migrated faster than the LOS of the parent KIM6+, suggesting the core was truncated. In addition, the analysis of LOS isolated from the galU mutant by mass spectrometry showed that aminoarabinose modification of lipid A is absent. Therefore, addition of aminoarabinose to lipid A and complete LOS core (galU), as well as enterobacterial common antigen (wecB and wecC), is important for survival of Y. pestis in macrophages.

  19. A site-specific, single-copy transgenesis strategy to identify 5' regulatory sequences of the mouse testis-determining gene Sry.

    Science.gov (United States)

    Quinn, Alexander; Kashimada, Kenichi; Davidson, Tara-Lynne; Ng, Ee Ting; Chawengsaksophak, Kallayanee; Bowles, Josephine; Koopman, Peter

    2014-01-01

    The Y-chromosomal gene SRY acts as the primary trigger for male sex determination in mammalian embryos. Correct regulation of SRY is critical: aberrant timing or level of Sry expression is known to disrupt testis development in mice and we hypothesize that mutations that affect regulation of human SRY may account for some of the many cases of XY gonadal dysgenesis that currently remain unexplained. However, the cis-sequences involved in regulation of Sry have not been identified, precluding a test of this hypothesis. Here, we used a transgenic mouse approach aimed at identifying mouse Sry 5' flanking regulatory sequences within 8 kb of the Sry transcription start site (TSS). To avoid problems associated with conventional pronuclear injection of transgenes, we used a published strategy designed to yield single-copy transgene integration at a defined, transcriptionally open, autosomal locus, Col1a1. None of the Sry transgenes tested was expressed at levels compatible with activation of Sox9 or XX sex reversal. Our findings indicate either that the Col1a1 locus does not provide an appropriate context for the correct expression of Sry transgenes, or that the cis-sequences required for Sry expression in the developing gonads lie beyond 8 kb 5' of the TSS.

  20. iDHS-EL: identifying DNase I hypersensitive sites by fusing three different modes of pseudo nucleotide composition into an ensemble learning framework.

    Science.gov (United States)

    Liu, Bin; Long, Ren; Chou, Kuo-Chen

    2016-08-15

    Regulatory DNA elements are associated with DNase I hypersensitive sites (DHSs). Accordingly, identification of DHSs will provide useful insights for in-depth investigation into the function of noncoding genomic regions. In this study, using the strategy of ensemble learning framework, we proposed a new predictor called iDHS-EL for identifying the location of DHS in human genome. It was formed by fusing three individual Random Forest (RF) classifiers into an ensemble predictor. The three RF operators were respectively based on the three special modes of the general pseudo nucleotide composition (PseKNC): (i) kmer, (ii) reverse complement kmer and (iii) pseudo dinucleotide composition. It has been demonstrated that the new predictor remarkably outperforms the relevant state-of-the-art methods in both accuracy and stability. For the convenience of most experimental scientists, a web server for iDHS-EL is established at http://bioinformatics.hitsz.edu.cn/iDHS-EL, which is the first web-server predictor ever established for identifying DHSs, and by which users can easily get their desired results without the need to go through the mathematical details. We anticipate that IDHS-EL: will become a very useful high throughput tool for genome analysis. bliu@gordonlifescience.org or bliu@insun.hit.edu.cn Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  1. A site-specific, single-copy transgenesis strategy to identify 5' regulatory sequences of the mouse testis-determining gene Sry.

    Directory of Open Access Journals (Sweden)

    Alexander Quinn

    Full Text Available The Y-chromosomal gene SRY acts as the primary trigger for male sex determination in mammalian embryos. Correct regulation of SRY is critical: aberrant timing or level of Sry expression is known to disrupt testis development in mice and we hypothesize that mutations that affect regulation of human SRY may account for some of the many cases of XY gonadal dysgenesis that currently remain unexplained. However, the cis-sequences involved in regulation of Sry have not been identified, precluding a test of this hypothesis. Here, we used a transgenic mouse approach aimed at identifying mouse Sry 5' flanking regulatory sequences within 8 kb of the Sry transcription start site (TSS. To avoid problems associated with conventional pronuclear injection of transgenes, we used a published strategy designed to yield single-copy transgene integration at a defined, transcriptionally open, autosomal locus, Col1a1. None of the Sry transgenes tested was expressed at levels compatible with activation of Sox9 or XX sex reversal. Our findings indicate either that the Col1a1 locus does not provide an appropriate context for the correct expression of Sry transgenes, or that the cis-sequences required for Sry expression in the developing gonads lie beyond 8 kb 5' of the TSS.

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

    African Journals Online (AJOL)

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

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

    African Journals Online (AJOL)

    Summary. In western Kenya, extant woodland habitats and their representative bird species are increasingly scarce outside of protected areas. With the assistance of satellite imagery we located several minimally impacted ecosystems on the Kavirondo Escarpment. (0°1.7' S, 34°56.5' E), which we then visited to examine ...

  4. [(3)H]chlorpromazine photolabeling of the torpedo nicotinic acetylcholine receptor identifies two state-dependent binding sites in the ion channel.

    Science.gov (United States)

    Chiara, David C; Hamouda, Ayman K; Ziebell, Michael R; Mejia, Luis A; Garcia, Galo; Cohen, Jonathan B

    2009-10-27

    Chlorpromazine (CPZ), a potent nicotinic acetylcholine receptor (nAChR) noncompetitive antagonist, binds with higher affinity in the ion channel in the desensitized state than in the closed channel state and with low affinity to additional sites in nAChR-rich membranes. For nAChR equilibrated with agonist, we confirm previous reports that [(3)H]CPZ occupies a site near the cytoplasmic end of the M2 ion channel domain, photolabeling positions M2-2, M2-6, and/or M2-9 in each subunit. We find that [(3)H]CPZ also binds at the extracellular end of the channel, photolabeling amino acids at positions M2-16 (alpha,gamma), M2-17 (alpha,beta,delta), and M2-20 (alpha,beta,delta). The photolabeling at the cytoplasmic end of the channel is fully inhibitable by phencyclidine or proadifen, whereas neither drug inhibits [(3)H]CPZ photolabeling at the extracellular end, establishing that positively charged drugs can bind simultaneously at the cytoplasmic and extracellular ends of the ion channel. [(3)H]CPZ photolabeling is not detected in the transmembrane domain outside the ion channel, but it photolabels alphaMet-386 and alphaSer-393 in the cytoplasmic alphaMA helix. In the nAChR equilibrated with alpha-bungarotoxin to stabilize the nAChR in a closed state, [(3)H]CPZ photolabels amino acids at M2-5 (alpha), M2-6 (alpha,beta,delta), and M2-9 (beta,delta), with no labeling at M2-2. These results provide novel information about the modes of drug binding within the nAChR ion channel and indicate that within the nAChR transmembrane domain, the binding of cationic aromatic amine antagonists can be restricted to the ion channel domain, in contrast to the uncharged, allosteric potentiators and inhibitors that also bind within the delta subunit helix bundle and at subunit interfaces.

  5. Linkage of human cytomegalovirus glycoprotein gO variant groups identified from worldwide clinical isolates with gN genotypes, implications for disease associations and evidence for N-terminal sites of positive selection

    International Nuclear Information System (INIS)

    Mattick, C.; Dewin, D.; Polley, S.; Sevilla-Reyes, E.; Pignatelli, S.; Rawlinson, W.; Wilkinson, G.; Dal Monte, P.; Gompels, U.A.

    2004-01-01

    Previously, we identified the glycoprotein gO gene, UL74, as a hypervariable locus in the human cytomegalovirus (HCMV) genome [Virology 293 (2002) 281]. Here, we analyze gO from 50 isolates from congenitally infected newborns, transplant recipients, and HIV/AIDS patients from Italy, Australia, and UK. These are compared to four gO groups described from USA transplantation patients [J. Virol. 76 (2002) 10841]. Phylogenetic analyses identified seven genotypes. Divergence between genotypes was up to 55% and within 3%. Discrete linkage was shown between seven hypervariable gO and gN genotypes, but not with gB. This suggests interactions, while gN and gO are known to form complexes with distinct conserved glycoproteins gM, gH/gL, respectively, both are involved in fusogenic entry and exit. Codon-based maximum likelihood models showed evidence for sites of positive selection. Further analyses of disease relationships should take into account these newly defined gO/gN groups

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

    Energy Technology Data Exchange (ETDEWEB)

    Guzowski, R.V. [Science Applications International Corp., San Diego, CA (United States)]|[Sandia National Labs., Albuquerque, NM (United States). Safety and Risk Assessment Dept.

    1994-12-31

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

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

    Directory of Open Access Journals (Sweden)

    Sandra Fuentes

    2016-04-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    1993-12-01

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

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

    Science.gov (United States)

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

    2017-10-01

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

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

    Directory of Open Access Journals (Sweden)

    Barbara Wappenschmidt

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

  11. Uterine rupture without previous caesarean delivery

    DEFF Research Database (Denmark)

    Thisted, Dorthe L. A.; H. Mortensen, Laust; Krebs, Lone

    2015-01-01

    OBJECTIVE: To determine incidence and patient characteristics of women with uterine rupture during singleton births at term without a previous caesarean delivery. STUDY DESIGN: Population based cohort study. Women with term singleton birth, no record of previous caesarean delivery and planned...... vaginal delivery (n=611,803) were identified in the Danish Medical Birth Registry (1997-2008). Medical records from women recorded with uterine rupture during labour were reviewed to ascertain events of complete uterine rupture. Relative Risk (RR) and adjusted Relative Risk Ratio (aRR) of complete uterine...... rupture with 95% confidence intervals (95% CI) were ascertained according to characteristics of the women and of the delivery. RESULTS: We identified 20 cases with complete uterine rupture. The incidence of complete uterine rupture among women without previous caesarean delivery was about 3...

  12. Multi-Institution Analysis of Infection Control Practices Identifies the Subset Associated with Best Surgical Site Infection Performance: A Texas Alliance for Surgical Quality Collaborative Project.

    Science.gov (United States)

    Davis, Catherine H; Kao, Lillian S; Fleming, Jason B; Aloia, Thomas A

    2017-08-16

    In an effort to reduce surgical site infection (SSI) rates, a large number of infection control practices (ICPs), including operating room attire policies, have been recommended. However, few have proven benefits and many are costly, time-consuming, and detrimental to provider morale. The goal of this multi-institution study was to determine which ICPs are associated with lower postoperative SSI rates. Twenty American College of Surgeons NSQIP and Texas Alliance for Surgical Quality-affiliated hospitals completed this Quality Improvement Assessment Board-approved study. Surgeon champions at each hospital ranked current surgery, anesthesia, and nursing adherence to 38 separate ICPs in 6 categories (attire, preoperative, intraoperative, preoperative, intraoperative, antibiotics, postoperative, and reporting) on 4-point scales for general surgery cases. These data were compared with the risk-adjusted general surgery SSI odds ratios contained in the July 2016 American College of Surgeons NSQIP hospital-level, risk-adjusted reports. Compliance rates were compared between the 7 best (median SSI odds ratio, 0.64; range, 0.56 to 0.70) and 7 worst (median SSI odds ratio, 1.16; range, 0.94 to 1.65) performers using ANOVA. Nearly all hospitals reported maximal adherence to hair removal with clippers (Surgical Care Improvement Project measure Inf-6) and to best-practice prophylactic antibiotic metrics (Surgical Care Improvement Project measure Inf-1-3). Variable adherence was identified across many ICPs and more frequent compliance with 8 ICPs correlated with lower SSI odds ratios, including preoperative shower; skin preparation technique; using clean instruments, gowns, and gloves for wound closure and dressing changes; and transparent internal reporting of SSI data. Operating room attire ICPs, including coverage of nonscrubbed provider head and arm hair, did not correlate with SSI rates. This analysis suggests that the subset of ICPs that focus on perioperative patient

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

    International Nuclear Information System (INIS)

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

    1987-09-01

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

  14. Concomitant and previous osteoporotic vertebral fractures.

    Science.gov (United States)

    Lenski, Markus; Büser, Natalie; Scherer, Michael

    2017-04-01

    Background and purpose - Patients with osteoporosis who present with an acute onset of back pain often have multiple fractures on plain radiographs. Differentiation of an acute osteoporotic vertebral fracture (AOVF) from previous fractures is difficult. The aim of this study was to investigate the incidence of concomitant AOVFs and previous OVFs in patients with symptomatic AOVFs, and to identify risk factors for concomitant AOVFs. Patients and methods - This was a prospective epidemiological study based on the Registry of Pathological Osteoporotic Vertebral Fractures (REPAPORA) with 1,005 patients and 2,874 osteoporotic vertebral fractures, which has been running since February 1, 2006. Concomitant fractures are defined as at least 2 acute short-tau inversion recovery (STIR-) positive vertebral fractures that happen concomitantly. A previous fracture is a STIR-negative fracture at the time of initial diagnostics. Logistic regression was used to examine the influence of various variables on the incidence of concomitant fractures. Results - More than 99% of osteoporotic vertebral fractures occurred in the thoracic and lumbar spine. The incidence of concomitant fractures at the time of first patient contact was 26% and that of previous fractures was 60%. The odds ratio (OR) for concomitant fractures decreased with a higher number of previous fractures (OR =0.86; p = 0.03) and higher dual-energy X-ray absorptiometry T-score (OR =0.72; p = 0.003). Interpretation - Concomitant and previous osteoporotic vertebral fractures are common. Risk factors for concomitant fractures are a low T-score and a low number of previous vertebral fractures in cases of osteoporotic vertebral fracture. An MRI scan of the the complete thoracic and lumbar spine with STIR sequence reduces the risk of under-diagnosis and under-treatment.

  15. Historic Sites and National Register of Historic Places, National Register of Historic Places - NRHP is a list of properties identified by the Federal Government as significant in American history and culture. These properties include districts, buildings, sites and objects of significance to the nation, etc., Published in 2007, 1:24000 (1in=2000ft) scale, Maryland Department of Planning.

    Data.gov (United States)

    NSGIC State | GIS Inventory — Historic Sites and National Register of Historic Places dataset current as of 2007. National Register of Historic Places - NRHP is a list of properties identified by...

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

    DEFF Research Database (Denmark)

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

    2012-01-01

    with extracervical metastases from carcinoma of unknown primary (CUP) site.Patients and Methods. From January 2006 to December 2010, 136 newly diagnosed CUP patients with extracervical metastases underwent (18)F-FDG PET/CT.A standard of reference (SR) was established by a multidisciplinary team to ensure....../CT and CT alone in regard to sensitivity, specificity, and accuracy.Conclusion. In the general CUP population with multiple extracervical metastases (18)F-FDG PET/CT does not represent a clear diagnostic advantage over CT alone regarding the ability to detect the primary tumor site....

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

    DEFF Research Database (Denmark)

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

    1989-01-01

    -fold lower affinity for Ca2+, as judged by the ability of Ca2+ to inhibit the reaction in the presence of 10 mM Mg2+. Wild type PRPP synthetase is subject to product inhibition by AMP, but AMP inhibition of the prsA1 mutant enzyme could not be detected. It has been previously proposed that a divalent...

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

    Science.gov (United States)

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

    2016-10-01

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

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

    DEFF Research Database (Denmark)

    Poongavanam, Vasanthanathan; Corona, Angela; Steinmann, Casper

    2018-01-01

    with innovative mechanisms. The HIV-1 reverse transcriptase (RT) associated ribonuclease H (RNase H) is the only viral encoded enzyme that still lacks an efficient inhibitor despite the fact that it is a well-validated target whose functional abrogation compromises viral infectivity. Identification of new drugs...... inhibited the RNase H function below 100 μM with three hits exhibiting IC50 values mode of inhibition. Site-directed mutagenesis studies provide valuable insight into the binding mode of newly...

  20. Use of a Phosphorylation Site Mutant To Identify Distinct Modes of Gene Repression by the Control of Virulence Regulator (CovR) in Streptococcus pyogenes.

    Science.gov (United States)

    Horstmann, Nicola; Sahasrabhojane, Pranoti; Yao, Hui; Su, Xiaoping; Shelburne, Samuel A

    2017-09-15

    Control of the virulence regulator/sensor kinase (CovRS) two-component system (TCS) serves as a model for investigating the impact of signaling pathways on the pathogenesis of Gram-positive bacteria. However, the molecular mechanisms by which CovR, an OmpR/PhoB family response regulator, controls virulence gene expression are poorly defined, partly due to the labile nature of its aspartate phosphorylation site. To better understand the regulatory effect of phosphorylated CovR, we generated the phosphorylation site mutant strain 10870-CovR-D53E, which we predicted to have a constitutive CovR phosphorylation phenotype. Interestingly, this strain showed CovR activity only for a subset of the CovR regulon, which allowed for classification of CovR-influenced genes into D53E-regulated and D53E-nonregulated groups. Inspection of the promoter sequences of genes belonging to each group revealed distinct promoter architectures with respect to the location and number of putative CovR-binding sites. Electrophoretic mobility shift analysis demonstrated that recombinant CovR-D53E protein retains its ability to bind promoter DNA from both CovR-D53E-regulated and -nonregulated groups, implying that factors other than mere DNA binding are crucial for gene regulation. In fact, we found that CovR-D53E is incapable of dimerization, a process thought to be critical to OmpR/PhoB family regulator function. Thus, our global analysis of CovR-D53E indicates dimerization-dependent and dimerization-independent modes of CovR-mediated repression, thereby establishing distinct mechanisms by which this critical regulator coordinates virulence gene expression. IMPORTANCE Streptococcus pyogenes causes a wide variety of diseases, ranging from superficial skin and throat infections to life-threatening invasive infections. To establish these various disease manifestations, Streptococcus pyogenes requires tightly coordinated production of its virulence factor repertoire. Here, the response regulator

  1. Identifying a reliable blubber measurement site to assess body condition in a marine mammal with topographically variable blubber, the Pacific walrus

    Science.gov (United States)

    Noren, Shawn R.; Udevitz, Mark S.; Triggs, Lisa; Paschke, Jessa; Oland, Lisa; Jay, Chadwick V.

    2015-01-01

    Pacific walruses may be unable to meet caloric requirements in the changing Arctic ecosystem, which could affect body condition and have population-level consequences. Body condition has historically been monitored by measuring blubber thickness over the xiphoid process (sternum). This may be an unreliable condition index because blubber at other sites along the body may be preferentially targeted to balance energetic demands. Animals in aquaria provided an opportunity for controlled study of how blubber topography is altered by caloric intake. Morphology, body mass, blubber thickness (21 sites), and caloric intake of five mature, nonpregnant, nonlactating female walruses were measured monthly (12 month minimum). Body condition (mass × standard length−1) was described by a model that included caloric intake and a seasonal effect, and scaled positively with estimates of total blubber mass. Blubber thicknesses (1.91–10.69 cm) varied topographically and were similar to values reported for free-ranging female walruses. Body condition was most closely related to blubber thickness measured dorsomedially in the region of the anterior insertion of the pectoral flippers (shoulders); sternum blubber thickness was a relatively poor indicator of condition. This study demonstrates the importance of validating condition metrics before using them to monitor free-ranging populations.

  2. Severe hypoglycemia identifies vulnerable patients with type 2 diabetes at risk for premature death and all-site cancer: the Hong Kong diabetes registry.

    Science.gov (United States)

    Kong, Alice P S; Yang, Xilin; Luk, Andrea; Ma, Ronald C W; So, Wing Yee; Ozaki, Risa; Ting, Rose; Cheung, Kitty; Ho, Chung Shun; Chan, Michael H M; Chow, Chun Chung; Chan, Juliana C N

    2014-04-01

    OBJECTIVE We examined the associations of clinical profiles in type 2 diabetic patients who developed severe hypoglycemia and their clinical outcomes, including death and all-site cancer. RESEARCH DESIGN AND METHODS A consecutive cohort of 8,767 type 2 diabetic patients with and without severe hypoglycemia in the 12 months before enrollment were recruited between 1995 and 2007, with follow-up until 2009. Severe hypoglycemia was defined by ICD-9 codes as hospitalizations resulting from hypoglycemia. Cox proportional hazards regression was used to calculate the hazard ratio (HR) and 95% CIs of clinical factors collected at enrollment for severe hypoglycemia. RESULTS In this cohort, mean age was 57.4 (SD 13.2) years and median disease duration of diabetes was 5 (interquartile range [IQR] 1-11) years. During a median follow-up of 6.71 (IQR 3.47-10.38) years, 235 patients had severe hypoglycemia (incidence 3.96 [95% CI 3.45-4.46] per 1,000 patient-years). At enrollment, patients with and without severe hypoglycemia had similar cancer rates. During follow-up, patients with severe hypoglycemia had a higher incidence of all-site cancer (13.4 vs. 6.4%, P < 0.0001) and mortality (32.8 vs. 11.2%, P < 0.0001) than those without severe hypoglycemia. After adjusting for confounders, old age, low BMI, high glycated hemoglobin, low triglyceride (TG), low LDL cholesterol (LDL-C), albuminuria, and chronic kidney disease were independent predictors for severe hypoglycemia. CONCLUSIONS In type 2 diabetes, severe hypoglycemia is associated with advanced age, renal dysfunction, poor glycemic control, and cancer subphenotypes (low BMI, low LDL-C, and low TG).

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

    African Journals Online (AJOL)

    Research Note Effects of previous cultivation on regeneration of Julbernadia globiflora and Brachystegia spiciformis in grazing areas of Mupfurudzi ... Plant attributes for Julbernadia globiflora and Brachystegia spiciformis were measured in previously cultivated and uncultivated sites making up rangelands of the scheme.

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

    Science.gov (United States)

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

    2017-01-01

    Although the HVTN 505 DNA/recombinant adenovirus type 5 vector HIV-1 vaccine trial showed no overall efficacy, analysis of breakthrough HIV-1 sequences in participants can help determine whether vaccine-induced immune responses impacted viruses that caused infection. We analyzed 480 HIV-1 genomes sampled from 27 vaccine and 20 placebo recipients and found that intra-host HIV-1 diversity was significantly lower in vaccine recipients (P ≤ 0.04, Q-values ≤ 0.09) in Gag, Pol, Vif and envelope glycoprotein gp120 (Env-gp120). Furthermore, Env-gp120 sequences from vaccine recipients were significantly more distant from the subtype B vaccine insert than sequences from placebo recipients (P = 0.01, Q-value = 0.12). These vaccine effects were associated with signatures mapping to CD4 binding site and CD4-induced monoclonal antibody footprints. These results suggest either (i) no vaccine efficacy to block acquisition of any viral genotype but vaccine-accelerated Env evolution post-acquisition; or (ii) vaccine efficacy against HIV-1s with Env sequences closest to the vaccine insert combined with increased acquisition due to other factors, potentially including the vaccine vector. PMID:29149197

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

    Science.gov (United States)

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

    2016-03-16

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

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

    Science.gov (United States)

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

    2017-01-01

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

  7. Metabolic network segmentation: A probabilistic graphical modeling approach to identify the sites and sequential order of metabolic regulation from non-targeted metabolomics data.

    Directory of Open Access Journals (Sweden)

    Andreas Kuehne

    2017-06-01

    Full Text Available In recent years, the number of large-scale metabolomics studies on various cellular processes in different organisms has increased drastically. However, it remains a major challenge to perform a systematic identification of mechanistic regulatory events that mediate the observed changes in metabolite levels, due to complex interdependencies within metabolic networks. We present the metabolic network segmentation (MNS algorithm, a probabilistic graphical modeling approach that enables genome-scale, automated prediction of regulated metabolic reactions from differential or serial metabolomics data. The algorithm sections the metabolic network into modules of metabolites with consistent changes. Metabolic reactions that connect different modules are the most likely sites of metabolic regulation. In contrast to most state-of-the-art methods, the MNS algorithm is independent of arbitrary pathway definitions, and its probabilistic nature facilitates assessments of noisy and incomplete measurements. With serial (i.e., time-resolved data, the MNS algorithm also indicates the sequential order of metabolic regulation. We demonstrated the power and flexibility of the MNS algorithm with three, realistic case studies with bacterial and human cells. Thus, this approach enables the identification of mechanistic regulatory events from large-scale metabolomics data, and contributes to the understanding of metabolic processes and their interplay with cellular signaling and regulation processes.

  8. Z-DNA-forming sites identified by ChIP-Seq are associated with actively transcribed regions in the human genome.

    Science.gov (United States)

    Shin, So-I; Ham, Seokjin; Park, Jihwan; Seo, Seong Hye; Lim, Chae Hyun; Jeon, Hyeongrin; Huh, Jounghyun; Roh, Tae-Young

    2016-07-03

    Z-DNA, a left-handed double helical DNA is structurally different from the most abundant B-DNA. Z-DNA has been known to play a significant role in transcription and genome stability but the biological meaning and positions of Z-DNA-forming sites (ZFSs) in the human genome has not been fully explored. To obtain genome-wide map of ZFSs, Zaa with two Z-DNA-binding domains was used for ChIP-Seq analysis. A total of 391 ZFSs were found and their functions were examined in vivo A large portion of ZFSs was enriched in the promoter regions and contain sequences with high potential to form Z-DNA. Genes containing ZFSs were occupied by RNA polymerase II at the promoters and showed high levels of expression. Moreover, ZFSs were significantly related to active histone marks such as H3K4me3 and H3K9ac. The association of Z-DNA with active transcription was confirmed by the reporter assay system. Overall, our results suggest that Z-DNA formation depends on chromatin structure as well as sequence composition, and is associated with active transcription in human cells. The global information about ZFSs positioning will provide a useful resource for further understanding of DNA structure-dependent transcriptional regulation. © The Author 2016. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

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

    Directory of Open Access Journals (Sweden)

    Flavo E. S. de Sousa

    2012-06-01

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

  10. Ocean Disposal Site Monitoring

    Science.gov (United States)

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

  11. Promoting Your Web Site.

    Science.gov (United States)

    Raeder, Aggi

    1997-01-01

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

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

    Data.gov (United States)

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

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

    Directory of Open Access Journals (Sweden)

    Chiara Luise

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

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

    Science.gov (United States)

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

    2018-02-06

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

  15. Placental complications after a previous cesarean section

    OpenAIRE

    Milošević Jelena; Lilić Vekoslav; Tasić Marija; Radović-Janošević Dragana; Stefanović Milan; Antić Vladimir

    2009-01-01

    Introduction The incidence of cesarean section has been rising in the past 50 years. With the increased number of cesarean sections, the number of pregnancies with the previous cesarean section rises as well. The aim of this study was to establish the influence of the previous cesarean section on the development of placental complications: placenta previa, placental abruption and placenta accreta, as well as to determine the influence of the number of previous cesarean sections on the complic...

  16. Genome-wide profiling of p63 DNA-binding sites identifies an element that regulates gene expression during limb development in the 7q21 SHFM1 locus.

    Directory of Open Access Journals (Sweden)

    Evelyn N Kouwenhoven

    2010-08-01

    Full Text Available Heterozygous mutations in p63 are associated with split hand/foot malformations (SHFM, orofacial clefting, and ectodermal abnormalities. Elucidation of the p63 gene network that includes target genes and regulatory elements may reveal new genes for other malformation disorders. We performed genome-wide DNA-binding profiling by chromatin immunoprecipitation (ChIP, followed by deep sequencing (ChIP-seq in primary human keratinocytes, and identified potential target genes and regulatory elements controlled by p63. We show that p63 binds to an enhancer element in the SHFM1 locus on chromosome 7q and that this element controls expression of DLX6 and possibly DLX5, both of which are important for limb development. A unique micro-deletion including this enhancer element, but not the DLX5/DLX6 genes, was identified in a patient with SHFM. Our study strongly indicates disruption of a non-coding cis-regulatory element located more than 250 kb from the DLX5/DLX6 genes as a novel disease mechanism in SHFM1. These data provide a proof-of-concept that the catalogue of p63 binding sites identified in this study may be of relevance to the studies of SHFM and other congenital malformations that resemble the p63-associated phenotypes.

  17. Important biological information uncovered in previously unaligned reads from chromatin immunoprecipitation experiments (ChIP-Seq)

    Science.gov (United States)

    Ouma, Wilberforce Zachary; Mejia-Guerra, Maria Katherine; Yilmaz, Alper; Pareja-Tobes, Pablo; Li, Wei; Doseff, Andrea I.; Grotewold, Erich

    2015-01-01

    Establishing the architecture of gene regulatory networks (GRNs) relies on chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-Seq) methods that provide genome-wide transcription factor binding sites (TFBSs). ChIP-Seq furnishes millions of short reads that, after alignment, describe the genome-wide binding sites of a particular TF. However, in all organisms investigated an average of 40% of reads fail to align to the corresponding genome, with some datasets having as much as 80% of reads failing to align. We describe here the provenance of previously unaligned reads in ChIP-Seq experiments from animals and plants. We show that a substantial portion corresponds to sequences of bacterial and metazoan origin, irrespective of the ChIP-Seq chromatin source. Unforeseen was the finding that 30%–40% of unaligned reads were actually alignable. To validate these observations, we investigated the characteristics of the previously unaligned reads corresponding to TAL1, a human TF involved in lineage specification of hemopoietic cells. We show that, while unmapped ChIP-Seq read datasets contain foreign DNA sequences, additional TFBSs can be identified from the previously unaligned ChIP-Seq reads. Our results indicate that the re-evaluation of previously unaligned reads from ChIP-Seq experiments will significantly contribute to TF target identification and determination of emerging properties of GRNs. PMID:25727450

  18. Hanford Site Development Plan

    Energy Technology Data Exchange (ETDEWEB)

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

    1990-01-01

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

  19. Hanford Site Development Plan

    International Nuclear Information System (INIS)

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

    1990-01-01

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

  20. 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.

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

    Directory of Open Access Journals (Sweden)

    Michael V Zaragoza

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

  2. 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.

  3. Automatic electromagnetic valve for previous vacuum

    International Nuclear Information System (INIS)

    Granados, C. E.; Martin, F.

    1959-01-01

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

  4. Thyroid disease awareness is associated with high rates of identifying subjects with previously undiagnosed thyroid dysfunction

    OpenAIRE

    Canaris, Gay J; Tape, Thomas G; Wigton, Robert S

    2013-01-01

    Background Conventional screening for hypothyroidism is controversial. Although hypothyroidism is underdiagnosed, many organizations do not recommend screening, citing low disease prevalence in unselected populations. We studied attendees at a thyroid health fair, hypothesizing that certain patient characteristics would enhance the yield of testing. Methods We carried out an observational study of participants at a Michigan health fair that focused on thyroid disease. We collected patient-rep...

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

    Science.gov (United States)

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

    2015-06-01

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

  6. 77 FR 14594 - Additions to the Identifying Information for an Individual Previously Designated Pursuant to the...

    Science.gov (United States)

    2012-03-12

    ...., Bogota, Colombia; c/o CUBICAFE S.A., Bogota, Colombia; c/o CUBI CAFE CLICK CUBE MEXICO, S.A. DE C.V., Mexico City, Distrito Federal, Mexico; c/o DESARROLLO MINERO RESPONSABLE C.I. S.A.S., Bogota, Colombia; c..., Colombia; c/o INVERPUNTO DEL VALLE S.A., Cali, Colombia; c/o INVERSIONES CIFUENTES Y CIA. S. EN C...

  7. INTRODUCTION Previous reports have documented a high ...

    African Journals Online (AJOL)

    pregnancy if they were married, educated, had dental insurance, previously used dental services when not pregnant, or had knowledge about the possible connection between oral health and pregnancy outcome8. The purpose of this study was to explore the factors determining good oral hygiene among pregnant women ...

  8. Empowerment perceptions of educational managers from previously ...

    African Journals Online (AJOL)

    The perceptions of educational manag ers from previously disadvantaged primary and high schools in the Nelson Mandela Metropole regarding the issue of empowerment are outlined and the perceptions of educational managers in terms of various aspects of empowerment at different levels reflected. A literature study ...

  9. Management of choledocholithiasis after previous gastrectomy.

    Science.gov (United States)

    Anwer, S; Egan, R; Cross, N; Guru Naidu, S; Somasekar, K

    2017-09-01

    Common bile duct stones in patients with a previous gastrectomy can be a technical challenge because of the altered anatomy. This paper presents the successful management of two such patients using non-traditional techniques as conventional endoscopic retrograde cholangiopancreatography was not possible.

  10. Laboratory Grouping Based on Previous Courses.

    Science.gov (United States)

    Doemling, Donald B.; Bowman, Douglas C.

    1981-01-01

    In a five-year study, second-year human physiology students were grouped for laboratory according to previous physiology and laboratory experience. No significant differences in course or board examination performance were found, though correlations were found between predental grade-point averages and grouping. (MSE)

  11. 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 ...

  12. 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 ...

  13. 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

  14. 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

  15. Pesticide Use Site Index

    Science.gov (United States)

    The Pesticide Use Site Index will help a company (or other applicant) identify which data requirements are needed to register a pesticide product. It provides information on pesticide use sites and pesticide major use patterns.

  16. Earliest direct evidence of monument building at the archaeological site of Nan Madol (Pohnpei, Micronesia) identified using 230Th/U coral dating and geochemical sourcing of megalithic architectural stone

    Science.gov (United States)

    McCoy, Mark D.; Alderson, Helen A.; Hemi, Richard; Cheng, Hai; Edwards, R. Lawrence

    2016-11-01

    Archaeologists commonly use the onset of the construction of large burial monuments as a material indicator of a fundamental shift in authority in prehistoric human societies during the Holocene. High- quality direct evidence of this transition is rare. We report new interdisciplinary research at the archaeological site of Nan Madol that allows us to specify where and when people began to construct monumental architecture in the remote islands of the Pacific. Nan Madol is an ancient administrative and mortuary center and the former capital of the island of Pohnpei. It was constructed over 83 ha of lagoon with artificial islets and other architecture built using columnar basalt and coral. We employed geochemical sourcing of basalt used as architectural stone and high-precision uranium-thorium series dates (230Th/U) on coral from the tomb of the first chief of the entire island to identify the beginning of monument building at Nan Madol in AD 1180-1200. Over the next several centuries (AD 1300-1600) monument building began on other islands across Oceania. Future research should be aimed at resolving the causes of these social transformations through higher quality data on monument building.

  17. Previously unknown organomagnesium compounds in astrochemical context

    OpenAIRE

    Ruf, Alexander

    2018-01-01

    We describe the detection of dihydroxymagnesium carboxylates (CHOMg) in astrochemical context. CHOMg was detected in meteorites via ultrahigh-resolving chemical analytics and represents a novel, previously unreported chemical class. Thus, chemical stability was probed via quantum chemical computations, in combination with experimental fragmentation techniques. Results propose the putative formation of green-chemical OH-Grignard-type molecules and triggered fundamental questions within chemica...

  18. [Placental complications after a previous cesarean section].

    Science.gov (United States)

    Milosević, Jelena; Lilić, Vekoslav; Tasić, Marija; Radović-Janosević, Dragana; Stefanović, Milan; Antić, Vladimir

    2009-01-01

    The incidence of cesarean section has been rising in the past 50 years. With the increased number of cesarean sections, the number of pregnancies with the previous cesarean section rises as well. The aim of this study was to establish the influence of the previous cesarean section on the development of placental complications: placenta previa, placental abruption and placenta accreta, as well as to determine the influence of the number of previous cesarean sections on the complication development. The research was conducted at the Clinic of Gynecology and Obstetrics in Nis covering 10-year-period (from 1995 to 2005) with 32358 deliveries, 1280 deliveries after a previous cesarean section, 131 cases of placenta previa and 118 cases of placental abruption. The experimental groups was presented by the cases of placenta previa or placental abruption with prior cesarean section in obstetrics history, opposite to the control group having the same conditions but without a cesarean section in medical history. The incidence of placenta previa in the control group was 0.33%, opposite to the 1.86% incidence after one cesarean section (pcesarean sections and as high as 14.28% after three cesarean sections in obstetric history. Placental abruption was recorded as placental complication in 0.33% pregnancies in the control group, while its incidence was 1.02% after one cesarean section (pcesarean sections. The difference in the incidence of intrapartal hysterectomy between the group with prior cesarean section (0.86%) and without it (0.006%) shows a high statistical significance (pcesarean section is an important risk factor for the development of placental complications.

  19. Identifying sarcopenia.

    Science.gov (United States)

    Abellan van Kan, Gabor; Houles, Mathieu; Vellas, Bruno

    2012-09-01

    The present review describes and discusses the currently available definitions for sarcopenia from consensus studies. Different sarcopenia definitions have been proposed in these last years. Six main approaches to an operative definition of sarcopenia have been identified. Although the first definitions were solely based on the assessment of the amount of muscle mass, current definitions seem to consistently recognize a bi-dimensional nature of sarcopenia. So, these approaches imply the need of simultaneously assessing both age-related quantitative (i.e. amount of muscle mass) and qualitative (i.e. muscle strength and function) declines of skeletal muscle. Although current consensus exists about a bi-dimensional nature, the proposed approaches to measure sarcopenia are characterized by methodological differences. The majority of the operative definitions proposes to assess muscle mass as an index of appendicular muscle mass divided by squared height (evaluated by dual energy X-ray absorptiometry), assess strength using hand-held dynamometers, and assess function by evaluating gait speed at habitual pace over a short distance. Nevertheless, the clinically relevant thresholds and how to combine the three aspects in an operative definition in order to identify sarcopenia are heterogeneous. A main drawback is that supportive empirical data are missing for these conceptual definitions regarding the risk-assessment of different clinically significant adverse outcomes.

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

    Data.gov (United States)

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

  1. 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.

  2. Books average previous decade of economic misery.

    Science.gov (United States)

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

    2014-01-01

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

  3. Induced vaginal birth after previous caesarean section

    Directory of Open Access Journals (Sweden)

    Akylbek Tussupkaliyev

    2016-11-01

    Full Text Available Introduction The rate of operative birth by Caesarean section is constantly rising. In Kazakhstan, it reaches 27 per cent. Research data confirm that the percentage of successful vaginal births after previous Caesarean section is 50–70 per cent. How safe the induction of vaginal birth after Caesarean (VBAC remains unclear. Methodology The studied techniques of labour induction were amniotomy of the foetal bladder with the vulsellum ramus, intravaginal administration of E1 prostaglandin (Misoprostol, and intravenous infusion of Oxytocin-Richter. The assessment of rediness of parturient canals was conducted by Bishop’s score; the labour course was assessed by a partogram. The effectiveness of labour induction techniques was assessed by the number of administered doses, the time of onset of regular labour, the course of labour and the postpartum period and the presence of complications, and the course of the early neonatal period, which implied the assessment of the child’s condition, described in the newborn development record. The foetus was assessed by medical ultrasound and antenatal and intranatal cardiotocography (CTG. Obtained results were analysed with SAS statistical processing software. Results The overall percentage of successful births with intravaginal administration of Misoprostol was 93 per cent (83 of cases. This percentage was higher than in the amniotomy group (relative risk (RR 11.7 and was similar to the oxytocin group (RR 0.83. Amniotomy was effective in 54 per cent (39 of cases, when it induced regular labour. Intravenous oxytocin infusion was effective in 94 per cent (89 of cases. This percentage was higher than that with amniotomy (RR 12.5. Conclusions The success of vaginal delivery after previous Caesarean section can be achieved in almost 70 per cent of cases. At that, labour induction does not decrease this indicator and remains within population boundaries.

  4. 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...

  5. Event Sequence Variability in Healthy Swallowing: Building on Previous Findings

    OpenAIRE

    Molfenter, Sonja M.; Leigh, Chelsea; Steele, Catriona M.

    2014-01-01

    This study builds on previous work by Kendall, Leonard and McKenzie, which investigated event sequence variability for 12 paired-events during swallowing by healthy volunteers. They identified four event pairs, which always occurred in a stereotyped order as well as a most-common occurring overall order of events during swallowing. In the current study, we investigate overall event sequencing and the same four paired-events in a sample of swallows by healthy, young (under 45 years old) volunt...

  6. Antenatal diagnosis of Patau syndrome with previous anomalous baby

    OpenAIRE

    Keerthi Kocherla; Vasantha Kocherla

    2014-01-01

    Patau syndrome is the least common and most severe of the viable autosomal trisomies with median survival of fewer than 3 days was first identified as a cytogenetic syndrome in 1960. Patau syndrome is caused by an extra copy of chromosome 13. In this case report, we present antenatal imaging findings and gross foetal specimen correlation of foetus with Patau syndrome confirmed by karyotyping in third gravida who had significant previous obstetric history of gastrochisis in monochorionic and...

  7. Prevalence of Infraumbilical Adhesions in Women With Previous Laparoscopy

    Science.gov (United States)

    Ku, Lowell; Wong, Herb; Liu, C. Y.; Phelps, John Y.

    2007-01-01

    Background and Objectives: The aim of this study is to evaluate the prevalence of intraabdominal adhesions to the umbilicus following gynecologic laparoscopy through an umbilical incision. Methods: A retrospective review was performed of all gynecologic laparoscopic procedures in a private practice setting to identify patients with a repeat laparoscopy who had a history of a previous laparoscopy through an umbilical incision. Patients with a history of other surgeries were excluded. All repeat laparoscopies used a left upper quadrant entry technique where the abdominal cavity was surveyed for adhesions. We also reviewed adverse events attributable to the left upper quadrant entry approach. Results: We identified 151 patients who underwent a second laparoscopy and had a previous umbilical scar. Thirty-two of the 151 (21.2%) patients with a history of a laparoscopy had evidence of adhesions to the umbilical undersurface. No adverse events or injuries were attributed to the left upper quadrant entry technique. Conclusions: Adhesions to the umbilical undersurface occur in 21.2% of patients who have undergone a prior laparoscopy through an umbilical incision. For this reason, we recommend an alternate location for entry in patients with an umbilical scar from a previous laparoscopy. PMID:17651555

  8. Rates of induced abortion in Denmark according to age, previous births and previous abortions

    Directory of Open Access Journals (Sweden)

    Marie-Louise H. Hansen

    2009-11-01

    Full Text Available Background: Whereas the effects of various socio-demographic determinants on a woman's risk of having an abortion are relatively well-documented, less attention has been given to the effect of previous abortions and births. Objective: To study the effect of previous abortions and births on Danish women's risk of an abortion, in addition to a number of demographic and personal characteristics. Data and methods: From the Fertility of Women and Couples Dataset we obtained data on the number of live births and induced abortions by year (1981-2001, age (16-39, county of residence and marital status. Logistic regression analysis was used to estimate the influence of the explanatory variables on the probability of having an abortion in a relevant year. Main findings and conclusion: A woman's risk of having an abortion increases with the number of previous births and previous abortions. Some interactions were was found in the way a woman's risk of abortion varies with calendar year, age and parity. The risk of an abortion for women with no children decreases while the risk of an abortion for women with children increases over time. Furthermore, the risk of an abortion decreases with age, but relatively more so for women with children compared to childless women. Trends for teenagers are discussed in a separate section.

  9. Percutaneous endoscopic jejunostomy in a patient with previous esophagectomy.

    Science.gov (United States)

    de la Torre, R A; Scott, J S; Unger, S W

    1991-04-01

    Establishment of a percutaneous endoscopic jejunostomy via direct jejunal puncture was accomplished in a 45-year-old woman five years after a partial esophagectomy with cervical esophagogastrostomy for adenocarcinoma of the esophagus. The patient had recurrence of the cancer at the anastomotic site with subsequent inability to eat, necessitating a feeding tube for prolonged enteral nutrition. Although percutaneous puncture of the jejunum has been previously described, it has been limited to patients who had undergone partial or complete gastrectomies with Bilroth II anastomoses. This case report of direct endoscopic jejunal tube placement in a patient after esophagectomy further establishes this procedure as a viable alternative to surgically placed feeding tubes in patients with altered gastric anatomy.

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

    DEFF Research Database (Denmark)

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

    2013-01-01

    Non-serotype b strains of Haemophilus influenzae are extremely rare causes of acute bacterial meningitis in immunocompetent individuals. We report a case of acute bacterial meningitis in a 14-year-old boy, who was previously healthy and had been immunised against H influenzae serotype b (Hib......). The causative pathogen was identified as H influenzae serotype f (Hif), and was successfully treated with ceftriaxone. An immunological evaluation revealed transient low levels of immunoglobulins but no apparent immunodeficiency was found 2 years after the clinical insult....

  11. The long-term consequences of previous hyperthyroidism

    DEFF Research Database (Denmark)

    Hjelm Brandt Kristensen, Frans

    2015-01-01

    vascular state. While it is biologically plausible that these changes may induce long-term consequences, the insight into morbidity as well as mortality in patients with previous hyperthyroidism is limited. The reasons for this are a combination of inadequately powered studies, varying definitions......,400 non-hyperthyroid control individuals (matched for age and sex), all identified from a random 5% sample of the Danish background population (n=339,481). In the second study population, 625 same-sex twin pairs, discordant for hyperthyroidism, were included. For each individual, the degree of co...

  12. Incidence of previously undetected disease in routine paediatric otolaryngology admissions.

    Science.gov (United States)

    Zeitoun, H; Robinson, P

    1996-06-01

    The process of clerking routine pre-operative admissions involves the house officer taking a full medical history and performing a full physical examination. The diagnostic yield is thought to be low, and the educational value to the house officer is also small. This study addresses the question as to whether routine physical examination is always indicated. One hundred and nine children admitted for routine Otolaryngology procedures were prospectively studied to identify the importance of examination in the pre-operative assessment of patients. The results showed that 51 per cent of the children admitted had risk factors. The medical history was sufficient to identify these risk factors in all patients with the exception of one cardiac condition. This study concludes that a suitable alternative to the current process of clerking such as a standardized nurse history could be safely and efficiently undertaken. Eliminating the tiny percentage of previously unrecognized disease would be a prerequisite for such a change.

  13. Area C borrow Site Habitat Assessment

    Energy Technology Data Exchange (ETDEWEB)

    Sackschewsky, Michael R.; Downs, Janelle L.

    2009-12-04

    A habitat quality assessment was performed within selected portions of the proposed Area C Borrow Source. The previously identified Bitterbrush / Indian ricegrass stabilized dune element occurrence was determined to be better described as a sagebrush /needle-and-thread grass element occurrence of fair to good quality. A new habitat polygon is suggested adjacent to this element occurrence, which would also be sagebrush/needle-and-thread grass, but of poor quality. The proposed site of initial borrow site development was found to be a very low quality community dominated by cheatgrass.

  14. Congruency sequence effects are driven by previous-trial congruency, not previous-trial response conflict

    OpenAIRE

    Weissman, Daniel H.; Carp, Joshua

    2013-01-01

    Congruency effects in distracter interference tasks are often smaller after incongruent trials than after congruent trials. However, the sources of such congruency sequence effects (CSEs) are controversial. The conflict monitoring model of cognitive control links CSEs to the detection and resolution of response conflict. In contrast, competing theories attribute CSEs to attentional or affective processes that vary with previous-trial congruency (incongruent vs. congruent). The present study s...

  15. 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

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

    Directory of Open Access Journals (Sweden)

    N Dabiri

    2008-04-01

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

  17. 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

  18. Event sequence variability in healthy swallowing: building on previous findings.

    Science.gov (United States)

    Molfenter, Sonja M; Leigh, Chelsea; Steele, Catriona M

    2014-04-01

    This study builds on previous work by Kendall, Leonard, and McKenzie, which investigated event sequence variability for 12 paired events during swallowing by healthy volunteers. They identified four event pairs that always occurred in a stereotyped order and a most common occurring overall order of events during swallowing. In the current study, we investigated overall event sequencing and the same four paired events in a sample of swallows by healthy young (under 45 years old) volunteers. Data were collected during a 16-swallow lateral videofluoroscopy protocol, which included manipulations of bolus volume, barium density, bolus viscosity, and swallow cueing. Our results agreed with previous findings that variable event sequencing is found in healthy swallowing, and, in regard to obligatory sequencing of two paired events, movement of the arytenoids toward the base of the epiglottis begins prior to upper esophageal sphincter (UES) opening and maximum hyolaryngeal approximation occurs after UES opening. However, our data failed to replicate the previous findings that there is obligatory sequencing of maximum pharyngeal constriction after maximal UES distension and the UES opens before bolus arrival at the UES. The most common observed overall event sequence reported by Kendall et al. was observed in only 4/293 swallows in our dataset. Manipulations of bolus volume, bolus viscosity, barium concentration, swallow cueing, and swallow repetitions could not completely account for the differences observed between the two studies.

  19. Prevalence and significance of previously undiagnosed rheumatic diseases in pregnancy.

    Science.gov (United States)

    Spinillo, Arsenio; Beneventi, Fausta; Ramoni, Véronique; Caporali, Roberto; Locatelli, Elena; Simonetta, Margherita; Cavagnoli, Chiara; Alpini, Claudia; Albonico, Giulia; Prisco, Elena; Montecucco, Carlomaurizio

    2012-06-01

    The objective of this study was to evaluate the rates of previously undiagnosed rheumatic diseases during the first trimester of pregnancy and their impact on the pregnancy outcome. Pregnant women in their first trimester were screened using a two-step approach using a self-administered 10-item questionnaire and subsequent testing for rheumatic autoantibodies (antinuclear antibody, anti-double-stranded DNA, anti-extractable nuclear antigen, anticardiolipin antibodies, anti-β2-glycoprotein I antibodies and lupus anticoagulant) and evaluation by a rheumatologist. Overall, the complications of pregnancy evaluated included fetal loss, pre-eclampsia, gestational diabetes, fetal growth restriction, delivery at less than 34 weeks, neonatal resuscitation and admission to the neonatal intensive care unit. Out of the 2458 women screened, the authors identified 62 (2.5%) women with previously undiagnosed undifferentiated connective tissue disease (UCTD) and 24 (0.98%) women with previously undiagnosed definite systemic rheumatic disease. The prevalences were seven (0.28%) for systemic lupus erythematosus and Sjogren's syndrome, six (0.24%) for rheumatoid arthritis, three (0.12%) for antiphospholipid syndrome and one (0.04%) for systemic sclerosis. In multiple exact logistic regression, after adjustment for potential confounders, the OR of overall complications of pregnancy were 2.81 (95% CI 1.29 to 6.18) in women with UCTD and 4.57 (95% CI 1.57 to 13.57) in those with definite diseases, respectively, compared with asymptomatic controls. In our population approximately 2.5% and 1% of first trimester pregnant women had a previously undiagnosed UCTD and definite systemic rheumatic disease, respectively. These conditions were associated with significant negative effects on the outcome of pregnancy.

  20. 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.

  1. Water Quality Monitoring Sites

    Data.gov (United States)

    Vermont Center for Geographic Information — Water Quality Monitoring Site identifies locations across the state of Vermont where water quality data has been collected, including habitat, chemistry, fish and/or...

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

    Science.gov (United States)

    Ray, Ann; Kinch, Lisa N; de Souza Santos, Marcela; Grishin, Nick V; Orth, Kim; Salomon, Dor

    2016-07-26

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

  3. 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

  4. 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.)

  5. Site Features

    Data.gov (United States)

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

  6. Accurate discrimination of bHLH domains in plants, animals, and fungi using biologically meaningful sites.

    Science.gov (United States)

    Sailsbery, Joshua K; Dean, Ralph A

    2012-08-24

    The highly conserved bHLH (basic Helix-Loop-Helix) domain, found in many transcription factors, has been well characterized separately in Plants, Animals, and Fungi. While conserved, even functionally constrained sites have varied since the Eukarya split. Our research identifies those slightly variable sites that were highly characteristic of Plants, Animals, or Fungi. Through discriminant analysis, we identified five highly discerning DNA-binding amino acid sites. Additionally, by incorporating Kingdom specific HMMs, we were able to construct a tool to quickly and accurately identify and classify bHLH sequences using these sites. We conclude that highly discerning sites identified through our analysis were likely under functional constraints specific to each Kingdom. We also demonstrated the utility of our tool by identifying and classifying previously unknown bHLH domains in both characterized genomes and from sequences in a large environmental sample.

  7. Intravitreal ranibizumab for diabetic macular oedema in previously vitrectomized eyes

    DEFF Research Database (Denmark)

    Laugesen, Caroline Schmidt; Ostri, Christoffer; Brynskov, Troels

    2017-01-01

    PURPOSE: There is little information about the efficacy of intravitreal vascular endothelial growth factor (VEGF) inhibition in vitrectomized eyes. This study aimed to evaluate the efficacy of anti-VEGF (ranibizumab) on diabetic macular oedema in previously vitrectomized eyes. METHODS: A nationwide...... retrospective review of medical records from 2010 to 2013. RESULTS: We identified 33 previously vitrectomized eyes in 28 patients treated with ranibizumab injections for diabetic macular oedema. Median follow-up was 323 days (interquartile range 72-1404 days). Baseline mean visual acuity was 0.57 logMAR (95% CI...... 0.13-1.01) before injections. After an average of 4.7 injections (range 1-15), mean visual acuity remained stable at 0.54 logMAR (95% CI 0.13-0.95) with a mean improvement of 0.03 (p = 0. 45, 95% CI -0.12 to 0.06). In 12 eyes (36%), visual acuity improved 0.1 logMAR or more, in 12 eyes (36%), vision...

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

    Directory of Open Access Journals (Sweden)

    Ann Ray

    2016-07-01

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

  9. 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.

  10. 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.

  11. Site decontamination

    International Nuclear Information System (INIS)

    Bicker, A.E.

    1981-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Tiffany J. Pan

    2015-01-01

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

  13. Site organization and site arrangement

    International Nuclear Information System (INIS)

    Boissonnet, B.; Macqueron, J.F.

    1976-01-01

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

  14. 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.

  15. Identifying discharge practice training needs.

    Science.gov (United States)

    Lees, L; Emmerson, K

    A training needs analysis tool was developed to identify nurses' discharge training needs and to improve discharge practice. The tool includes 49 elements of discharge practice subdivided into four areas: corporate, operational, clinical and nurse-led discharge. The tool was disseminated to 15 wards on two hospital sites with assistance from the practice development team. Analysis of discharge training is important to assess discharge training needs and to identify staff who may assist with training.

  16. Alternate site selection process for UMTRA [Uranium Mill Tailings Remedial Action] project sites

    International Nuclear Information System (INIS)

    1988-06-01

    The purpose of this document is to describe the guidelines and processes to be used by the Department of Energy (DOE) with input from the affected states and tribes to select alternate disposal sites in compliance with each established cooperative agreement. This document supersedes two previous DOE documents, Criteria for Evaluating Disposal Sites (DOE, 1982) and Alternate Site Selection Process (ASSP) for UMTRA Project Sites (DOE, 1986). This revision of the ASSP was prepared in response to the proposed groundwater protection standards that amend 40 CF 192. The principal modifications are to the ASSP screening criteria for hydrological and geological conditions at candidate disposal sites. The revised screening and selection criteria will assist the project in selecting disposal sites where the probability of compliance with the proposed groundwater standards is high. The ASSP described in Section 2.0 consists of three phases: Phases I -- designation of a search region; Phase II -- preliminary screening of the designated search region; and Phase III -- identification and evaluation of candidate sites. Section 3.0 discusses how the results of the ASSP will be reported. This process provides a technically sound and publicly defensible approach for identifying potentially suitable disposal sites. 4 refs., 1 fig., 3 tabs

  17. Mutagenesis of the Agrobacterium VirE2 single-stranded DNA-binding protein identifies regions required for self-association and interaction with VirE1 and a permissive site for hybrid protein construction.

    Science.gov (United States)

    Zhou, X R; Christie, P J

    1999-07-01

    The VirE2 single-stranded DNA-binding protein (SSB) of Agrobacterium tumefaciens is required for delivery of T-DNA to the nuclei of susceptible plant cells. By yeast two-hybrid and immunoprecipitation analyses, VirE2 was shown to self-associate and to interact with VirE1. VirE2 mutants with small deletions or insertions of a 31-residue oligopeptide (i31) at the N or C terminus or with an i31 peptide insertion at Leu236 retained the capacity to form homomultimers. By contrast, VirE2 mutants with modifications outside a central region located between residues 320 and 390 retained the capacity to interact with VirE1. These findings suggest the tertiary structure of VirE2 is important for homomultimer formation whereas a central domain mediates formation of a complex with VirE1. The capacity of VirE2 mutants to interact with full-length VirE2 in the yeast Saccharomyces cerevisiae correlated with the abundance of the mutant proteins in A. tumefaciens, suggesting that VirE2 is stabilized by homomultimerization in the bacterium. We further characterized the promoter and N- and C-terminal sequence requirements for synthesis of functional VirE2. A PvirB::virE2 construct yielded functional VirE2 protein as defined by complementation of a virE2 null mutation. By contrast, PvirE or Plac promoter constructs yielded functional VirE2 only if virE1 was coexpressed with virE2. Deletion of 10 or 9 residues from the N or C terminus of VirE2, respectively, or addition of heterologous peptides or proteins to either terminus resulted in a loss of protein function. However, an i31 peptide insertion at Tyr39 had no effect on protein function as defined by the capacity of the mutant protein to (i) interact with native VirE2, (ii) interact with VirE1, (iii) accumulate at abundant levels in A. tumefaciens, and (iv) restore wild-type virulence to a virE2 null mutant. We propose that Tyr39 of VirE2 corresponds to a permissive site for insertion of heterologous peptides or proteins of interest

  18. 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

  19. Site assessment

    DEFF Research Database (Denmark)

    Villanueva, Héctor; Gómez Arranz, Paula

    This report describes the site assessment of given position in a given site, for a wind turbine with a well-defined hub height and rotor diameter. The analysis is carried out in accordance to IEC 61400-12-1 [1], and both an obstacle assessment and a terrain assessment are performed.......This report describes the site assessment of given position in a given site, for a wind turbine with a well-defined hub height and rotor diameter. The analysis is carried out in accordance to IEC 61400-12-1 [1], and both an obstacle assessment and a terrain assessment are performed....

  20. Site assessment

    DEFF Research Database (Denmark)

    Villanueva, Héctor; Vesth, Allan

    This report describes the site assessment of given position in a given site, for a wind turbine with a well-defined hub height and rotor diameter. The analysis is carried out in accordance to IEC 61400-12-1 [1], and both an obstacle assessment and a terrain assessment are performed......This report describes the site assessment of given position in a given site, for a wind turbine with a well-defined hub height and rotor diameter. The analysis is carried out in accordance to IEC 61400-12-1 [1], and both an obstacle assessment and a terrain assessment are performed...

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

    Science.gov (United States)

    Wagner, Orvin E.

    2002-04-01

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

  2. Discovery of an Important Previously Unknown Longitudinal Wave.

    Science.gov (United States)

    Wagner, Orvin

    2002-03-01

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

  3. The IncF plasmid pRSB225 isolated from a municipal wastewater treatment plant's on-site preflooder combining antibiotic resistance and putative virulence functions is highly related to virulence plasmids identified in pathogenic E. coli isolates.

    Science.gov (United States)

    Wibberg, Daniel; Szczepanowski, Rafael; Eikmeyer, Felix; Pühler, Alfred; Schlüter, Andreas

    2013-03-01

    The IncF antibiotic resistance and virulence plasmid pRSB225, isolated from an unknown bacterium released with the purified wastewater from a municipal sewage treatment plant into the environment has been analysed at the genomic level by pyrosequencing. The 164,550bp plasmid comprises 210 coding sequences (cds). It is composed of three replicons (RepFIA, RepFIB, and RepFII) and encodes further plasmid-specific functions for stable maintenance and inheritance and conjugative plasmid transfer. The plasmid is self-transmissible and shows a narrow host range limited to the family Enterobacteriaceae. The accessory modules of the plasmid mainly comprise genes conferring resistance to ampicillin (bla(TEM-1b)), chloramphenicol (catA1), erythromycin (mphA), kanamycin and neomycin (aphA1), streptomycin (strAB), sulphonamides (sul2), tetracycline (tetA(B)) and trimethoprim (dfrA14), as well as mercuric ions (mer genes). In addition, putative virulence-associated genes coding for iron uptake (iutA/iucABCD, sitABCD, and a putative high-affinity Fe²⁺ uptake system) and for a toxin/antitoxin system (vagCD) were identified on the plasmid. All antibiotic and heavy metal resistance genes are located either on class 1 (Tn10-remnant, Tn4352B) and class 2 transposons (Tn2-remnant, Tn21, Tn402-remnant) or a class 1 integron, whereas almost all putative virulence genes are associated with IS elements (IS1, IS26), indicating that transposition and/or recombination events were responsible for acquisition of the accessory pRSB225 modules. Particular modules of plasmid pRSB225 are related to corresponding segments of different virulence plasmids harboured by pathogenic Escherichia coli strains. Moreover, pRSB225 modules were also detected in entero-aggregative-haemorrhagic E. coli (EAHEC) draft genome sequences suggesting that IncF plasmids related to pRSB225 mediated gene transfer into pathogenic E. coli derivatives. Copyright © 2012 Elsevier Inc. All rights reserved.

  4. Site Calibration

    DEFF Research Database (Denmark)

    Kock, Carsten Weber; Vesth, Allan

    This Site Calibration report is describing the results of a measured site calibration for a site in Denmark. The calibration is carried out by DTU Wind Energy in accordance with Ref.[3] and Ref.[4]. The measurement period is given. The site calibration is carried out before a power performance...... measurement on a given turbine to clarify the influence from the terrain on the ratio between the wind speed at the center of the turbine hub and at the met mast. The wind speed at the turbine is measured by a temporary mast placed at the foundation for the turbine. The site and measurement equipment...... is detailed described in [1] and [2]. All parts of the sensors and the measurement system have been installed by DTU Wind Energy....

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

    Science.gov (United States)

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

    2017-07-01

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

  6. 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

  7. 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

  8. 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.

  9. 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.

  10. 22 CFR 40.91 - Certain aliens previously removed.

    Science.gov (United States)

    2010-04-01

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

  11. 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.

  12. 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.

  13. 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

  14. Determining root correspondence between previously and newly detected objects

    Science.gov (United States)

    Paglieroni, David W.; Beer, N Reginald

    2014-06-17

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

  15. Site development

    International Nuclear Information System (INIS)

    Noack, J.

    1975-01-01

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

  16. Site selection

    International Nuclear Information System (INIS)

    Olsen, C.W.

    1983-07-01

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

  17. Superfund Sites

    Data.gov (United States)

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

  18. Examination of previously published data to identify patterns in the social representation of "Loud music" in young adults across countries.

    Science.gov (United States)

    Manchaiah, Vinaya; Zhao, Fei; Oladeji, Susan; Ratinaud, Pierre

    2018-01-01

    The current study was aimed at understanding the patterns in the social representation of loud music reported by young adults in different countries. The study included a sample of 534 young adults (18-25 years) from India, Iran, Portugal, United Kingdom, and United States. Participants were recruited using a convince sampling, and data were collected using the free association task. Participants were asked to provide up to five words or phrases that come to mind when thinking about "loud music." The data were first analyzed using the qualitative content analysis. This was followed by quantitative cluster analysis and chi-square analysis. The content analysis suggested 19 main categories of responses related to loud music. The cluster analysis resulted in for main clusters, namely: (1) emotional oriented perception; (2) problem oriented perception; (3) music and enjoyment oriented perception; and (4) positive emotional and recreation-oriented perception. Country of origin was associated with the likelihood of participants being in each of these clusters. The current study highlights the differences and similarities in young adults' perception of loud music. These results may have implications to hearing health education to facilitate healthy listening habits.

  19. Materials Deterioration in Tropic versus Conus Sites,

    Science.gov (United States)

    1980-06-01

    RADIATION COASTAL EXPOSURE SITE OCEAN SPRINGS, MS SUBTROPICAL MARINE CLIMATE, HIGH PREVIOUS SUMMER HEAT, HUMIDITY AND MANGROVE RAINFALL SITE RESULTS KEY...WEST, FL TROPICAL MARINE CLIMATE DURING FORT SHERMAN CERTAIN MONTHS COASTAL EXPO- SURE SITE Figure 3. Analogy Between CONUS and Panama Exposure Sites...Sherman Coastal Site for 2 Weeks, 520X. Figure 13. Photomicrograph of Fungi on Surface of Jungle Fatigue Strip Exposed at Fort Sherman Coastal Site for

  20. 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

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

    African Journals Online (AJOL)

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

  2. CT Perfusion Characteristics Identify Metastatic Sites in Liver

    Directory of Open Access Journals (Sweden)

    Yuan Wang

    2015-01-01

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

  3. CT Perfusion Characteristics Identify Metastatic Sites in Liver.

    Science.gov (United States)

    Wang, Yuan; Hobbs, Brian P; Ng, Chaan S

    2015-01-01

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

  4. Human stool contains a previously unrecognized diversity of novel astroviruses

    Directory of Open Access Journals (Sweden)

    Zhao Guoyan

    2009-10-01

    Full Text Available Abstract Human astroviruses are a leading cause of gastrointestinal disease. Since their discovery in 1975, 8 closely related serotypes have been described in humans, and more recently, two new astrovirus species, astrovirus MLB1 and astrovirus VA1, were identified in diarrhea patients. In this study, we used consensus astrovirus primers targeting the RNA polymerase to define the diversity of astroviruses present in pediatric patients with diarrhea on two continents. From 416 stool specimens comprising two different cohorts from Vellore, India, 35 samples were positive. These positive samples were analyzed further by either sequencing of the ~400 bp amplicon generated by the consensus PCR or by performing additional RT-PCR specific for individual astroviruses. 19 samples contained the classic human astrovirus serotypes 1-8 while 7 samples were positive for the recently described astrovirus MLB1. Strikingly, from samples that were positive in the consensus PCR screen but negative in the specific PCR assays, five samples contained sequences that were highly divergent from all previously described astroviruses. Sequence analysis suggested that three novel astroviruses, tentatively named astroviruses VA2, MLB2 and VA3, were present in these five patient specimens (AstV-VA2 in 2 patients, AstV-MLB2 in 2 patients and AstV-VA3 in one patient. Using the same RT-PCR screening strategy, 13 samples out of 466 tested stool specimens collected in St. Louis, USA were positive. Nine samples were positive for the classic human astroviruses. One sample was positive for AstV-VA2, and 3 samples were positive for AstV-MLB2 demonstrating that these two viruses are globally widespread. Collectively, these findings underscore the tremendous diversity of astroviruses present in fecal specimens from diarrhea patients. Given that a significant fraction of diarrhea etiologies is currently unknown, it is plausible that these or other yet unrecognized astroviruses may be

  5. 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.

  6. 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)

  7. Lunar Polar Landing Sites

    Science.gov (United States)

    Kamps, Oscar; Foing, Bernard H.; Flahaut, Jessica

    2016-07-01

    An important step for a scientific mission is to assess on where the mission should be conducted. This study on landing site selection focuses on a mission to the poles of the Moon where an in-situ mission should be conducted to answer the questions with respect to volatiles and ices. The European interest for a mission to the poles of the Moon is presented in the mission concept called Heracles. This mission would be a tele-operated, sample return mission where astronauts will controlling a rover from an Orion capsule in cislunar orbit. The primary selection of landing sites was based on the scientific interest of areas near the poles. The maximum temperature map from Diviner was used to select sites where CO^2¬ should always be stable. This means that the maximum temperature is lower than 54K which is the sublimation temperature for CO^2¬ in lunar atmospheric pressure. Around these areas 14 potential regions of interest were selected. Further selection was based on the epoch of the surface in these regions of interest. It was thought that it would be of high scientific value if sites are sampled which have another epoch than already sampled by one of the Apollo or Luna missions. Only 6 sites on both North as South Pole could contain stable CO^2 ¬and were older than (Pre-)Necterian. Before a landing site and rover traverse was planned these six sites were compared on their accessibility of the areas which could contain stable CO^2. It was assumed that slope lower than 20^o is doable to rove. Eventually Amundsen and Rozhdestvenskiy West were selected as regions of interest. Assumptions for selecting landing sites was that area should have a slope lower than 5^o, a diameter of 1km, in partial illuminated area, and should not be isolated but inside an area which is in previous steps marked as accessible area to rove. By using multiple tools in ArcGIS it is possible to present the area's which were marked as potential landing sites. The closest potential landing

  8. 2 CFR 1.215 - Relationship to previous issuances.

    Science.gov (United States)

    2010-01-01

    ... 2 Grants and Agreements 1 2010-01-01 2010-01-01 false Relationship to previous issuances. 1.215 Section 1.215 Grants and Agreements ABOUT TITLE 2 OF THE CODE OF FEDERAL REGULATIONS AND SUBTITLE A Introduction toSubtitle A § 1.215 Relationship to previous issuances. Although some of the guidance was...

  9. 2 CFR 230.45 - Relationship to previous issuance.

    Science.gov (United States)

    2010-01-01

    ... 2 Grants and Agreements 1 2010-01-01 2010-01-01 false Relationship to previous issuance. 230.45 Section 230.45 Grants and Agreements OFFICE OF MANAGEMENT AND BUDGET CIRCULARS AND GUIDANCE Reserved COST PRINCIPLES FOR NON-PROFIT ORGANIZATIONS (OMB CIRCULAR A-122) § 230.45 Relationship to previous issuance. (a...

  10. 49 CFR 173.23 - Previously authorized packaging.

    Science.gov (United States)

    2010-10-01

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

  11. 75 FR 76056 - FEDERAL REGISTER CITATION OF PREVIOUS ANNOUNCEMENT:

    Science.gov (United States)

    2010-12-07

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

  12. Triple outlet right ventricle: a previously unknown cardiac malformation.

    Science.gov (United States)

    Tingo, Jennifer E; Carroll, Sheila J; Crystal, Matthew A

    2015-03-01

    We present the case of an infant with three distinct outflow tracts from the right ventricle. Three outlets from the heart have been previously named the "Tritruncal Heart". We review the two previously reported cases of tritruncal hearts and describe the anatomy, diagnosis, surgical management, and outcome of our case. Embryologic implications are also discussed.

  13. Identifying Functional Cysteine Residues in the Mitochondria.

    Science.gov (United States)

    Bak, Daniel W; Pizzagalli, Mattia D; Weerapana, Eranthie

    2017-04-21

    The mitochondria are dynamic organelles that regulate oxidative metabolism and mediate cellular redox homeostasis. Proteins within the mitochondria are exposed to large fluxes in the surrounding redox environment. In particular, cysteine residues within mitochondrial proteins sense and respond to these redox changes through oxidative modifications of the cysteine thiol group. These oxidative modifications result in a loss in cysteine reactivity, which can be monitored using cysteine-reactive chemical probes and quantitative mass spectrometry (MS). Analysis of cell lysates treated with cysteine-reactive probes enable the identification of hundreds of cysteine residues, however, the mitochondrial proteome is poorly represented (proteins and suppression of mitochondrial peptide MS signals by highly abundant cytosolic peptides. Here, we apply a mitochondrial isolation and purification protocol to substantially increase coverage of the mitochondrial cysteine proteome. Over 1500 cysteine residues from ∼450 mitochondrial proteins were identified, thereby enabling interrogation of an unprecedented number of mitochondrial cysteines. Specifically, these mitochondrial cysteines were ranked by reactivity to identify hyper-reactive cysteines with potential catalytic and regulatory functional roles. Furthermore, analyses of mitochondria exposed to nitrosative stress revealed previously uncharacterized sites of protein S-nitrosation on mitochondrial proteins. Together, the mitochondrial cysteine enrichment strategy presented herein enables detailed characterization of protein modifications that occur within the mitochondria during (patho)physiological fluxes in the redox environment.

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

    Science.gov (United States)

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

    2009-04-01

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

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

    Science.gov (United States)

    Fromhage, Lutz; Schneider, Jutta M.

    2005-09-01

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

  16. Site selection

    CERN Multimedia

    CERN PhotoLab

    1968-01-01

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

  17. Site Restoration

    Energy Technology Data Exchange (ETDEWEB)

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

    2001-04-01

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

  18. Site Restoration

    International Nuclear Information System (INIS)

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

    2001-01-01

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

  19. Site calibration

    DEFF Research Database (Denmark)

    Gómez Arranz, Paula; Georgieva Yankova, Ginka

    between the wind speed at the center of the turbine hub and at the met mast. The wind speed at the turbine is measured by a temporary mast placed at the foundation for the turbine. The site and measurement equipment is detailed described in [2]. The possible measurement sector for power performance...

  20. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-07-28

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

  2. Adolescents previously involved in Satanism experiencing mental health problems

    Directory of Open Access Journals (Sweden)

    H Heathcote

    1999-09-01

    Full Text Available No research has previously been done regarding the phenomenon of adolescents who have previously been involved in Satanism and who experience obstacles in their strive for mental health. Adolescents previously involved in Satanism present behavioral problems like aggressive outbursts, depression, “ psychosis” or suicide attempts, that could lead to suicide. In the phenomenonanalysis semi-structured, phenomenological interviews were performed with the respondents and their parents. The respondents were requested to write a naïve sketch about their life. After completion of the data-control, guidelines for nursing staff were set.

  3. 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

  4. Influence of previous participation in physical activity on its ...

    African Journals Online (AJOL)

    ... participation can influence perceptions of PA among the students. Physical activity promotion programmes should consider the role of these factors which should be emphasised from childhood. Keywords: physical activity, students, perceived benefits, perceived barriers, previous participation, sedentary lifestyle, Rwanda

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

    African Journals Online (AJOL)

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

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

    Science.gov (United States)

    1985-01-01

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

  7. Delivery outcomes at term after one previous cesarean section.

    Science.gov (United States)

    Yamani-Zamzami, Tarik Y

    2007-12-01

    To determine the maternal and perinatal outcomes at term in women with one previous cesarean delivery and with no history of vaginal birth. This is a case-control study conducted at King Abdul-Aziz University Hospital, Jeddah, Kingdom of Saudi Arabia, between January 1, 1999 and December 31, 2002. One hundred sixty-two women with one previous cesarean delivery and with no previous vaginal birth were compared with 324 control women. The cesarean section rate was higher in the study group 40 (24.7%) versus 23 (7.1%) in the control group and was statistically significant (phistory of vaginal delivery are considered less favorable, the vaginal birth after cesarean section success rate may be even lower if the indication for previous primary cesarean delivery was failure to progress, and may be associated with increased risk of uterine rupture. Further study is required to confirm our findings.

  8. Site and neighborhood environments for walking among older adults.

    Science.gov (United States)

    Wang, Zhe; Lee, Chanam

    2010-11-01

    Walking has significant health and mobility benefits for older adults. Previous environment-walking studies have focused on neighborhood environments, overlooking proximate site-level characteristics. This study examines both the neighborhood and site-level environments. A survey was conducted with 114 older adults from five assisted-living facilities in Houston, TX. A subset of 61 participants' environments was examined using Geographic Information Systems (GIS). Multivariate analyses identified positive correlates of walking at the site level including yard landscaping and corner-lots, and neighborhood-level correlates including walking destinations, safety from crime, and sidewalks. Both site-level and neighborhood environmental supports appear important in promoting walking among older adults. Copyright © 2010 Elsevier Ltd. All rights reserved.

  9. [Influence of previous abdominopelvic surgery on gynecological laparoscopic operation].

    Science.gov (United States)

    Jin, Haoran; Shi, Wei; Zhou, Yingfang; Wu, Beisheng; Peng, Chao

    2014-09-01

    To investigate the influence of previous abdominopelvic surgery on gynecological laparoscopic operation. A retrospective analysis of 3 283 cases of gynecological diseases by laparoscopic operation patients in Peking University First Hospital from 2007 January to 2012 December, among them, 719 (21.90%) patients with previous abdominopelvic surgery history (study Group), 2 564 (78.10%)patients have no history of abdominopelvic surgery (control group). Study group 719 patients, previous operation times: one time in 525 cases, 194 cases were multiple; previous operation: 185 cases of gynecological surgery, 305 cases of obstetric surgery, 108 cases of general surgery, and 121 complex surgery (include at least two kinds of surgery); previous operative approach: 650 cases laparotomy and 69 cases laparoscopy. Compared two groups of patients with abdominopelvic adhesion and the gynecologic laparoscopic operation situation, analyzed the influence of previous abdominopelvic surgery on abdominopelvic adhesion on and gynecological laparoscopic operation. The incidence of abdominopelvic adhesion in the patients with previous abdominopelvic surgery was 51.2% (368/719), which was significantly higher than that of 8.2% (211/2 564)in patients without previous abdominopelvic surgery (P surgery (23.1%, 166/719) was significantly higher than that in the control group (3.3% , 85/2 564;P laparotomy was 0.6% (4/719) significantly more than the control groups (0.1%, 2/2 564; P = 0.023). Compared with other groups, patients with gynecological or complex surgery or multiple operation history presented more severe abdominopelvic adhesion both in the score and degree (P laparotomy showed no statistical difference between the two groups (P > 0.05). The laparoscopic operation could be carried out successfully and safely in patients with a history of various abdominopelvic operations, but the conversion rate increases, for patients with a history of multiple operation because of pelvic adhesion

  10. Site Practice

    DEFF Research Database (Denmark)

    Wahedi, Haseebullah

    2016-01-01

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

  11. Identification of multidrug resistance in previously treated tuberculosis patients: a mixed methods study in Cambodia

    Science.gov (United States)

    Royce, S; Khann, S; Yadav, RP; Mao, ET; Cattamanchi, A; Sam, S; Handley, MA

    2014-01-01

    SUMMARY Setting Previously treated tuberculosis (TB) patients are a priority for drug susceptibility testing (DST) to identify cases with multidrug resistance (MDR). In Cambodia, a recent study found that only one-third of smear-positive previously treated patients had DST results. Objective To quantify the gaps in detecting MDR in previously treated TB patients in Cambodia, and describe health workers’ perspectives on barriers, facilitators and potential interventions. Design We analyzed case notifications in Cambodia (2004–2012) and conducted semi-structured interviews with key stakeholders Results The proportion of previously treated notifications varied significantly across provinces 2010–12, in the context of longer term trends of decreasing relapse and increasing “other” retreatment notifications. Correct classification of patients’ TB treatment history and ensuring specimens from previously-treated patients are collected and reach the laboratory could nearly double the number of detected MDR-TB cases. Identified barriers include patients’ reluctance to disclose and staff difficulty eliciting treatment history, partly due to availability of streptomycin only in hospitals. Facilitators include trained health workers, collection of sputum for DST even if previously treated patients are not taking streptomycin, streamlining sputum transportation and promptly reporting results. Conclusion Improved monitoring, supportive supervision, and correctly classifying previously treated patients are essential for improving detection of MDR-TB. PMID:25299861

  12. 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).

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

    LENUS (Irish Health Repository)

    Ooi, Poh Veh

    2011-01-01

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

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

    LENUS (Irish Health Repository)

    Ooi, Poh Veh

    2012-01-31

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

  15. 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.

  16. Previous Land Use and Invasive Species Impacts on Long-term Afforestation Success

    Directory of Open Access Journals (Sweden)

    Joshua B. Nickelson

    2015-09-01

    Full Text Available The conversion of agricultural lands to forests has increased worldwide over the past few decades for multiple reasons including increasing forest connectivity and wildlife habitat. However, previous land cover and competing vegetation often impede afforestation. We established 219 plots in 29 Quercus plantations on four previous land cover types (LCT: Clover, Soybeans, Woody Brush, and Herbaceous Weeds. Plantations were located in Illinois, USA and were sampled 15–18 years after planting. Sampling data for all trees (planted and volunteer included species, diameter, and vine presence on the main bole of the tree. Free-to-grow status was recorded for all Quercus species and estimated cover of two invasive species, Elaeagnus umbellata and Lonicera japonica, was documented on each plot. There was a strong relationship between total tree density and invasive species cover across all sites. Stocking success was lower and E. umbellata cover was higher on Woody Brush sites compared to Clover and Soybean cover types. Additionally, significantly more free-to-grow Quercus saplings occurred in Clover and Soybean cover types compared to the Woody Brush sites. The results indicate that previous land cover plays a critical role in forest afforestation. Furthermore, while historically, volunteer tree species were thought to be detrimental to the development of planted species these results suggest that with the increasing prevalence of invasive species worldwide the role of volunteer species in afforestation should be reconsidered and silvicultural protocols adjusted accordingly.

  17. Ribosome signatures aid bacterial translation initiation site identification.

    Science.gov (United States)

    Giess, Adam; Jonckheere, Veronique; Ndah, Elvis; Chyżyńska, Katarzyna; Van Damme, Petra; Valen, Eivind

    2017-08-30

    While methods for annotation of genes are increasingly reliable, the exact identification of translation initiation sites remains a challenging problem. Since the N-termini of proteins often contain regulatory and targeting information, developing a robust method for start site identification is crucial. Ribosome profiling reads show distinct patterns of read length distributions around translation initiation sites. These patterns are typically lost in standard ribosome profiling analysis pipelines, when reads from footprints are adjusted to determine the specific codon being translated. Utilising these signatures in combination with nucleotide sequence information, we build a model capable of predicting translation initiation sites and demonstrate its high accuracy using N-terminal proteomics. Applying this to prokaryotic translatomes, we re-annotate translation initiation sites and provide evidence of N-terminal truncations and extensions of previously annotated coding sequences. These re-annotations are supported by the presence of structural and sequence-based features next to N-terminal peptide evidence. Finally, our model identifies 61 novel genes previously undiscovered in the Salmonella enterica genome. Signatures within ribosome profiling read length distributions can be used in combination with nucleotide sequence information to provide accurate genome-wide identification of translation initiation sites.

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

    International Nuclear Information System (INIS)

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

    1998-01-01

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

  19. Oriented scanning is the leading mechanism underlying 5' splice site selection in mammals.

    Directory of Open Access Journals (Sweden)

    Keren Borensztajn

    2006-09-01

    Full Text Available Splice site selection is a key element of pre-mRNA splicing. Although it is known to involve specific recognition of short consensus sequences by the splicing machinery, the mechanisms by which 5' splice sites are accurately identified remain controversial and incompletely resolved. The human F7 gene contains in its seventh intron (IVS7 a 37-bp VNTR minisatellite whose first element spans the exon7-IVS7 boundary. As a consequence, the IVS7 authentic donor splice site is followed by several cryptic splice sites identical in sequence, referred to as 5' pseudo-sites, which normally remain silent. This region, therefore, provides a remarkable model to decipher the mechanism underlying 5' splice site selection in mammals. We previously suggested a model for splice site selection that, in the presence of consecutive splice consensus sequences, would stimulate exclusively the selection of the most upstream 5' splice site, rather than repressing the 3' following pseudo-sites. In the present study, we provide experimental support to this hypothesis by using a mutational approach involving a panel of 50 mutant and wild-type F7 constructs expressed in various cell types. We demonstrate that the F7 IVS7 5' pseudo-sites are functional, but do not compete with the authentic donor splice site. Moreover, we show that the selection of the 5' splice site follows a scanning-type mechanism, precluding competition with other functional 5' pseudo-sites available on immediate sequence context downstream of the activated one. In addition, 5' pseudo-sites with an increased complementarity to U1snRNA up to 91% do not compete with the identified scanning mechanism. Altogether, these findings, which unveil a cell type-independent 5'-3'-oriented scanning process for accurate recognition of the authentic 5' splice site, reconciliate apparently contradictory observations by establishing a hierarchy of competitiveness among the determinants involved in 5' splice site selection.

  20. 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

  1. 2 CFR 225.45 - Relationship to previous issuance.

    Science.gov (United States)

    2010-01-01

    ... 2 Grants and Agreements 1 2010-01-01 2010-01-01 false Relationship to previous issuance. 225.45 Section 225.45 Grants and Agreements OFFICE OF MANAGEMENT AND BUDGET CIRCULARS AND GUIDANCE Reserved COST PRINCIPLES FOR STATE, LOCAL, AND INDIAN TRIBAL GOVERNMENTS (OMB CIRCULAR A-87) § 225.45 Relationship to...

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

    African Journals Online (AJOL)

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

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

    African Journals Online (AJOL)

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

  4. Balance and bilateral skills of selected previously disadvantaged ...

    African Journals Online (AJOL)

    Balance and bilateral skills of selected previously disadvantaged children aged 9 to 12 years. Eileen K Africa, Karel J Van Deventer. Abstract. The main aim of the study was to design an appropriate motor skills development programme that could be implemented in any primary school to improve the fundamental motor ...

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

    African Journals Online (AJOL)

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

  6. Suburethral sling procedures after previous surgery for urinary ...

    African Journals Online (AJOL)

    Objective. To compare the outcome of suburethral sling procedures (tension-free vaginal tape (TVT), obturator tape (Ob-tape)) for stress urinary incontinence (SUI) in women with previous surgery for SUI or pelvic organ prolapse (POP). Methods. A comparative, descriptive, retrospective study was done using information ...

  7. 5 CFR 532.405 - Use of highest previous rate.

    Science.gov (United States)

    2010-01-01

    ... 5 Administrative Personnel 1 2010-01-01 2010-01-01 false Use of highest previous rate. 532.405 Section 532.405 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT CIVIL SERVICE REGULATIONS... rate may be based upon a rate of pay received during a temporary promotion, so long as the temporary...

  8. 24 CFR 1710.552 - Previously accepted state filings.

    Science.gov (United States)

    2010-04-01

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

  9. 5 CFR 9701.352 - Use of highest previous rate.

    Science.gov (United States)

    2010-01-01

    ... HUMAN RESOURCES MANAGEMENT SYSTEM Pay and Pay Administration Pay Administration § 9701.352 Use of... 5 Administrative Personnel 3 2010-01-01 2010-01-01 false Use of highest previous rate. 9701.352 Section 9701.352 Administrative Personnel DEPARTMENT OF HOMELAND SECURITY HUMAN RESOURCES MANAGEMENT...

  10. Bilateral orbital infarction and retinal detachment in a previously ...

    African Journals Online (AJOL)

    In this report, we present a case of an 11‑year‑old previously undiagnosed sickle cell disease Nigerian girl with severe acute bilateral orbital infarction and retinal detachment to highlight that hemoglobinopathy induced orbital infarction should be considered in African children with acute onset proptosis with or without ...

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

    Science.gov (United States)

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

    1999-08-01

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

  12. The effect of previous traumatic injury on homicide risk.

    Science.gov (United States)

    Griffin, Russell L; Davis, Gregory G; Levitan, Emily B; MacLennan, Paul A; Redden, David T; McGwin, Gerald

    2014-07-01

    Research has reported that a strong risk factor for traumatic injury is having a previous injury (i.e., recidivism). To date, the only study examining the relationship between recidivism and homicide reported strong associations, but was limited by possible selection bias. The current matched case-control study utilized coroner's data from 2004 to 2008. Subjects were linked to trauma registry data to determine whether the person had a previous traumatic injury. Conditional logistic regression was used to estimate odds ratios (ORs) and 95% confidence intervals (95% CIs) for the association between homicide and recidivism. Homicide risk was increased for those having a previous traumatic injury (OR 1.81, 95% CI 1.09-2.99) or a previous intentional injury (OR 2.53, 95% CI 1.24-5.17). These results suggest an association between homicide and injury recidivism, and that trauma centers may be an effective setting for screening individuals for secondary prevention efforts of homicide through violence prevention programs. © 2014 American Academy of Forensic Sciences.

  13. Control of feed intake as affected by previous treatment | Pienaar ...

    African Journals Online (AJOL)

    An experiment was conducted with eighteen rumen cannulated sheep fed on a chopped lucerne diet. Previous level of intake significantly influenced the level at which sheep initially established voluntary feed intake. This difference had disappeared after three weeks on an ad lib. intake. Perturbation analysis of the results ...

  14. "Battered Women" and Previous Victimization: Is the Question Relevant?

    Science.gov (United States)

    Gudim, Laurie, Comp.; And Others

    This report discusses battered women and the role of their previous victimization. After a literature review on family violence in general, these topics are discussed: (1) family violence and the patriarchy; (2) the historical background of family violence; (3) intergenerational cycle of violence; and (4) psychological literature's four ways…

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

    African Journals Online (AJOL)

    Age, education, religion, parity, prior contraception, and interval from the last delivery were significantly associated with the current choice of contraception (P 0.05). Overall, when comparing the pattern among those with a previous operative delivery and those without, ...

  16. Process cells dismantling of EUREX pant: previous activities

    International Nuclear Information System (INIS)

    Gili, M.

    1998-01-01

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

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

    African Journals Online (AJOL)

    Previous utilization of service does not improve timely booking in antenatal care: Cross sectional study on timing of antenatal care booking at public health facilities in ... Methods: A cross sectional study was conducted to collect data from 630 pregnant women who were attending antenatal care service at 10 governmental ...

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

    African Journals Online (AJOL)

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

  19. Mondor's Disease of the Breast in a Nigerian Woman Previously ...

    African Journals Online (AJOL)

    2017-09-14

    Sep 14, 2017 ... Case Report. How to cite this article: Olarinoye-Akorede SA, Silas BT. Mondor's disease of the breast in a Nigerian woman previously treated for invasive ductal carcinoma in the ... and the new creations are licensed under the identical terms. For reprints .... malignancy. Financial support and sponsorship.

  20. 44 CFR 402.5 - Forwarding commodities previously shipped.

    Science.gov (United States)

    2010-10-01

    ... 44 Emergency Management and Assistance 1 2010-10-01 2010-10-01 false Forwarding commodities... commodities previously shipped. Order T-1 applies to transportation on or discharge from ships documented... ship or aircraft, before the issuance of Order T-1, had transported restricted commodities manifested...

  1. Reoperative sentinel lymph node biopsy after previous mastectomy.

    Science.gov (United States)

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

    2008-10-01

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

  2. Detection and identification of previously unrecognized microbial pathogens.

    OpenAIRE

    Relman, D. A.

    1998-01-01

    Features of a number of important but poorly explained human clinical syndromes strongly indicate a microbial etiology. In these syndromes, the failure of cultivation-dependent microbial detection methods reveals our ignorance of microbial growth requirements. Sequence-based molecular methods, however, offer alternative approaches for microbial identification directly from host specimens found in the setting of unexplained acute illnesses, chronic inflammatory disease, and from anatomic sites...

  3. Limitations of previously published systematic reviews evaluating the outcome of endodontic treatment

    NARCIS (Netherlands)

    Wu, M.K.; Shemesh, H.; Wesselink, P.R.

    2009-01-01

    The aim of this work was to identify the limitations of previously published systematic reviews evaluating the outcome of root canal treatment. Traditionally, periapical radiography has been used to assess the outcome of root canal treatment with the absence of a periapical radiolucency being

  4. 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.

  5. 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

  6. High prevalence of genetic variants previously associated with LQT syndrome in new exome data

    DEFF Research Database (Denmark)

    Refsgaard, Lena; Holst, Anders G; Sadjadieh, Golnaz

    2012-01-01

    Exome Sequencing Project (ESP) has provided important knowledge on this topic. We aimed to investigate the prevalence of previously LQTS-associated variants in ESP (5400 individuals), in order to identify possible false-positive LQTS variants. With this aim, we performed a search for previously...... published LQTS-associated variants in ESP. In addition, a PolyPhen-2 prediction was conducted, and the four most prevalent LQTS-associated variants with significant functional effects present in ESP were genotyped in a second control population. We identified 33 missense variants previously associated...... with LQTS in ESP. These 33 variants affected 173 alleles and this corresponded to a LQTS prevalence of 1:31 in the ESP population. PolyPhen-2 predicted 30% of the 33 variants present in ESP to be benign compared with 13% among LQTS-associated variants not present in ESP (P=0.019). Genotyping of the four...

  7. Site Restoration

    International Nuclear Information System (INIS)

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

    2002-01-01

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

  8. Site Restoration

    Energy Technology Data Exchange (ETDEWEB)

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

    2002-04-01

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

  9. Mochovce site

    International Nuclear Information System (INIS)

    1997-01-01

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

  10. 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......-insulin-dependent diabetes mellitus). Diabetes did not develop in any of the controls. Predictive factors for diabetes development were fasting glucose level at diagnosis (high glucose, high risk), preterm delivery, and an oral glucose tolerance test result that showed diabetes 2 months post partum. In a subgroup...

  11. Thoughts on identifiers

    CERN Document Server

    CERN. Geneva

    2005-01-01

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

  12. SITE-94. Mineralogy of the Aespoe site

    International Nuclear Information System (INIS)

    Andersson, Karin

    1996-12-01

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

  13. Identifiability in stochastic models

    CERN Document Server

    1992-01-01

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

  14. 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.

  15. Previously unreported abnormalities in Wolfram Syndrome Type 2.

    Science.gov (United States)

    Akturk, Halis Kaan; Yasa, Seda

    2017-01-01

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

  16. Nicotine Elicits Methamphetamine-Seeking in Rats Previously Administered Nicotine

    OpenAIRE

    Neugebauer, N. M.; Harrod, S. B.; Bardo, M. T.

    2009-01-01

    Research has indicated a high correlation between psychostimulant use and tobacco cigarette smoking in human substance abusers. The objective of the current study was to examine the effects of acute and repeated nicotine administration on responding for intravenous methamphetamine (0.03 mg/kg/infusion) in a rodent model of self-administration, as well as the potential of nicotine to induce reinstatement of previously extinguished drug-taking behavior in male Sprague-Dawley rats. In addition, ...

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

    OpenAIRE

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

    2015-01-01

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

  18. Previous climatic alterations are caused by the sun

    International Nuclear Information System (INIS)

    Groenaas, Sigbjoern

    2003-01-01

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

  19. Previously infertile couples and the newborn intensive care unit.

    Science.gov (United States)

    Lind, R F; Pruitt, R L; Greenfeld, D

    1989-05-01

    Having a newborn child admitted to a newborn intensive care unit can be a traumatic experience for parents; however, parents who previously have been infertile face unique problems in coping with this situation. The authors discuss the difficulties parents must overcome in resolving their crises and in developing a good relationship with their child, or, in some cases, coming to terms with the child's death or ongoing disability. In addition, the authors offer suggestions for effective social work intervention.

  20. 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.

  1. Corrective Action Plan for Corrective Action Unit 214: Bunkers and Storage Areas, Nevada Test Site, Nevada - Revision 0 - March 2005

    Energy Technology Data Exchange (ETDEWEB)

    U.S. Department of Energy, National Nuclear Security Administration, Nevada Site Office; Bechtel Nevada

    2005-03-01

    Corrective Action Unit 214, Bunkers and Storage Areas, is identified in the Federal Facility Agreement and Consent Order of 1996. Corrective Action Unit 214 consists of nine Corrective Action Sites located in Areas 5, 11, and 25 of the Nevada Test Site. The Nevada Test Site is located approximately 105 kilometers (65 miles) northwest of Las Vegas, Nevada, in Nye County. Corrective Action Unit 214 was previously characterized in 2004, and results were presented in the Corrective Action Decision Document for 214. Site characterization indicated that soil and/or debris exceeded clean-up criteria for Total Petroleum Hydrocarbons, pesticides, metals, and radiological contamination.

  2. Optimization of hydraulic machinery by exploiting previous successful designs

    Energy Technology Data Exchange (ETDEWEB)

    Kyriacou, S A; Giannakoglou, K C [National Technical University of Athens, Parallel CFD and Optimization Unit, PO Box 64069, Athens 15710 (Greece); Weissenberger, S; Grafenberger, P, E-mail: stelios.Kyriacou@gmail.co [Andritz HYDRO, RD, Lunzerstrasse 78, 4031 Linz (Austria)

    2010-08-15

    A design-optimization method for hydraulic machinery is proposed. Optimal designs are obtained using the appropriate CFD evaluation software driven by an evolutionary algorithm which is also assisted by artificial neural networks used as surrogate evaluation models or metamodels. As shown in a previous IAHR paper by the same authors, such an optimization method substantially reduces the CPU cost, since the metamodels can discard numerous non-promising candidate solutions generated during the evolution, at almost negligible CPU cost, without evaluating them by means of the costly CFD tool. The present paper extends the optimization method of the previous paper by making it capable to accommodate and exploit pieces of useful information archived during previous relevant successful designs. So, instead of parameterizing the geometry of the hydraulic machine components, which inevitably leads to many design variables, enough to slow down the design procedure, in the proposed method all new designs are expressed as weighted combinations of the archived ones. The archived designs act as the design space bases. The role of the optimization algorithms is to find the set (or sets, for more than one objectives, where the Pareto front of non-dominated solutions is sought) of weight values, corresponding to the hydraulic machine configuration(s) with optimal performance. Since the number of weights is much less that the number of design variables of the conventional shape parameterization, the design space dimension reduces and the CPU cost of the metamodel-assisted evolutionary algorithm is much lower. The design of a Francis runner is used to demonstrate the capabilities of the proposed method.

  3. Cutaneous protothecosis in a patient with previously undiagnosed HIV infection.

    Science.gov (United States)

    Fong, Kenneth; Tee, Shang-Ian; Ho, Madeline S L; Pan, Jiun Yit

    2015-08-01

    Protothecosis is an uncommon condition resulting from infection by achlorophyllous algae of the Prototheca species. Immunocompromised individuals are generally most susceptible to protothecal infection and tend to develop severe and disseminated disease. However, the association between protothecosis and HIV-induced immunosuppression is not clear, with only a handful of cases having been described to date. Here we report a case of cutaneous protothecosis in a Chinese man with previously undiagnosed HIV infection that responded well to oral itraconazole. © 2014 The Australasian College of Dermatologists.

  4. HEART TRANSPLANTATION IN PATIENTS WITH PREVIOUS OPEN HEART SURGERY

    Directory of Open Access Journals (Sweden)

    R. Sh. Saitgareev

    2016-01-01

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

  5. Fulminant Pneumococcal Pericarditis in a Previously Healthy Patient.

    Science.gov (United States)

    Trpkov, Cvetan; Nath, Ermin; Moon, Michael; Windram, Jonathan; Graham, Michelle M

    2017-04-01

    Purulent pericarditis is a rare acutely life-threatening condition. Initial symptoms, signs, and investigations can be nonspecific. Echocardiography is invaluable for establishing the diagnosis and initial management. We present a case of a previously healthy patient with purulent pericarditis caused by Streptococcus pneumoniae in the absence of a primary focus of infection. The patient deteriorated rapidly with cardiac tamponade and septic shock and was managed successfully by a combined medical and surgical approach. Copyright © 2016 Canadian Cardiovascular Society. Published by Elsevier Inc. All rights reserved.

  6. 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 restoration work will employ capping with a barrier layer.

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

    Czech Academy of Sciences Publication Activity Database

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

    2007-01-01

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

  8. 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

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

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    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.

  10. 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

    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...

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

    Science.gov (United States)

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

    1987-01-01

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

  12. Efforts to promote vaginal delivery after a previous cesarean section.

    Science.gov (United States)

    Hamai, Yoko; Imanishi, Yukio

    2012-01-01

    The aim of this study was to examine the results of vaginal delivery in patients with a past history of cesarean section. The type of delivery, interventions during delivery, and the prognoses of the mothers and babies were examined in 145 women with a history of cesarean section over the 10-year period from January 2000 to December 2009. A scheduled cesarean section was performed in 27 cases. Vaginal delivery was recommended in 118 cases and the success rate was 94.9% (112/118). Uterine rupture was observed in one patient who experienced a natural rupture at home and whose previous cesarean section was an inverse T incision. No cases required a blood transfusion or hysterectomy. The prognoses of both mothers and babies were good and the vaginal delivery success rate was 94.9%. Uterine rupture was observed in one case. Vaginal delivery with previous cesarean section should be considered in cases with expectation and informed consent. © 2011 The Authors. Journal of Obstetrics and Gynaecology Research © 2011 Japan Society of Obstetrics and Gynecology.

  13. Investigating the effect of previous treatments on wheat biomass over multiple spatial frequencies

    Science.gov (United States)

    Milne, A. E.; Castellanos, M. T.; Cartagena, M. C.; Tarquis, A. M.; Lark, R. M.

    2010-09-01

    In this study we use the maximum overlap discrete packet transform (MODWPT) to investigate residual effects on wheat biomass of fertigation treatments applied to a previous crop. The wheat crop covered nine subplots from a previous experiment on melon response to fertigation. Each subplot had previously received a different level of applied nitrogen. Many factors affect wheat biomass, causing it to vary at different spatial frequencies. We hypothesize that these will include residual effects from fertilizer application (at relatively low spatial frequencies) and the local influence of individual plants from the previous melon crop (at high frequency). To test this hypothesis we use the MODWPT to identify the dominant spatial frequencies of wheat biomass variation, and analyse the relationship to both the previous fertilizer application and the location of individual melon plants in the previous crop. The MODWPT is particularly appropriate for this because it allows us first to identify the key spatial frequencies in the wheat biomass objectively and to analyse them, and their relationship to hypothesized driving factors without any assumptions of uniformity (stationarity) of wheat-biomass variation. The results showed that the applied nitrogen dominated the wheat biomass response, and that there was a noticeable component of wheat-biomass variation at the spatial frequency that corresponds to the melon cropping. We expected wheat biomass to be negatively correlated with the position of melons in the previous crop, due to uptake of the applied nitrogen. The MODWPT, which allows us to detect changes in correlation between variables at different frequencies, showed that such a relationship was found across part of the experiment but not uniformly.

  14. 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

  15. 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...

  16. 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

  17. 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...

  18. Repeat coronary angiography with previously normal arteries: a futile exercise?

    Science.gov (United States)

    Rowe, Rebecca; Parviz, Yasir; Iqbal, Javaid; Heppenstall, James; Teare, Dawn; Gunn, Julian

    2015-02-15

    Up to 20% of coronary angiograms reveal normal arteries. How long they stay normal is poorly understood. This study investigated the fate of normal coronary arteries and determined the rate of development of coronary artery disease. We interrogated the angiographic archive of the South Yorkshire Cardiothoracic Centre between 2004 and 2013 to identify patients with truly normal coronary arteries who underwent repeat coronary angiography more than 1 year later. Follow up angiograms were scored for the severity and extent of CAD (graded per segment as 0%, 1-50%, >50%). Risk factors for the development of coronary artery disease were documented. Univariate predictors of disease development were identified and entered into a logistic regression model to identify independent predictors. Out of over 25,000 angiographic procedures in the archives we found 6068 patients reported to have normal coronary arteries. Of these, 162 patients had also undergone subsequent repeat coronary angiography. Of these, 97 had truly normal (smooth) coronary arteries at baseline and had undergone repeat angiography >1 year later. At a median 51 months, 87 continued to have normal arteries, and all the remaining 10 had mild disease only (average 37% stenosis in an average 1.2 segments). No patients developed any significant (>50% stenosis) disease. Advanced age, time between angiograms, and smoking status were identified as independent predictors of development of CAD. Truly normal coronary arteries do not progress to significant disease within a time frame of 4 years. Repeat coronary angiography within that period is probably not indicated. © 2014 Wiley Periodicals, Inc.

  19. 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

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

    Science.gov (United States)

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

    2013-12-01

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

  1. Identifying Individual Clown Fish

    OpenAIRE

    Liu, Xiao; Fisher, Robert

    2016-01-01

    This paper presents a clustering approach to estimating the number of individuals present in a set of Amphiprion clarkii (clownfish) observed live from a Taiwanese coral reef. Previous approaches to individual identification have addressed species where there are many individuals with some distinctive pattern and few observations of each. By contrast, fish observations from a fixed camera tend to produce many observations of a few individuals, whose differences in appearance are more quantita...

  2. 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.

  3. Deepwater Gulf of Mexico more profitable than previously thought

    International Nuclear Information System (INIS)

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

    1997-01-01

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

  4. Surgical treatment of breast cancer in previously augmented patients.

    Science.gov (United States)

    Karanas, Yvonne L; Leong, Darren S; Da Lio, Andrew; Waldron, Kathleen; Watson, James P; Chang, Helena; Shaw, William W

    2003-03-01

    The incidence of breast cancer is increasing each year. Concomitantly, cosmetic breast augmentation has become the second most often performed cosmetic surgical procedure. As the augmented patient population ages, an increasing number of breast cancer cases among previously augmented women can be anticipated. The surgical treatment of these patients is controversial, with several questions remaining unanswered. Is breast conservation therapy feasible in this patient population and can these patients retain their implants? A retrospective review of all breast cancer patients with a history of previous augmentation mammaplasty who were treated at the Revlon/UCLA Breast Center between 1991 and 2001 was performed. During the study period, 58 patients were treated. Thirty patients (52 percent) were treated with a modified radical mastectomy with implant removal. Twenty-eight patients (48 percent) underwent breast conservation therapy, which consisted of lumpectomy, axillary lymph node dissection, and radiotherapy. Twenty-two of the patients who underwent breast conservation therapy initially retained their implants. Eleven of those 22 patients (50 percent) ultimately required completion mastectomies with implant removal because of implant complications (two patients), local recurrences (five patients), or the inability to obtain negative margins (four patients). Nine additional patients experienced complications resulting from their implants, including contracture, erosion, pain, and rupture. The data illustrate that breast conservation therapy with maintenance of the implant is not ideal for the majority of augmented patients. Breast conservation therapy with explantation and mastopexy might be appropriate for rare patients with large volumes of native breast tissue. Mastectomy with immediate reconstruction might be a more suitable choice for these patients.

  5. Effect of previous induced abortions on postabortion contraception selection.

    Science.gov (United States)

    Keene, Melissa; Roston, Alicia; Keith, Louis; Patel, Ashlesha

    2015-05-01

    The objective was to compare contraceptive method selection in women undergoing their first pregnancy termination versus women undergoing repeat pregnancy termination in an urban abortion clinic. We hypothesized that women undergoing repeat abortions will select highly effective contraceptives (intrauterine device, subdermal implant, tubal ligation) more often than patients undergoing their first abortion. We conducted a retrospective analysis of all women undergoing first-trimester surgical abortion at John H. Stroger, Jr., Hospital of Cook County from October 1, 2009, to October 31, 2011. We compared contraceptive method selection in the postabortion period after receipt of contraceptive counseling for 7466 women, stratifying women by history of no prior abortion versus one or more abortions. Of the 7466 women, 48.6% (3625) had no history of previous abortion. After controlling for age, race and number of living children, women with a history of abortion were more likely to select a highly effective method [odds ratio (OR) 1.19, 95% confidence interval (CI) 1.06-1.33]. Most significantly, having living children was the strongest predictor of a highly effective method with an OR of 3.17 (95% CI 2.69-3.75). In women having a first-trimester abortion, the factors most predictive of selecting a highly effective method for postabortion contraception include history of previous abortion and having living children. The latter holds true independent of abortion history. This paper is unique in its ability to demonstrate the high interest in highly effective contraceptive selection in high-risk, low-income women with prior abortion history. Efforts to integrate provision of highly effective methods of contraception for postabortion care are essential for the reduction of future unintended pregnancies. Copyright © 2015 Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

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

    2017-07-01

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

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

    Science.gov (United States)

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

    2014-01-01

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

  8. Site Characterization Work Plan for Gasbuggy, New Mexico

    Energy Technology Data Exchange (ETDEWEB)

    DOE/NV

    2000-12-14

    Project Gasbuggy was the first of three joint government-industry experiments conducted to test the effectiveness of nuclear explosives to fracture deeply buried, low-permeability natural gas reservoirs to stimulate production. The scope of this work plan is to document the environmental objectives and the proposed technical site investigation strategies that will be utilized for the site characterization of the Project Gasbuggy Site. Its goal is the collection of data in sufficient quantity and quality to determine current site conditions, support a risk assessment for the site surfaces, and evaluate if further remedial action is required to achieve permanent closure of the site that is both protective of human health and the environment. The Gasbuggy Site is located approximately 55 air miles east of Farmington, New Mexico, in Rio Arriba County within the Carson National Forest in the northeast portion of the San Juan Basin. Historically, Project Gasbuggy consisted of the joint government-industry detonation of a nuclear device on December 10, 1967, followed by reentry drilling and gas production testing and project evaluation activities in post-detonation operations from 1967 to 1976. Based on historical documentation, no chemical release sites other than the mud pits were identified; additionally, there was no material buried at the Gasbuggy Site other than drilling fluids and construction debris. Although previous characterization and restoration activities including sensitive species surveys, cultural resources surveys, surface geophysical surveys, and limited soil sampling and analysis were performed in 1978 and again in 2000, no formal closure of the site was achieved. Also, these efforts did not adequately address the site's potential for chemical contamination at the surface/shallow subsurface ground levels or the subsurface hazards for potential migration outside of the current site subsurface intrusion restrictions. Additional investigation

  9. Modelling multi-site transmission of the human papillomavirus and its impact on vaccination effectiveness.

    Science.gov (United States)

    Lemieux-Mellouki, P; Drolet, M; Jit, M; Gingras, G; Brisson, M

    2017-12-01

    Previous HPV models have only included genital transmission, when evidence suggests that transmission between several anatomical sites occurs. We compared model predictions of population-level HPV vaccination effectiveness against genital HPV16 infection in women, using a 1) uni-site (genital site), and a 2) multi-site model (genital and one extragenital site). We developed a uni-site and a multi-site deterministic HPV transmission model, assuming natural immunity was either site-specific or systemic. Both models were calibrated to genital HPV16 prevalence (5%-7.5%), whilst the multi-site model was calibrated to HPV16 prevalence representative of oral (0%-1%) and anal (1%-7.5%) sites. For each model, we identified 2500 parameter sets that fit endemic genital and extragenital prevalences within pre-specified target ranges. In the Base-case analysis, vaccination was girls-only with 40% coverage. Vaccine efficacy was 100% for all sites with lifetime protection. The outcome was the relative reduction in genital HPV16 prevalence among women at post-vaccination equilibrium (RRprev). RRprev was stratified by extragenital prevalence pre-vaccination. Under assumptions of site-specific immunity, RRprev with the multi-site model was generally greater than with the uni-site model. Differences between the uni-site and multi-site models were greater when transmission from the extragenital site to the genital site was high. Under assumptions of systemic immunity, the multi-site and uni-site models yielded similar RRprev in the scenario without immunity after extragenital infection. In the scenario with systemic immunity after extragenital infection, the multi-site model yielded lower predictions of RRprev than the uni-site model. Modelling genital-site only transmission may overestimate vaccination impact if extragenital infections contribute to systemic natural immunity or underestimate vaccination impact if a high proportion of genital infections originate from extragenital

  10. Site Characterization Progress Report No.20

    Energy Technology Data Exchange (ETDEWEB)

    DOE

    1999-10-01

    This is the 20th progress report issued by the U.S. Department of Energy. This report provides a summary-level discussion of Yucca Mountain Site Characterization Project progress. Accomplishments this period are presented in a format that identifies important progress achieved and conveys how that progress supports the near-term objectives in the U.S. Department of Energy's schedule. Greater detail is documented in the cited references and in deliverables listed in Appendix A to this report. Readers may request specific U.S. Department of Energy-approved program documents that are listed in Section 7, References, and Appendix A by contacting the Office of Civilian Radioactive Waste Management Information Line at 1-800-225-6972. This document provides a discussion of recently completed and ongoing activities conducted by the Yucca Mountain Site Characterization Project during the six-month reporting period from October 1, 1998, through March 31, 1999. Some information presented herein is by necessity preliminary, because some deliverables and reports that support the discussions have not been finalized. Projected future deliverables and reports are listed in Appendix B and are noted in the text as works in progress. Appendix C lists the status of milestone reports referenced in previous progress reports. A glossary of Yucca Mountain Site Characterization Project-specific terms used in this report is given in Appendix D.

  11. Identifying Knowledge and Communication

    Directory of Open Access Journals (Sweden)

    Eduardo Coutinho Lourenço de Lima

    2006-12-01

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

  12. TWRS Privatization Phase 1 Master Site Plan

    International Nuclear Information System (INIS)

    PARAZIN, R.J.

    1999-01-01

    The U.S. Department of Energy (DOE) has chosen to accomplish the Tank Waste Remediation System disposal mission via privatization. The disposal mission has been divided into two privatization phases. Phase I, a 'proof of concept' phase, will establish and demonstrate the technical, commercial, and procurement capabilities necessary far privatization to proceed. Once established, privatization will be expanded in the form of a second phase (Phase II) to dispose of the remainder of the tank waste. In conjunction with preparation of the Tank Waste Remediation System (TWRS) Privatization Request for Proposals (RFP)(RL, 1996), a location was selected for the Phase I demonstration facilities (Shord, 1996). The location selected was the area previously developed and characterized for the Grout Disposal Site, adjoining the 200 East Area. The site is of sufficient size for a Private Contractor (PC) to carry out pretreatment, immobilization, and vitrification operations and possesses the required characteristics (e.g., close to feed tanks) to best facilitate the Phase I operations. This overall long-range Master Site Plan (MSP) has been developed to establish a ''baseline'' for the (TWRS) Privatization Phase I (TPPI) PC Site. The MSP depicts the planned layout for the PC Site along with various interfaces between the site and other Hanford utilities and functions. The complete integration of TPPl MSP with overall Hanford Site planning process will assist in establishing the PC site and the necessary priorities to meet the Hanford cleanup mission. The MSP has been developed systematically into a comprehensive, safe, flexible, logical and cost-effective plan. The general philosophy behind the preparation of a MSP for the TPPl program is that it will serve as a single source documentation of the planning for the development of the TPPl complex. The effort will plan temporary and permanent land use, utilities, and traffic flow for the overall program. It will identify needs

  13. 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

  14. Environmental assessment: Davis Canyon site, Utah

    International Nuclear Information System (INIS)

    1986-05-01

    In February 1983, the US Department of Energy (DOE) identified the Davis Canyon site in Utah as one of the nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high- level radioactive waste. To determine their suitability, the Davis Canyon site and the eight other potentially acceptable sites have been evaluated in accordance with the DOE's General Guidelines for the Recommendation of Sites for the Nuclear Waste Repositories. These evaluations were reported in draft environmental assessments (EAs), which were issued for public review and comment. After considering the comments received on the draft EAs, the DOE prepared the final EA. The Davis Canyon site is in the Paradox Basin, which is one of five distinct geohydrologic settings considered for the first repository. This setting contains one other potentially acceptable site -- the Lavender Canyon site. Although the Lavender Canyon site is suitable for site characterization, the DOE has concluded that the Davis Canyon site is the preferred site in the Paradox Basin. On the basis of the evaluations reported in this EA, the DOE has found that the Davis Canyon site is not disqualified under the guidelines. Furthermore, the DOE has found that the site is suitable for site characterization because the evidence does not support a conclusion that the site will not be able to meet each of the qualifying conditions specified in the guidelines. On the basis of these findings, the DOE is nominating the Davis Canyon site as one of the five sites suitable for characterization

  15. Environmental assessment: Davis Canyon site, Utah

    Energy Technology Data Exchange (ETDEWEB)

    none,

    1986-05-01

    In February 1983, the US Department of Energy (DOE) identified the Davis Canyon site in Utah as one of the nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high- level radioactive waste. To determine their suitability, the Davis Canyon site and the eight other potentially acceptable sites have been evaluated in accordance with the DOE's General Guidelines for the Recommendation of Sites for the Nuclear Waste Repositories. These evaluations were reported in draft environmental assessments (EAs), which were issued for public review and comment. After considering the comments received on the draft EAs, the DOE prepared the final EA. The Davis Canyon site is in the Paradox Basin, which is one of five distinct geohydrologic settings considered for the first repository. This setting contains one other potentially acceptable site -- the Lavender Canyon site. Although the Lavender Canyon site is suitable for site characterization, the DOE has concluded that the Davis Canyon site is the preferred site in the Paradox Basin. On the basis of the evaluations reported in this EA, the DOE has found that the Davis Canyon site is not disqualified under the guidelines. Furthermore, the DOE has found that the site is suitable for site characterization because the evidence does not support a conclusion that the site will not be able to meet each of the qualifying conditions specified in the guidelines. On the basis of these findings, the DOE is nominating the Davis Canyon site as one of the five sites suitable for characterization.

  16. Environmental assessment: Davis Canyon site, Utah

    International Nuclear Information System (INIS)

    1986-05-01

    In February 1983, the US Department of Energy (DOE) identified the Davis Canyon site in Utah as one of the nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high-level radioactive waste. To determine their suitability, the Davis Canyon site and the eight other potentially acceptable sites have been evaluated in accordance with the DOE's General Guidelines for the Recommendation of Sites for the Nuclear Waste Repositories. These evaluations were reported in draft environmental assessments (EAs), which were issued for public review and comment. After considering the comments received on the draft EAs, the DOE prepared the final EA. The Davis Canyon site is in the Paradox Basin, which is one of five distinct geohydrologic settings considering for the first repository. This setting contains one other potentially acceptable site -- the Lavender Canyon site. Although the Lavender Canyon site is suitable for site characterization, the DOE has concluded that the Davis Canyon site is the preferred site in the Paradox Basin. On the basis of the evaluations reported in this EA, the DOE has found that the Davis Canyon site is not disqualified under the guidelines. Furthermore, the DOE has found that the site is suitable for site characterization because the evidence does not support a conclusion that the site will not be able to meet each of the qualifying conditions specified in the guidelines. On the basis of these findings, the DOE is nominating the Davis Canyon site as one of five sites suitable for characterization

  17. Environmental assessment: Davis Canyon site, Utah

    Energy Technology Data Exchange (ETDEWEB)

    none,

    1986-05-01

    In February 1983, the US Department of Energy (DOE) identified the Davis Canyon site in Utah as one of the nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high-level radioactive waste. To determine their suitability, the Davis Canyon site and the eight other potentially acceptable sites have been evaluated in accordance with the DOE's General Guidelines for the Recommendation of Sites for the Nuclear Waste Repositories. These evaluations were reported in draft environmental assessments (EAs), which were issued for public review and comment. After considering the comments received on the draft EAs, the DOE prepared the final EA. The Davis Canyon site is in the Paradox Basin, which is one of five distinct geohydrologic settings considering for the first repository. This setting contains one other potentially acceptable site -- the Lavender Canyon site. Although the Lavender Canyon site is suitable for site characterization, the DOE has concluded that the Davis Canyon site is the preferred site in the Paradox Basin. On the basis of the evaluations reported in this EA, the DOE has found that the Davis Canyon site is not disqualified under the guidelines. Furthermore, the DOE has found that the site is suitable for site characterization because the evidence does not support a conclusion that the site will not be able to meet each of the qualifying conditions specified in the guidelines. On the basis of these findings, the DOE is nominating the Davis Canyon site as one of five sites suitable for characterization.

  18. Identifying learning styles.

    Science.gov (United States)

    Hughes, Grace

    2016-12-14

    What was the nature of the CPD activity, practice-related feedback and/or event and/or experience in your practice? The article explored different learning styles and outlined some of the models that can be used to identify them. It discussed the limitations of these models, indicating that although they can be helpful in identifying a student's preferred learning style, this is not 'fixed' and might change over time. Learning is also influenced by other factors, such as culture and age.

  19. 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

  20. 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

  1. 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.

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

    Science.gov (United States)

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

    2013-10-01

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

  3. Do attitudes of families concerned influence features of children who claim to remember previous lives?

    Science.gov (United States)

    Pasricha, Satwant K

    2011-01-01

    Reported cases of nearly 2600 children (subjects) who claim to remember previous lives have been investigated in cultures with and without belief in reincarnation. The authenticity in most cases has been established. To study the influence of attitudes of parents of the subjects, families of the deceased person with whom they are identified and attention paid by others on the features of the cases. The study is based on field investigations. Data is derived from analysis of a larger series of an ongoing project. Information on initial and subsequent attitudes of subjects' mothers was available for 292 and 136 cases, respectively; attitudes of 227 families of deceased person (previous personality) with whom he is identified, and the extent of attention received from outsiders for 252 cases. Observations and interviews with multiple firsthand informants on both sides of the case as well as some neutral informants supplemented by examination of objective data were the chief methods of investigation. The initial attitude of mothers varied from encouragement (21%) to neutral or tolerance (51%) to discouragement (28%). However, it changed significantly from neutrality to taking measures to induce amnesia in their children for previous life memories due to various psychosocial pressures and prevalent beliefs. Families of the previous personalities, once convinced, showed complete acceptance in a majority of cases. Outside attention was received in 58% cases. The positive attitude of parents might facilitate expression of memories but subsequently attitudes of persons concerned do not seem to alter features of the cases.

  4. High prevalence of peripheral arterial disease in patients with previous cerebrovascular or coronary event

    DEFF Research Database (Denmark)

    Mehlsen, Jesper; Wiinberg, Niels; Joergensen, Bjarne S

    2010-01-01

    The presence of peripheral arterial disease (PAD) in patients with other manifestations of cardiovascular disease identifies a population at increased risk of complications both during acute coronary events and on a long-term basis and possibly a population in whom secondary prevention...... of cardiovascular events should be addressed aggressively. The present study was aimed at providing a valid estimate on the prevalence of PAD in patients attending their general practitioner and having previously suffered a cardio- or cerebrovascular event....

  5. 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

  6. spatially identifying vulnerable areas

    African Journals Online (AJOL)

    System (SMDSS) to identify factors that make forest and game reserves vulnerable to rampant human induced ... Commission Act, 1999 (Act 571); and Wildlife Resources (Amendment) (Declaration of Game Reserves). Regulations, 1976 ..... A dynamic simulation model of land-use changes in Sudano-sahelian countries of ...

  7. Identifying and Managing Risk.

    Science.gov (United States)

    Abraham, Janice M.

    1999-01-01

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

  8. Radon anomalies prior to earthquakes (1). Review of previous studies

    International Nuclear Information System (INIS)

    Ishikawa, Tetsuo; Tokonami, Shinji; Yasuoka, Yumi; Shinogi, Masaki; Nagahama, Hiroyuki; Omori, Yasutaka; Kawada, Yusuke

    2008-01-01

    The relationship between radon anomalies and earthquakes has been studied for more than 30 years. However, most of the studies dealt with radon in soil gas or in groundwater. Before the 1995 Hyogoken-Nanbu earthquake, an anomalous increase of atmospheric radon was observed at Kobe Pharmaceutical University. The increase was well fitted with a mathematical model related to earthquake fault dynamics. This paper reports the significance of this observation, reviewing previous studies on radon anomaly before earthquakes. Groundwater/soil radon measurements for earthquake prediction began in 1970's in Japan as well as foreign countries. One of the most famous studies in Japan is groundwater radon anomaly before the 1978 Izu-Oshima-kinkai earthquake. We have recognized the significance of radon in earthquake prediction research, but recently its limitation was also pointed out. Some researchers are looking for a better indicator for precursors; simultaneous measurements of radon and other gases are new trials in recent studies. Contrary to soil/groundwater radon, we have not paid much attention to atmospheric radon before earthquakes. However, it might be possible to detect precursors in atmospheric radon before a large earthquake. In the next issues, we will discuss the details of the anomalous atmospheric radon data observed before the Hyogoken-Nanbu earthquake. (author)

  9. Cerebral Metastasis from a Previously Undiagnosed Appendiceal Adenocarcinoma

    Directory of Open Access Journals (Sweden)

    Antonio Biroli

    2012-01-01

    Full Text Available Brain metastases arise in 10%–40% of all cancer patients. Up to one third of the patients do not have previous cancer history. We report a case of a 67-years-old male patient who presented with confusion, tremor, and apraxia. A brain MRI revealed an isolated right temporal lobe lesion. A thorax-abdomen-pelvis CT scan showed no primary lesion. The patient underwent a craniotomy with gross-total resection. Histopathology revealed an intestinal-type adenocarcinoma. A colonoscopy found no primary lesion, but a PET-CT scan showed elevated FDG uptake in the appendiceal nodule. A right hemicolectomy was performed, and the specimen showed a moderately differentiated mucinous appendiceal adenocarcinoma. Whole brain radiotherapy was administrated. A subsequent thorax-abdomen CT scan revealed multiple lung and hepatic metastasis. Seven months later, the patient died of disease progression. In cases of undiagnosed primary lesions, patients present in better general condition, but overall survival does not change. Eventual identification of the primary tumor does not affect survival. PET/CT might be a helpful tool in detecting lesions of the appendiceal region. To the best of our knowledge, such a case was never reported in the literature, and an appendiceal malignancy should be suspected in patients with brain metastasis from an undiagnosed primary tumor.

  10. Influence of Previous Knowledge in Torrance Tests of Creative Thinking

    Directory of Open Access Journals (Sweden)

    María Aranguren

    2015-07-01

    Full Text Available The aim of this work is to analyze the influence of study field, expertise and recreational activities participation in Torrance Tests of Creative Thinking (TTCT, 1974 performance. Several hypotheses were postulated to explore the possible effects of previous knowledge in TTCT verbal and TTCT figural university students’ outcomes. Participants in this study included 418 students from five study fields: Psychology;Philosophy and Literature, Music; Engineering; and Journalism and Advertising (Communication Sciences. Results found in this research seem to indicate that there in none influence of the study field, expertise and recreational activities participation in neither of the TTCT tests. Instead, the findings seem to suggest some kind of interaction between certain skills needed to succeed in specific studies fields and performance on creativity tests, such as the TTCT. These results imply that TTCT is a useful and valid instrument to measure creativity and that some cognitive process involved in innovative thinking can be promoted using different intervention programs in schools and universities regardless the students study field.

  11. New Strategies for Cultivation and Detection of Previously Uncultured Microbes

    Science.gov (United States)

    Stevenson, Bradley S.; Eichorst, Stephanie A.; Wertz, John T.; Schmidt, Thomas M.; Breznak, John A.

    2004-01-01

    An integrative approach was used to obtain pure cultures of previously uncultivated members of the divisions Acidobacteria and Verrucomicrobia from agricultural soil and from the guts of wood-feeding termites. Some elements of the cultivation procedure included the following: the use of agar media with little or no added nutrients; relatively long periods of incubation (more than 30 days); protection of cells from exogenous peroxides; and inclusion of humic acids or a humic acid analogue (anthraquinone disulfonate) and quorum-signaling compounds (acyl homoserine lactones) in growth media. The bacteria were incubated in the presence of air and in hypoxic (1 to 2% O2 [vol/vol]) and anoxic atmospheres. Some bacteria were incubated with elevated concentrations of CO2 (5% [vol/vol]). Significantly more Acidobacteria were found on isolation plates that had been incubated with 5% CO2. A simple, high-throughput, PCR-based surveillance method (plate wash PCR) was developed. This method greatly facilitated detection and ultimate isolation of target bacteria from as many as 1,000 colonies of nontarget microbes growing on the same agar plates. Results illustrate the power of integrating culture methods with molecular techniques to isolate bacteria from phylogenetic groups underrepresented in culture. PMID:15294811

  12. Measles Outbreak among Previously Immunized Adult Healthcare Workers, China, 2015

    Directory of Open Access Journals (Sweden)

    Zhengyi Zhang

    2016-01-01

    Full Text Available Measles is caused by measles virus belonging to genus Morbillivirus of the family Paramyxoviridae. Vaccination has played a critical role in controlling measles infection worldwide. However, in the recent years, outbreaks of measles infection still occur in many developing countries. Here, we report an outbreak of measles among healthcare workers and among the 60 measles infected patients 50 were healthcare workers including doctors, nurses, staff, and medics. Fifty-one patients (85% tested positive for IgM antibodies against the measles virus and 50 patients (83.3% tested positive for measles virus RNA. Surprisingly, 73.3% of the infected individuals had been previously immunized against measles. Since there is no infection division in our hospital, the fever clinics are located in the Emergency Division. In addition, the fever and rash were not recognized as measles symptoms at the beginning of the outbreak. These factors result in delay in isolation and early confirmation of the suspected patients and eventually a measles outbreak in the hospital. Our report highlights the importance of following a two-dose measles vaccine program in people including the healthcare workers. In addition, vigilant attention should be paid to medical staff with clinical fever and rash symptoms to avoid a possible nosocomial transmission of measles infection.

  13. Multispecies Coevolution Particle Swarm Optimization Based on Previous Search History

    Directory of Open Access Journals (Sweden)

    Danping Wang

    2017-01-01

    Full Text Available A hybrid coevolution particle swarm optimization algorithm with dynamic multispecies strategy based on K-means clustering and nonrevisit strategy based on Binary Space Partitioning fitness tree (called MCPSO-PSH is proposed. Previous search history memorized into the Binary Space Partitioning fitness tree can effectively restrain the individuals’ revisit phenomenon. The whole population is partitioned into several subspecies and cooperative coevolution is realized by an information communication mechanism between subspecies, which can enhance the global search ability of particles and avoid premature convergence to local optimum. To demonstrate the power of the method, comparisons between the proposed algorithm and state-of-the-art algorithms are grouped into two categories: 10 basic benchmark functions (10-dimensional and 30-dimensional, 10 CEC2005 benchmark functions (30-dimensional, and a real-world problem (multilevel image segmentation problems. Experimental results show that MCPSO-PSH displays a competitive performance compared to the other swarm-based or evolutionary algorithms in terms of solution accuracy and statistical tests.

  14. Coronary collateral vessels in patients with previous myocardial infarction

    International Nuclear Information System (INIS)

    Nakatsuka, M.; Matsuda, Y.; Ozaki, M.

    1987-01-01

    To assess the degree of collateral vessels after myocardial infarction, coronary angiograms, left ventriculograms, and exercise thallium-201 myocardial scintigrams of 36 patients with previous myocardial infarction were reviewed. All 36 patients had total occlusion of infarct-related coronary artery and no more than 70% stenosis in other coronary arteries. In 19 of 36 patients with transient reduction of thallium-201 uptake in the infarcted area during exercise (Group A), good collaterals were observed in 10 patients, intermediate collaterals in 7 patients, and poor collaterals in 2 patients. In 17 of 36 patients without transient reduction of thallium-201 uptake in the infarcted area during exercise (Group B), good collaterals were seen in 2 patients, intermediate collaterals in 7 patients, and poor collaterals in 8 patients (p less than 0.025). Left ventricular contractions in the infarcted area were normal or hypokinetic in 10 patients and akinetic or dyskinetic in 9 patients in Group A. In Group B, 1 patient had hypokinetic contraction and 16 patients had akinetic or dyskinetic contraction (p less than 0.005). Thus, patients with transient reduction of thallium-201 uptake in the infarcted area during exercise had well developed collaterals and preserved left ventricular contraction, compared to those in patients without transient reduction of thallium-201 uptake in the infarcted area during exercise. These results suggest that the presence of viable myocardium in the infarcted area might be related to the degree of collateral vessels

  15. Motivational activities based on previous knowledge of students

    Science.gov (United States)

    García, J. A.; Gómez-Robledo, L.; Huertas, R.; Perales, F. J.

    2014-07-01

    Academic results depend strongly on the individual circumstances of students: background, motivation and aptitude. We think that academic activities conducted to increase motivation must be tuned to the special situation of the students. Main goal of this work is analyze the students in the first year of the Degree in Optics and Optometry in the University of Granada and the suitability of an activity designed for those students. Initial data were obtained from a survey inquiring about the reasons to choose this degree, their knowledge of it, and previous academic backgrounds. Results show that: 1) the group is quite heterogeneous, since students have very different background. 2) Reasons to choose the Degree in Optics and Optometry are also very different, and in many cases were selected as a second option. 3) Knowledge and motivations about the Degree are in general quite low. Trying to increase the motivation of the students we designed an academic activity in which we show different topics studied in the Degree. Results show that students that have been involved in this activity are the most motivated and most satisfied with their election of the degree.

  16. Pertussis-associated persistent cough in previously vaccinated children.

    Science.gov (United States)

    Principi, Nicola; Litt, David; Terranova, Leonardo; Picca, Marina; Malvaso, Concetta; Vitale, Cettina; Fry, Norman K; Esposito, Susanna

    2017-11-01

    To evaluate the role of Bordetella pertussis infection, 96 otherwise healthy 7- to 17-year-old subjects who were suffering from a cough lasting from 2 to 8 weeks were prospectively recruited. At enrolment, a nasopharyngeal swab and an oral fluid sample were obtained to search for pertussis infection by the detection of B. pertussis DNA and/or an elevated titre of anti-pertussis toxin IgG. Evidence of pertussis infection was found in 18 (18.7 %; 95 % confidence interval, 11.5-28.0) cases. In 15 cases, the disease occurred despite booster administration. In two cases, pertussis was diagnosed less than 2 years after the booster injection, whereas in the other cases it was diagnosed between 2 and 9 years after the booster dose. This study used non-invasive testing to show that pertussis is one of the most important causes of long-lasting cough in school-age subjects. Moreover, the protection offered by acellular pertussis vaccines currently wanes more rapidly than previously thought.

  17. Optimal temperature for malaria transmission is dramaticallylower than previously predicted

    Science.gov (United States)

    Mordecai, Eerin A.; Paaijmans, Krijin P.; Johnson, Leah R.; Balzer, Christian; Ben-Horin, Tal; de Moor, Emily; McNally, Amy; Pawar, Samraat; Ryan, Sadie J.; Smith, Thomas C.; Lafferty, Kevin D.

    2013-01-01

    The ecology of mosquito vectors and malaria parasites affect the incidence, seasonal transmission and geographical range of malaria. Most malaria models to date assume constant or linear responses of mosquito and parasite life-history traits to temperature, predicting optimal transmission at 31 °C. These models are at odds with field observations of transmission dating back nearly a century. We build a model with more realistic ecological assumptions about the thermal physiology of insects. Our model, which includes empirically derived nonlinear thermal responses, predicts optimal malaria transmission at 25 °C (6 °C lower than previous models). Moreover, the model predicts that transmission decreases dramatically at temperatures > 28 °C, altering predictions about how climate change will affect malaria. A large data set on malaria transmission risk in Africa validates both the 25 °C optimum and the decline above 28 °C. Using these more accurate nonlinear thermal-response models will aid in understanding the effects of current and future temperature regimes on disease transmission.

  18. 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

  19. 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...

  20. Is previous hyperthyroidism associated with long-term cognitive dysfunction?

    DEFF Research Database (Denmark)

    Lillevang-Johansen, Mads; Petersen, Inge; Christensen, Kaare

    2014-01-01

    OBJECTIVE: Hyperthyroidism has been suggested to adversely affect cognitive function. However, this association could also be caused by genetic and environmental factors affecting both the development of hyperthyroidism and cognitive functioning. By investigating twin pairs discordant...... for hyperthyroidism, this potential confounding can be minimized. The aim of the study was to examine if hyperthyroidism is associated with long-term cognitive dysfunction. DESIGN: Twin case-control study. PATIENTS: Twin pairs discordant for hyperthyroidism were identified by record-linkage between The Danish...... National Patient Registry and 3036 twin pairs from The Danish Twin Registry, who had participated in nationwide surveys on health conditions. MEASUREMENTS: Among other investigations, survey participants had carried out cognitive tests including a Mini-Mental State Exam (MMSE) and six separate cognitive...

  1. Effect of Previous Gastrectomy on the Performance of Postoperative Colonoscopy

    Science.gov (United States)

    Kim, Sunghwan; Choi, Jeongmin; Kim, Tae Han; Suh, Yun-Suhk; Im, Jong Pil; Lee, Hyuk-Joon; Kim, Sang Gyun; Jeong, Seung-Yong; Kim, Joo Sung; Yang, Han-Kwang

    2016-01-01

    Purpose The purpose of this study was to determine the effect of a prior gastrectomy on the difficulty of subsequent colonoscopy, and to identify the surgical factors related to difficult colonoscopies. Materials and Methods Patients with a prior gastrectomy who had undergone a colonoscopy between 2011 and 2014 (n=482) were matched (1:6) to patients with no history of gastrectomy (n=2,892). Cecal insertion time, intubation failure, and bowel clearance score were compared between the gastrectomy and control groups, as was a newly generated comprehensive parameter for a difficult/incomplete colonoscopy (cecal intubation failure, cecal insertion time >12.9 minutes, or very poor bowel preparation scale). Surgical factors including surgical approach, extent of gastrectomy, extent of lymph node dissection, and reconstruction type, were analyzed to identify risk factors for colonoscopy performance. Results A history of gastrectomy was associated with prolonged cecal insertion time (8.7±6.4 vs. 9.7±6.5 minutes; P=0.002), an increased intubation failure rate (0.1% vs. 1.9%; P<0.001), and a poor bowel preparation rate (24.7 vs. 29.0; P=0.047). Age and total gastrectomy (vs. partial gastrectomy) were found to be independent risk factors for increased insertion time, which slowly increased throughout the postoperative duration (0.35 min/yr). Total gastrectomy was the only independent risk factor for the comprehensive parameter of difficult/incomplete colonoscopy. Conclusions History of gastrectomy is related to difficult/incomplete colonoscopy performance, especially in cases of total gastrectomy. In any case, it may be that a pre-operative colonoscopy is desirable in selected patients scheduled for gastrectomy; however, it should be performed by an expert endoscopist each time. PMID:27752394

  2. Association between previous splenectomy and gastric dilatation-volvulus in dogs: 453 cases (2004-2009).

    Science.gov (United States)

    Sartor, Angela J; Bentley, Adrienne M; Brown, Dorothy C

    2013-05-15

    To evaluate the association between previous splenectomy and gastric dilatation-volvulus (GDV) in dogs. Multi-institutional retrospective case-control study. Animals-151 dogs treated surgically for GDV and 302 control dogs with no history of GDV. Computerized records of dogs evaluated via exploratory laparotomy or abdominal ultrasonography were searched, and dogs with GDV and dogs without GDV (control dogs) were identified. Two control dogs were matched with respect to age, body weight, sex, neuter status, and breed to each dog with GDV. Data were collected on the presence or absence of the spleen for both dogs with GDV and control dogs. Conditional logistic regression analysis was used to investigate the association of previous splenectomy with GDV. 6 (4%) dogs in the GDV group and 3 (1%) dogs in the control group had a history of previous splenectomy. The odds of GDV in dogs with a history of previous splenectomy in this population of dogs were 5.3 times those of dogs without a history of previous splenectomy (95% confidence interval, 1.1 to 26.8). For the patients in the present study, there was an increased odds of GDV in dogs with a history of splenectomy. Prophylactic gastropexy may be considered in dogs undergoing a splenectomy, particularly if other risk factors for GDV are present.

  3. Contaminated Sites in Iowa

    Data.gov (United States)

    Iowa State University GIS Support and Research Facility — Sites contaminated by hazardous materials or wastes. These sites are those administered by the Contaminated Sites Section of Iowa DNR. Many are sites which are...

  4. Serratia liquefaciens Infection of a Previously Excluded Popliteal Artery Aneurysm

    Directory of Open Access Journals (Sweden)

    A. Coelho

    Full Text Available : Introduction: Popliteal artery aneurysms (PAAs are rare in the general population, but they account for nearly 70% of peripheral arterial aneurysms. There are several possible surgical approaches including exclusion of the aneurysm and bypass grafting, or endoaneurysmorrhaphy and interposition of a prosthetic conduit. The outcomes following the first approach are favorable, but persistent blood flow in the aneurysm sac has been documented in up to one third of patients in the early post-operative setting. Complications from incompletely excluded aneurysms include aneurysm enlargement, local compression symptoms, and sac rupture. Notably infection of a previously excluded and bypassed PAA is rare. This is the third reported case of PAA infection after exclusion and bypass grafting and the first due to Serratia liquefaciens. Methods: Relevant medical data were collected from the hospital database. Results: This case report describes a 54 year old male patient, diagnosed with acute limb ischaemia due to a thrombosed PAA, submitted to emergency surgery with exclusion and venous bypass. A below the knee amputation was necessary 3 months later. Patient follow-up was lost until 7 years following surgical repair, when he was diagnosed with aneurysm sac infection with skin fistulisation. He had recently been diagnosed with alcoholic hepatic cirrhosis Child–Pugh Class B. The patient was successfully treated by aneurysm resection, soft tissue debridement and systemic antibiotics. Conclusion: PAA infection is a rare complication after exclusion and bypass procedures but should be considered in any patient with evidence of local or systemic infection. When a PAA infection is diagnosed, aneurysmectomy, local debridement, and intravenous antibiotic therapy are recommended. The “gold standard” method of PAA repair remains controversial. PAA excision or endoaneurysmorrhaphy avoids complications from incompletely excluded aneurysms, but is associated with

  5. Sacrococcygeal pilonidal disease: analysis of previously proposed risk factors

    Directory of Open Access Journals (Sweden)

    Ali Harlak

    2010-01-01

    Full Text Available PURPOSE: Sacrococcygeal pilonidal disease is a source of one of the most common surgical problems among young adults. While male gender, obesity, occupations requiring sitting, deep natal clefts, excessive body hair, poor body hygiene and excessive sweating are described as the main risk factors for this disease, most of these need to be verified with a clinical trial. The present study aimed to evaluate the value and effect of these factors on pilonidal disease. METHOD: Previously proposed main risk factors were evaluated in a prospective case control study that included 587 patients with pilonidal disease and 2,780 healthy control patients. RESULTS: Stiffness of body hair, number of baths and time spent seated per day were the three most predictive risk factors. Adjusted odds ratios were 9.23, 6.33 and 4.03, respectively (p<0.001. With an adjusted odds ratio of 1.3 (p<.001, body mass index was another risk factor. Family history was not statistically different between the groups and there was no specific occupation associated with the disease. CONCLUSIONS: Hairy people who sit down for more than six hours a day and those who take a bath two or less times per week are at a 219-fold increased risk for sacrococcygeal pilonidal disease than those without these risk factors. For people with a great deal of hair, there is a greater need for them to clean their intergluteal sulcus. People who engage in work that requires sitting in a seat for long periods of time should choose more comfortable seats and should also try to stand whenever possible.

  6. Gastrointestinal tolerability with ibandronate after previous weekly bisphosphonate treatment

    Directory of Open Access Journals (Sweden)

    Richard Derman

    2009-09-01

    Full Text Available Richard Derman1, Joseph D Kohles2, Ann Babbitt31Department of Obstetrics and Gynecology, Christiana Hospital, Newark, DE, USA; 2Roche, Nutley, NJ, USA; 3Greater Portland Bone and Joint Specialists, Portland, ME, USAAbstract: Data from two open-label trials (PRIOR and CURRENT of women with postmenopausal osteoporosis or osteopenia were evaluated to assess whether monthly oral and quarterly intravenous (IV ibandronate dosing improved self-reported gastrointestinal (GI tolerability for patients who had previously experienced GI irritation with bisphosphonate (BP use. In PRIOR, women who had discontinued daily or weekly BP treatment due to GI intolerance received monthly oral or quarterly IV ibandronate for 12 months. The CURRENT subanalysis included women receiving weekly BP treatment who switched to monthly oral ibandronate for six months. GI symptom severity and frequency were assessed using the Osteoporosis Patient Satisfaction Questionnaire™. In PRIOR, mean GI tolerability scores increased significantly at month 1 from screening for both treatment groups (oral: 79.3 versus 54.1; IV: 84.4 versus 51.0; p < 0.001 for both. Most patients reported improvement in GI symptom severity and frequency from baseline at all post-screening assessments (>90% at Month 10. In the CURRENT subanalysis >60% of patients reported improvements in heartburn or acid reflux and >70% indicated improvement in other stomach upset at month 6. Postmenopausal women with GI irritability with daily or weekly BPs experienced improvement in symptoms with extended dosing monthly or quarterly ibandronate compared with baseline.Keywords: ibandronate, osteoporosis, bisphosphonate, gastrointestinal

  7. Analysis of the Fracture Zones and Structural Lineament Using Multi-offset VSP in the KURT Site

    International Nuclear Information System (INIS)

    Kim, Kyung Su; Koh, Yong Kwon; Bae, Dae Seok; Kim, Geon Young; Park, Kyung Woo; Ji, Sung Hoon; Ryu, Ji Hun

    2009-08-01

    We identified the geologic structure and fracture zones using multi-offset VSP at DB-1 in KURT site. The fracture zones at 154 m and 220 m depth in DB-1 were confirmed and the fracture zone near 780 m was expected. The deep-angle fracture found in previous survey also checked

  8. 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 illumi...

  9. Global Microbial Identifier

    DEFF Research Database (Denmark)

    Wielinga, Peter; Hendriksen, Rene S.; Aarestrup, Frank Møller

    2017-01-01

    -source systems. There is therefore an obvious need to develop a global system of whole microbial genome databases to aggregate, share, mine and use microbiological genomic data, to address global public health and clinical challenges, and most importantly to identify and diagnose infectious diseases. The global...... of microorganisms, for the identification of relevant genes and for the comparison of genomes to detect outbreaks and emerging pathogens. To harness the full potential of WGS, a shared global database of genomes linked to relevant metadata and the necessary software tools needs to be generated, hence the global...... microbial identifier (GMI) initiative. This tool will ideally be used in amongst others in the diagnosis of infectious diseases in humans and animals, in the identification of microorganisms in food and environment, and to track and trace microbial agents in all arenas globally. This will require...

  10. 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.

  11. Identifying anterior segment crystals.

    OpenAIRE

    Hurley, I W; Brooks, A M; Reinehr, D P; Grant, G B; Gillies, W E

    1991-01-01

    A series of 22 patients with crystals in the anterior segment of the eye was examined by specular microscopy. Of 10 patients with hypermature cataract and hyperrefringent bodies in the anterior chamber cholesterol crystals were identified in four patients and in six of the 10 in whom aspirate was obtained cholesterol crystals were demonstrated in three, two of these having shown crystals on specular microscopy. In 10 patients with intracorneal crystalline deposits, cholesterol crystals were f...

  12. Encrypting personal identifiers.

    OpenAIRE

    Meux, E

    1994-01-01

    STUDY SETTING. A statewide patient discharge database contained only one unique identifier: the social security number (SSN). A method was developed to transform (encrypt) the SSN so that it could be made publicly available, for purposes of linking discharge records, without revealing the SSN itself. The method of encrypting the SSN into a Record Linkage Number (RLN) is described. PRINCIPAL FINDINGS. The same RLN will always result from the same SSN; it is highly improbable that the same RLN ...

  13. [German language physician rating sites].

    Science.gov (United States)

    Strech, D; Reimann, S

    2012-08-01

    In physician rating sites (PRS), patients are able to share their experiences and indicate their satisfaction in qualitative and quantitative form. This information should support other patients in the search for a suitable physician and can serve as a form of anonymous feedback for physicians. Medical association representatives are often concerned that such reviews primarily aim at defamation. Furthermore, there are various aspects of medical work that cannot be adequately evaluated solely through the patients. In the United States of America, the majority of such previous reviews were shown to be positive. It has yet to be examined in the German and English speaking regions where distinct criteria presently allow patients to express their satisfaction through PRS. Based on the systematic review of patient satisfaction questionnaires, a set of criteria was created that represents the dimensions of patient satisfaction. German and English language physician rating sites were systematically researched using the Internet search machines "Google" and "Yahoo". The identified PRS were then evaluated with the help of the aforementioned set of criteria. In order to survey the tendency of the amount and content of reviews, a stratified sample of members of the Panel Doctor's Association in Hamburg and Thuringia was generated. A total of 298 randomly selected physicians were searched for in 6 German-language PRS regarding potential reviews. Some of the key features of the relation-ship between physicians and patients, such as medical competence, information, and consultation, were surveyed by more than three-fourths of the German-speaking PRS; however, other features such as communication were only sampled by one. As opposed to formal points of view, office facilities and organisation were assessed by all PRS. General reviews on treatment success and satisfaction were displayed in more than half of the reviews. Between 75% and 98% of physicians from the random sampling

  14. Splice site mutations in the ATP7A gene.

    Directory of Open Access Journals (Sweden)

    Tina Skjørringe

    Full Text Available 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 identified in 12 patients with milder phenotypes were predicted to have no significant effect on splicing, which concurs with the presence of wild-type transcript in 7 out of 9 patients investigated in vivo. Both the in silico predictions and the in vivo results support the hypothesis previously suggested by us and others, that the presence of some wild-type transcript is correlated to a milder phenotype.

  15. 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

  16. Tubal anastomosis after previous sterilization: a systematic review.

    Science.gov (United States)

    van Seeters, Jacoba A H; Chua, Su Jen; Mol, Ben W J; Koks, Carolien A M

    2017-05-01

    Female sterilization is one of the most common contraceptive methods. A small number of women, however, opt for reversal of sterilization procedures after they experience regret. Procedures can be performed by laparotomy or laparoscopy, with or without robotic assistance. Another commonly utilized alternative is IVF. The choice between surgery and IVF is often influenced by reimbursement politics for that particular geographic location. We evaluated the fertility outcomes of different surgical methods available for the reversal of female sterilization, compared these to IVF and assessed the prognostic factors for success. Two search strategies were employed. Firstly, we searched for randomized and non-randomized clinical studies presenting fertility outcomes of sterilization reversal up to July 2016. Data on the following outcomes were collected: pregnancy rate, ectopic pregnancy rate, cost of the procedure and operative time. Eligible study designs included prospective or retrospective studies, randomized controlled trials, cohort studies, case-control studies and case series. No age restriction was applied. Exclusion criteria were patients suffering from tubal infertility from any other reason (e.g. infection, endometriosis and adhesions from previous surgery) and studies including sterilization reversal procedures were then evaluated: female age, BMI and duration and method of sterilization. Secondly, we searched for randomized and non-randomized clinical studies that compared reversal of sterilization to IVF and evaluated them for pregnancy outcomes and cost effectiveness. We included 37 studies that investigated a total of 10 689 women. No randomized controlled trials were found. Most studies were retrospective cohort studies of a moderate quality. The pooled pregnancy rate after sterilization reversal was 42-69%, with heterogeneity seen from the different methods utilized. The reported ectopic pregnancy rate was 4-8%. The only prognostic factor affecting the

  17. 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.

  18. Understanding intercellular communication in the brain: Identified ...

    Indian Academy of Sciences (India)

    Understanding intercellular communication in the brain: Identified neuromuscular synapses of the fruitfly. Drosophila serve as a model. The transmission of information between nerve cells in the brain takes place at specialized sites of contact, the synapses. Spatial interactions between synapses and temporal modulation of ...

  19. Identifying particular places through experimental walking

    Directory of Open Access Journals (Sweden)

    Henrik Schultz

    2016-11-01

    Full Text Available Experimental walking can be used to identify particular places, design strategies and spatial visions for urban landscapes. Walking designers can explore sites and, in particular, their temporal dynamics and atmospheric particularities – both essential elements in making particular places. This article illustrates the benefits of this method, using the changing German city of Freiburg as an example.

  20. On identified predictive control

    Science.gov (United States)

    Bialasiewicz, Jan T.

    1993-01-01

    Self-tuning control algorithms are potential successors to manually tuned PID controllers traditionally used in process control applications. A very attractive design method for self-tuning controllers, which has been developed over recent years, is the long-range predictive control (LRPC). The success of LRPC is due to its effectiveness with plants of unknown order and dead-time which may be simultaneously nonminimum phase and unstable or have multiple lightly damped poles (as in the case of flexible structures or flexible robot arms). LRPC is a receding horizon strategy and can be, in general terms, summarized as follows. Using assumed long-range (or multi-step) cost function the optimal control law is found in terms of unknown parameters of the predictor model of the process, current input-output sequence, and future reference signal sequence. The common approach is to assume that the input-output process model is known or separately identified and then to find the parameters of the predictor model. Once these are known, the optimal control law determines control signal at the current time t which is applied at the process input and the whole procedure is repeated at the next time instant. Most of the recent research in this field is apparently centered around the LRPC formulation developed by Clarke et al., known as generalized predictive control (GPC). GPC uses ARIMAX/CARIMA model of the process in its input-output formulation. In this paper, the GPC formulation is used but the process predictor model is derived from the state space formulation of the ARIMAX model and is directly identified over the receding horizon, i.e., using current input-output sequence. The underlying technique in the design of identified predictive control (IPC) algorithm is the identification algorithm of observer/Kalman filter Markov parameters developed by Juang et al. at NASA Langley Research Center and successfully applied to identification of flexible structures.

  1. Identifying phenomenal consciousness.

    Science.gov (United States)

    Schier, Elizabeth

    2009-03-01

    This paper examines the possibility of finding evidence that phenomenal consciousness is independent of access. The suggestion reviewed is that we should look for isomorphisms between phenomenal and neural activation spaces. It is argued that the fact that phenomenal spaces are mapped via verbal report is no problem for this methodology. The fact that activation and phenomenal space are mapped via different means does not mean that they cannot be identified. The paper finishes by examining how data addressing this theoretical question could be obtained.

  2. Random Cell Identifiers Assignment

    Directory of Open Access Journals (Sweden)

    Robert Bestak

    2012-01-01

    Full Text Available Despite integration of advanced functions that enable Femto Access Points (FAPs to be deployed in a plug-and-play manner, the femtocell concept still cause several opened issues to be resolved. One of them represents an assignment of Physical Cell Identifiers (PCIs to FAPs. This paper analyses a random based assignment algorithm in LTE systems operating in diverse femtocell scenarios. The performance of the algorithm is evaluated by comparing the number of confusions for various femtocell densities, PCI ranges and knowledge of vicinity. Simulation results show that better knowledge of vicinity can significantly reduce the number of confusions events.

  3. 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

  4. Assessment of candidate sites for disposal of treated effluents at the Hanford Site, Washington

    International Nuclear Information System (INIS)

    Davis, J.D.

    1992-01-01

    A rigidly defined evaluation process was used to recommend a preferred location to dispose of treated effluents from facilities in the 200 Areas of the US Department of Energy's Hanford Site in Washington State. First, siting constraints were defined based on functional design considerations and siting guidelines. Then, criteria for selecting a preferred site from among several candidates were identified and their relative importance defined. Finally, the weighted criteria were applied and a site was selected for detailed characterization by subsurface investigations

  5. 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...

  6. 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.

  7. 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).

  8. Participation in physical activity: perceptions of women with a previous history of gestational diabetes mellitus.

    Science.gov (United States)

    Graco, Marnie; Garrard, Jan; Jasper, Andrea E

    2009-04-01

    Women with a history of gestational diabetes mellitus (GDM) have an increased risk of developing type 2 diabetes mellitus (T2DM). Regular physical activity plays an important role in preventing T2DM. This study aimed to explore the perceptions of physical activity among women with previous GDM, in the context of preventing T2DM. Individual semi-structured interviews were conducted with 10 women with previous GDM who had not been diagnosed with T2DM. Data were analysed using a modified grounded theory approach. Women perceived diet to be significantly more important for the prevention of T2DM than physical activity. They underestimated the role of physical activity in preventing diabetes, which may have resulted from the lack of information they received following their pregnancy. Women consistently placed the needs of their families before their own, despite acknowledging their future health risks. The most commonly cited constraints on physical activity participation were lack of time, partner support, and appropriate childcare. They identified a need for 'family-friendly' community-based physical activity programs for mothers, more accessible childcare, and more information about the role of physical activity in diabetes prevention. Awareness of the role of physical activity for the prevention of diabetes was low. Physical activity promotion for women with previous GDM needs to be shaped around the opportunities and constraints identified by this population group.

  9. Identified EM Earthquake Precursors

    Science.gov (United States)

    Jones, Kenneth, II; Saxton, Patrick

    2014-05-01

    recurrence, duration, and frequency response. At the Southern California field sites, one loop antenna was positioned for omni-directional reception and also detected a strong First Schumann Resonance; however, additional Schumann Resonances were absent. At the Timpson, TX field sites, loop antennae were positioned for directional reception, due to earthquake-induced, hydraulic fracturing activity currently conducted by the oil and gas industry. Two strong signals, one moderately strong signal, and approximately 6-8 weaker signals were detected in the immediate vicinity. The three stronger signals were mapped by a biangulation technique, followed by a triangulation technique for confirmation. This was the first antenna mapping technique ever performed for determining possible earthquake epicenters. Six and a half months later, Timpson experienced two M4 (M4.1 and M4.3) earthquakes on September 2, 2013 followed by a M2.4 earthquake three days later, all occurring at a depth of five kilometers. The Timpson earthquake activity now has a cyclical rate and a forecast was given to the proper authorities. As a result, the Southern California and Timpson, TX field results led to an improved design and construction of a third prototype antenna. With a loop antenna array, a viable communication system, and continuous monitoring, a full fracture cycle can be established and observed in real-time. In addition, field data could be reviewed quickly for assessment and lead to a much more improved earthquake forecasting capability. The EM precursors determined by this method appear to surpass all prior precursor claims, and the general public will finally receive long overdue forecasting.

  10. New study reveals twice as many asteroids as previously believed

    Science.gov (United States)

    2002-05-01

    The ISO satellite Credits: ESA ISO An artist's impression of the ISO spacecraft. The ISO Deep Asteroid Search indicates that there are between 1.1 million and 1.9 million 'space rocks' larger than 1 kilometre in diameter in the so-called 'main asteroid belt', about twice as many as previously believed. However, astronomers think it is premature to revise current assessments of the risk of the Earth being hit by an asteroid. Despite being in our own Solar System, asteroids can be more difficult to study than very distant galaxies. With sizes of up to one thousand kilometres in diameter, the brightness of these rocky objects may vary considerably in just a few minutes. They move very quickly with respect to the stars - they have been dubbed 'vermin of the sky' because they often appear as trails on long exposure images. This elusiveness explains why their actual number and size distribution remains uncertain. Most of the almost 40,000 asteroids catalogued so far (1) orbit the Sun forming the 'main asteroid belt', between Mars and Jupiter, too far to pose any threat to Earth. However, space-watchers do keep a closer eye on another category of asteroids, the 'Near Earth Asteroids' or 'NEAs', which are those whose orbits cross, or are likely to cross, that of our planet. The ISO Deep Asteroid Search (IDAS), the first systematic search for these objects performed in infrared light, focused on main belt asteroids. Because it is impossible to simply point the telescope at the whole main belt and count, astronomers choose selected regions of the belt and then use a theoretical model to extrapolate the data to the whole belt. Edward Tedesco (TerraSystems, Inc., New Hampshire, United States) and François-Xavier Desert (Observatoire de Grenoble, France) observed their main belt selected areas in 1996 and 1997 with ESA's ISO. They found that in the middle region of the belt the density of asteroids was 160 asteroids larger than 1 kilometre per square degree - an area of the

  11. Orchidopexy in late childhood often associated with previously normal testicular position.

    Science.gov (United States)

    van der Plas, Evelyn; Zijp, Gerda; Froeling, Frank; de Wilde, Jeroen; van der Voort, Laszla; Hack, Wilfried

    2013-08-01

    The aim of this study was to determine retrospectively, the prevalence of acquired undescended testis (UDT) in boys who underwent late orchidopexies, that is, performed after the age of 2 years. We included all patients who were 2 years or older when they underwent orchidopexy (ORP) for UDT at the Juliana Children's Hospital during 1996 to 2009. Previous testis position from birth until the date of ORP was obtained from youth health care records. We identified 660 boys who underwent ORP after the age of 2 years for undescended testis. For 421 of these 660 boys, the previous testicular position could be retrieved from the health records. In 143 of these 421 boys (34%), the operated testis had never been scrotal (congenital UDT), whereas in the other 278 boys (66%), a previous scrotal position had been documented twice or more (acquired UDT). Our results show that two-thirds of the boys that underwent ORP after the age of 2 had previously normal descended testes. This finding may offer an additional explanation for the discrepancy between the incidence of congenital UDT and the high rate of ORP in mid and late childhood. Georg Thieme Verlag KG Stuttgart · New York.

  12. Environmental assessment overview: Richton Dome site, Mississippi

    Energy Technology Data Exchange (ETDEWEB)

    none,

    1986-05-01

    In February 1983, the US Department of Energy (DOE) identified the Richton Dome site in Mississippi as one of the nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high-level radioactive waste. To determine their suitability, the Richton Dome site and the eight other potentially acceptable sites have been evaluated in accordance with the DOE's General Guidelines for the Recommendation of Sites for the Nuclear Waste Repositories. The site is in the Gulf interior region, which is one of five distinct geohydrologic settings considered for the first repository. On the basis of the evaluations reported in this EA, the DOE has found that the Richton Dome site is not disqualified under the guidelines. On the basis of these findings, the DOE is nominating the Richton Dome site as one of five sites suitable for characterization. 3 figs.

  13. Environmental assessment overview: Richton Dome site, Mississippi

    International Nuclear Information System (INIS)

    1986-05-01

    In February 1983, the US Department of Energy (DOE) identified the Richton Dome site in Mississippi as one of the nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high-level radioactive waste. To determine their suitability, the Richton Dome site and the eight other potentially acceptable sites have been evaluated in accordance with the DOE's General Guidelines for the Recommendation of Sites for the Nuclear Waste Repositories. The site is in the Gulf interior region, which is one of five distinct geohydrologic settings considered for the first repository. On the basis of the evaluations reported in this EA, the DOE has found that the Richton Dome site is not disqualified under the guidelines. On the basis of these findings, the DOE is nominating the Richton Dome site as one of five sites suitable for characterization. 3 figs

  14. Environmental assessment overview, Davis Canyon site, Utah

    International Nuclear Information System (INIS)

    1986-05-01

    In February 1983, the US Department of Energy (DOE) identified the Davis Canyon site in Utah as one of the nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high-level radioactive waste. To determine their suitability, the Davis Canyon site and the eight other potentially acceptable sites have been evaluated in accordance with the DOE's General Guidelines for the Recommendation of Sites for the Nuclear Waste Repositories. The Davis Canyon site is in the Paradox Basin, which is one of five distinct geohydrologic settings considered for the first repository. On the basis of the evaluations reported in this EA, the DOE has found that the Davis Canyon site is not disqualified under the guidelines. On the basis of these findings, the DOE is nominating the Davis Canyon site as one of five sites suitable for characterization. 3 figs

  15. Sudden Cardiac Death in Young Adults With Previous Hospital-Based Psychiatric Inpatient and Outpatient Treatment

    DEFF Research Database (Denmark)

    Risgaard, Bjarke; Waagstein, Kristine; Winkel, Bo Gregers

    2015-01-01

    Introduction: Psychiatric patients have premature mortality compared to the general population. The incidence of sudden cardiac death (SCD) in psychiatric patients is unknown in a nationwide setting. The aim of this study was to compare nationwide SCD incidence rates in young individuals with and......Introduction: Psychiatric patients have premature mortality compared to the general population. The incidence of sudden cardiac death (SCD) in psychiatric patients is unknown in a nationwide setting. The aim of this study was to compare nationwide SCD incidence rates in young individuals...... with and without previous psychiatric disease. Method: Nationwide, retrospective cohort study including all deaths in people aged 18–35 years in 2000–2006 in Denmark. The unique Danish death certificates and autopsy reports were used to identify SCD cases. Psychiatric disease was defined as a previous psychiatric...

  16. Survival after early-stage breast cancer of women previously treated for depression

    DEFF Research Database (Denmark)

    Suppli, Nis Frederik Palm; Johansen, Christoffer; Kessing, Lars Vedel

    2017-01-01

    Purpose The aim of this nationwide, register-based cohort study was to determine whether women treated for depression before primary early-stage breast cancer are at increased risk for receiving treatment that is not in accordance with national guidelines and for poorer survival. Material...... and Methods We identified 45,325 women with early breast cancer diagnosed in Denmark from 1998 to 2011. Of these, 744 women (2%) had had a previous hospital contact (as an inpatient or outpatient) for depression and another 6,068 (13%) had been treated with antidepressants. Associations between previous...... treatment of depression and risk of receiving nonguideline treatment of breast cancer were assessed in multivariable logistic regression analyses. We compared the overall survival, breast cancer-specific survival, and risk of death by suicide of women who were and were not treated for depression before...

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

    DEFF Research Database (Denmark)

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

    2014-01-01

    Study Design. Population based prospective cohort study.Objective. We explored the cross-sectional relationships between lumbar multifidus (LM) intramuscular adipose tissue (IMAT) infiltration and LBP at three successive time points and investigated the role of IMAT in predicting the occurrence....... At each time point, participants underwent magnetic resonance imaging and reported ever having had LBP, LBP in the previous year, non-trivial LBP in the previous year, or a history of pain radiating into the legs. Pixel intensity and frequencies from T1-weighted magnetic resonance images identified...... at age 45 or age 49 and LM IMAT did not predict future LBP.Conclusion. The relationship between LM IMAT and lbp/leg pain is inconsistent and may be modified by age....

  18. Addressing concerns related to geologic hazards at the site of the proposed Transuranic Waste Facility , TA-63, Los Alamos National Laboratory: focus on the current Los Alamos Seismic Network earthquake catalog, proximity of identified seismic events to the proposed facility , and evaluation of prev

    Energy Technology Data Exchange (ETDEWEB)

    Roberts, Peter M. [Los Alamos National Laboratory; Schultz-Fellenz, Emily S. [Los Alamos National Laboratory; Kelley, Richard E. [Los Alamos National Laboratory

    2012-04-02

    This technical paper presents the most recent and updated catalog of earthquakes measured by the Los Alamos Seismic Network at and around Los Alamos National Laboratory (LANL), with specific focus on the site of the proposed transuranic waste facility (TWF) at Technical Area 63 (TA-63). Any questions about the data presented herein, or about the Los Alamos Seismic Network, should be directed to the authors of this technical paper. LANL and the Los Alamos townsite sit atop the Pajarito Plateau, which is bounded on its western edge by the Pajarito fault system, a 35-mile-long system locally comprised of the down-to-the-east Pajarito fault (the master fault) and subsidiary down-to-the-west Rendija Canyon, Guaje Mountain, and Sawyer Canyon faults (Figure 1). This fault system forms the local active western margin of the Rio Grande rift near Los Alamos, and is potentially seismogenic (e.g., Gardner et al., 2001; Reneau et al., 2002; Lewis et al., 2009). The proposed TWF area at TA-63 is situated on an unnamed mesa in the north-central part of LANL between Twomile Canyon to the south, Ten Site Canyon to the north, and the headwaters of Canada del Buey to the east (Figure 2). The local bedrock is the Quaternary Bandelier Tuff, formed in two eruptive pulses from nearby Valles caldera, the eastern edge of which is located approximately 6.5 miles west-northwest of the technical area. The older member (Otowi Member) of the Bandelier Tuff has been dated at 1.61 Ma (Izett and Obradovich 1994). The younger member (Tshirege Member) of the Bandelier Tuff has been dated at 1.256 Ma (age from Phillips et al. 2007) and is widely exposed as the mesa-forming unit around Los Alamos. Several discrete cooling units comprise the Tshirege Member. Commonly accepted stratigraphic nomenclature for the Tshirege Member is described in detail by Broxton and Reneau (1995), Gardner et al. (2001), and Lewis et al. (2009). The Tshirege Member cooling unit exposed at the surface at TA-63 is Qbt3

  19. Integrative Analysis of CRISPR/Cas9 Target Sites in the Human HBB Gene

    Directory of Open Access Journals (Sweden)

    Yumei Luo

    2015-01-01

    Full Text Available Recently, the clustered regularly interspaced short palindromic repeats (CRISPR system has emerged as a powerful customizable artificial nuclease to facilitate precise genetic correction for tissue regeneration and isogenic disease modeling. However, previous studies reported substantial off-target activities of CRISPR system in human cells, and the enormous putative off-target sites are labor-intensive to be validated experimentally, thus motivating bioinformatics methods for rational design of CRISPR system and prediction of its potential off-target effects. Here, we describe an integrative analytical process to identify specific CRISPR target sites in the human β-globin gene (HBB and predict their off-target effects. Our method includes off-target analysis in both coding and noncoding regions, which was neglected by previous studies. It was found that the CRISPR target sites in the introns have fewer off-target sites in the coding regions than those in the exons. Remarkably, target sites containing certain transcriptional factor motif have enriched binding sites of relevant transcriptional factor in their off-target sets. We also found that the intron sites have fewer SNPs, which leads to less variation of CRISPR efficiency in different individuals during clinical applications. Our studies provide a standard analytical procedure to select specific CRISPR targets for genetic correction.

  20. Nucleosome structure incorporated histone acetylation site prediction in Arabidopsis thaliana.

    Science.gov (United States)

    Zhao, Chen; Liu, Hui; Li, Jiang; Deng, Youping; Shi, Tieliu

    2010-11-02

    Acetylation is a crucial post-translational modification for histones, and plays a key role in gene expression regulation. Due to limited data and lack of a clear acetylation consensus sequence, a few researches have focused on prediction of lysine acetylation sites. Several systematic prediction studies have been conducted for human and yeast, but less for Arabidopsis thaliana. Concerning the insufficient observation on acetylation site, we analyzed contributions of the peptide-alignment-based distance definition and 3D structure factors in acetylation prediction. We found that traditional structure contributes little to acetylation site prediction. Identified acetylation sites of histones in Arabidopsis thaliana are conserved and cross predictable with that of human by peptide based methods. However, the predicted specificity is overestimated, because of the existence of non-observed acetylable site. Here, by performing a complete exploration on the factors that affect the acetylability of lysines in histones, we focused on the relative position of lysine at nucleosome level, and defined a new structure feature to promote the performance in predicting the acetylability of all the histone lysines in A. thaliana. We found a new spacial correlated acetylation factor, and defined a ε-N spacial location based feature, which contains five core spacial ellipsoid wired areas. By incorporating the new feature, the performance of predicting the acetylability of all the histone lysines in A. Thaliana was promoted, in which the previous mispredicted acetylable lysines were corrected by comparing to the peptide-based prediction.

  1. 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.

  2. In situ hybridization of bat chromosomes with human (TTAGGGn probe, after previous digestion with Alu I

    Directory of Open Access Journals (Sweden)

    Karina de Cassia Faria

    2002-01-01

    Full Text Available The purpose of this work was to verify the ability of the enzyme Alu I to cleave and/or remove satellite DNA sequences from heterochromatic regions in chromosomes of bats, by identifying the occurrence of modifications in the pattern of fluorescence in situ hybridization with telomeric DNA. The localization and fluorescence intensity of the telomeric DNA sites of the Alu-digested and undigested chromosomes of species Eumops glaucinus, Carollia perspicillata, and Platyrrhinus lineatus were analyzed. Telomeric sequences were detected at the termini of chromosomes of all three species, although, in C. perspicillata, the signals were very faint or absent in most chromosomes. This finding was interpreted as being due to a reduced number of copies of the telomeric repeat, resulting from extensive telomeric association and/or rearrangements undergone by the chromosomes of Carollia. Fluorescent signals were also observed in centromeric and pericentromeric regions in several two-arm chromosomes of E. glaucinus and C. perspicillata. In E. glaucinus and P. lineatus, some interstitial and terminal telomeric sites were observed to be in association with regions of constitutive heterochromatin and ribosomal DNA (NORs. After digestion, these telomeric sites showed a significant decrease in signal intensity, indicating that enzyme Alu I cleaves and/or removes part of the satellite DNA present in these regions. These results suggest that the telomeric sequence is a component of the heterochromatin, and that the C-band- positive regions of bat chromosomes have a different DNA composition.

  3. Radiograph identifying means

    International Nuclear Information System (INIS)

    Sheldon, A.D.

    1983-01-01

    A flexible character-indentable plastics embossing tape is backed by and bonded to a lead strip, not more than 0.025 inches thick, to form a tape suitable for identifying radiographs. The lead strip is itself backed by a relatively thin and flimsy plastics or fabric strip which, when removed, allows the lead plastic tape to be pressure-bonded to the surface to be radiographed. A conventional tape-embossing gun is used to indent the desired characters in succession into the lead-backed tape, without necessarily severing the lead; and then the backing strip is peeled away to expose the layer of adhesive which pressure-bonds the indented tape to the object to be radiographed. X-rays incident on the embossed tape will cause the raised characters to show up dark on the subsequently-developed film, whilst the raised side areas will show up white. Each character will thus stand out on the developed film. (author)

  4. Tricuspid Valve Repair With Artificial Chorda After Previous Ventricular Septal Defect Repair.

    Science.gov (United States)

    Sassa, Toshiharu; Okamoto, Ken; Tazume, Hirokazu; Noguchi, Ryo; Koga, Ayumi; Fukui, Toshihiro

    2017-04-01

    We evaluated a 49-year-old man with severe tricuspid valve regurgitation and coronary artery disease who had undergone congenital ventricular septal defect repair four decades previously. We found an enlarged, prolapsed commissure between the anterior and septal leaflets and a ruptured septal leaflet chorda. Two mattress sutures closed the commissure, with the leaflets' height matched by inverting the prolapsed site ventricularly. After implanting the annuloplasty band, we undertook chordal replacement using expanded polytetrafluoroethylene sutures. Artificial chorda length was determined using a small tourniquet and the saline test. Two coronary artery bypass grafts were also implanted. Postoperative echocardiography demonstrated no tricuspid regurgitation. Copyright © 2017 The Society of Thoracic Surgeons. Published by Elsevier Inc. All rights reserved.

  5. India: From SITE to INSAT.

    Science.gov (United States)

    Chaudhri, M. M.

    1986-01-01

    Identifies core of India's illiteracy problem and describes use of educational technology to educate rural children. Highlights include descriptions of the Satellite Instructional Television Experiment (SITE) project; motivation behind low-cost educational aids development in rural areas; an educational radio pilot project; and development and…

  6. Incidence of cancer in adolescent idiopathic scoliosis patients treated 25 years previously

    DEFF Research Database (Denmark)

    Simony, Ane; Hansen, Emil Jesper; Christensen, Steen Bach

    2016-01-01

    PURPOSE: To report the incidence of cancer in a cohort of adolescent idiopathic scoliosis (AIS) patients treated 25 years previously. METHODS: 215 consecutive AIS patients treated between 1983 and 1990 were identified and requested to return for clinical and radiographic examination. The incidence...... of cancer was determined through chart review and follow-up interviews. Using the original radiographic log file that included patient position, mAs, kV and the total number of X-rays taken, a radiation physicist calculated the total radiation dose during treatment and follow-up adjusted for BMI and sex...

  7. 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.

  8. Laryngeal distribution of recurrent respiratory papillomatosis in a previously untreated cohort.

    Science.gov (United States)

    Benedict, Peter A; Ruiz, Ryan; Yoo, MiJin; Verma, Avanti; Ahmed, Omar H; Wang, Binhuan; Dion, Gregory R; Voigt, Andrew; Merati, Albert; Rosen, Clark A; Amin, Milan R; Branski, Ryan C

    2018-01-01

    To describe the distribution of recurrent respiratory papillomatosis (RRP) lesions across 21 laryngeal anatomic regions in previously untreated patients at initial presentation to provide insight regarding the natural history of RRP. Multi-institutional, retrospective case series. Initial laryngoscopic examination videos of 83 previously untreated patients with adult-onset RRP were reviewed. Papilloma locations were recorded using a 21-region laryngeal schematic. Multivariate analyses by anatomic subsite were conducted for the entire population and for subgroups stratified by sex, age, and proton pump inhibitor (PPI) usage. Heat maps were generated, hierarchically color coding the anatomic distribution of disease. In this cohort, RRP was most likely to occur on the true vocal folds (TVFs) and anterior commissure (P < .0001, odds ratio [OR]: 7.02); within the TVFs, the membranous vocal folds (MVFs) were most likely to be affected (P < .0001, OR: 3.56). The cohort was predominantly male (80.7%); males had a higher average number of affected sites (P = .005) and were more likely to have lesions in any laryngeal subsite (P < .0001, OR: 2.88,) compared to females. PPI users were more likely than nonusers to have disease in any laryngeal subsite (P = .0037, OR: 1.62), particularly in the posterior and subglottic regions (P = .0061, OR: 2.53). Age was not correlated with lesion prevalence or distribution. In untreated patients presenting to three laryngology clinics, the MVFs were most likely to be affected by RRP. Males had more anatomic sites affected by papilloma than females. The influence of PPI use on RRP distribution warrants further investigation. 4. Laryngoscope, 128:138-143, 2018. © 2017 The American Laryngological, Rhinological and Otological Society, Inc.

  9. Urinary tract infections in hospital pediatrics: many previous antibiotherapy and antibiotics resistance, including fluoroquinolones.

    Science.gov (United States)

    Garraffo, A; Marguet, C; Checoury, A; Boyer, S; Gardrat, A; Houivet, E; Caron, F

    2014-02-01

    We studied antibiotic resistance in pediatric UTIs and we evaluated the impact of antibiotic exposure in the previous 12 months, very little French data being available for this population. We conducted a multicenter prospective study including children consulting for, or admitted in 2 hospitals. Prior antibiotic exposure was documented from their health record. One hundred and ten patients (73 girls), 11 days to 12 years of age, were included in 10 months. Ninety-six percent presented with pyelonephritis, associated to uropathy for 25%. Escherichia coli was predominant (78%), followed by Proteus spp. and Enterococcus spp. The antibiotic resistance rate of E. coli was high and close to that reported for adults with complicated UTIs: amoxicillin 60%, amoxicillin-clavulanate 35%, cefotaxim 5%, trimethoprim-sulfametoxazole 26%, nalidixic acid 9%, ciprofloxacin 7%, gentamycin 1%, nitrofurantoin and fosfomycin 0%. The antibiotic exposure in the previous 12 months involved 62 children (56%) most frequently with β-lactams (89%) for a respiratory tract infection (56%). A clear relationship between exposure and resistance was observed for amoxicillin (71% vs. 46%), first generation (65% vs. 46%) and third generation (9% vs. 3%) cephalosporins, or trimethoprim-sulfamethoxazole (36% vs. 15%). However, antibiotic exposure could not account alone for the results, as suggested by the 7% of ciprofloxacin resistance, observed without any identified previous treatment. Bacterial species and antibiotic resistance level in children are similar to those reported for adults. Antibiotic exposure in the previous 12 months increases the risk of resistance but other factors are involved (previous antibiotic therapies and fecal-oral or mother-to-child transmission). Copyright © 2013 Elsevier Masson SAS. All rights reserved.

  10. 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.

  11. The Importance of Business Model Factors for Cloud Computing Adoption: Role of Previous Experiences

    Directory of Open Access Journals (Sweden)

    Bogataj Habjan Kristina

    2017-08-01

    Full Text Available Background and Purpose: Bringing several opportunities for more effective and efficient IT governance and service exploitation, cloud computing is expected to impact the European and global economies significantly. Market data show that despite many advantages and promised benefits the adoption of cloud computing is not as fast and widespread as foreseen. This situation shows the need for further exploration of the potentials of cloud computing and its implementation on the market. The purpose of this research was to identify individual business model factors with the highest impact on cloud computing adoption. In addition, the aim was to identify the differences in opinion regarding the importance of business model factors on cloud computing adoption according to companies’ previous experiences with cloud computing services.

  12. Double tracks test site characterization report

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    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).

  13. 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.

  14. Low-dose computed tomography image restoration using previous normal-dose scan

    Science.gov (United States)

    Ma, Jianhua; Huang, Jing; Feng, Qianjin; Zhang, Hua; Lu, Hongbing; Liang, Zhengrong; Chen, Wufan

    2011-01-01

    the previous normal-dose scan via the presented ndiNLM algorithm is noticeable as compared to a similar approach without using the previous normal-dose scan.Conclusions: For low-dose CT image restoration, the presented ndiNLM method is robust in preserving the spatial resolution and identifying the low-contrast structure. The authors can draw the conclusion that the presented ndiNLM algorithm may be useful for some clinical applications such as in perfusion imaging, radiotherapy, tumor surveillance, etc. PMID:21992386

  15. 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

  16. 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.

  17. 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.

  18. 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

  19. Environmental assessment: Richton Dome site, Mississippi

    Energy Technology Data Exchange (ETDEWEB)

    none,

    1986-05-01

    In February 1983, the US Department of Energy (DOE) identified the Richton Dome site in Mississippi as one of the nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high-level radioactive waste. To determine their suitability, the Richton Dome site and the eight other potentially acceptable sites have been evaluated in accordance with the DOE's General Guidelines for the Recommendation of Sites for the Nuclear Waste Repositories. These evaluations were reported in draft environmental assessments (EAs), which were issued for public review and comment. After considering the comments received on the draft EAs, the DOE prepared the final EAs. The site is in the Gulf interior region, which is one of five distinct geohydrologic settings considered for the first repository. This setting contains two other potentially acceptable sites--the Cypress Creek Dome site in Mississippi and the Vacherie Dome site in Louisiana. Although the Cypress Creek Dome and the Vacherie Dome sites are suitable for site characterization, the DOE has concluded that the Richton Dome site is the preferred site in the Gulf interior region. On the basis of the evaluations reported in this EA, the DOE has found that the Richton Dome site is not disqualified under the guidelines.

  20. Environmental assessment: Richton Dome Site, Mississippi

    Energy Technology Data Exchange (ETDEWEB)

    none,

    1986-05-01

    In February 1983, the US Department of Energy (DOE) identified the Richton Dome site in Mississippi as one of the nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high-level radioactive waste. To determine their suitability, the Richton Dome site and the eight other potentially acceptable sites have been evaluated in accordance with the DOE's General Guidelines for the Recommendation of Sites for the Nuclear Waste Repositories. These evaluations were reported in draft environmental assessments (EAs), which were issued for public review and comment. After considering the comments received on the draft EAs, the DOE prepared the final EAs. The site is in the Gulf interior region, which is one of five distinct geohydrologic settings considered for the first repository. This setting contains two other potentially acceptable sites--the Cypress Creek Dome site in Mississippi and the Vacherie Dome site in Louisiana. Although the Cypress Creek Dome and the Vacherie Dome sites are suitable for site characterization, the DOE has concluded that the Richton Dome site is the preferred site in the Gulf interior region. On the basis of the evaluations reported in this EA, the DOE has found that the Richton Dome site is not disqualified under the guidelines.

  1. Environmental assessment: Richton Dome site, Mississippi

    International Nuclear Information System (INIS)

    1986-05-01

    In February 1983, the US Department of Energy (DOE) identified the Richton Dome site in Mississippi as one of the nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high-level radioactive waste. To determine their suitability, the Richton Dome site and the eight other potentially acceptable sites have been evaluated in accordance with the DOE's General Guidelines for the Recommendation of Sites for the Nuclear Waste Repositories. These evaluations were reported in draft environmental assessments (EAs), which were issued for public review and comment. After considering the comments received on the draft EAs, the DOE prepared the final EAs. The site is in the Gulf interior region, which is one of five distinct geohydrologic settings considered for the first repository. This setting contains two other potentially acceptable sites--the Cypress Creek Dome site in Mississippi and the Vacherie Dome site in Louisiana. Although the Cypress Creek Dome and the Vacherie Dome sites are suitable for site characterization, the DOE has concluded that the Richton Dome site is the preferred site in the Gulf interior region. On the basis of the evaluations reported in this EA, the DOE has found that the Richton Dome site is not disqualified under the guidelines

  2. Environmental assessment: Richton Dome Site, Mississippi

    International Nuclear Information System (INIS)

    1986-05-01

    In February 1983, the US Department of Energy (DOE) identified the Richton Dome site in Mississippi as one of the nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high-level radioactive waste. To determine their suitability, the Richton Dome site and the eight other potentially acceptable sites have been evaluated in accordance with the DOE's General Guidelines for the Recommendation of Sites for the Nuclear Waste Repositories. These evaluations were reported in draft environmental assessments (EAs), which were issued for public review and comment. After considering the comments received on the draft EAs, the DOE prepared the final EAs. The site is in the Gulf interior region, which is one of five distinct geohydrologic settings considered for the first repository. This setting contains two other potentially acceptable sites--the Cypress Creek Dome site in Mississippi and the Vacherie Dome site in Louisiana. Although the Cypress Creek Dome and the Vacherie Dome sites are suitable for site characterization, the DOE has concluded that the Richton Dome site is the preferred site in the Gulf interior region. On the basis of the evaluations reported in this EA, the DOE has found that the Richton Dome site is not disqualified under the guidelines

  3. 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.

  4. 75 FR 39143 - Airworthiness Directives; Arrow Falcon Exporters, Inc. (previously Utah State University); AST...

    Science.gov (United States)

    2010-07-08

    ... (previously Precision Helicopters, LLC); Robinson Air Crane, Inc.; San Joaquin Helicopters (previously Hawkins... (Previously Hawkins & Powers Aviation); S.M. &T. Aircraft (Previously Us Helicopter Inc., UNC Helicopters, Inc...

  5. Identification of an assembly site for migratory and tropical seabirds in the South Atlantic Ocean

    Directory of Open Access Journals (Sweden)

    B. John Hughes

    2015-07-01

    Full Text Available Seabirds are good indicators of wider biodiversity and where they assemble in large numbers signifies sites important to many marine faunal species. Few such large assemblage sites have been identified and none in pelagic waters has been identified in the tropical Atlantic Ocean despite their importance for resident seabirds and those ‘on passage’ during migration. Here, we identify the likely location of just such an assembly site and provide preliminary information about the distribution of pelagic seabirds around Ascension Island in the tropical South Atlantic Ocean using a combination of trans-equatorial seabird migrant tracking data, records of at-sea surveys and land counts of seabirds returning from foraging trips. We found that waters north–north-west of Ascension Island are used more often by seabirds than those south and east of the island. Three-fifths of the species recorded in the assembly site breed at mid- or high-latitudes and some of these migratory seabirds stopover possibly to wait for favourable winds that facilitate onward flight. Our findings are important because to the best of our knowledge no seabird assembly sites have previously been identified in tropical Atlantic Ocean pelagic waters. We provide evidence to support the aspirations of the Marine Reserves Coalition that waters in the vicinity of Ascension Island should be recognised as a sanctuary for marine wildlife and we highlight an area that is worthy of further targeted investigation.

  6. Superfund Site Information - Site Sampling Data

    Data.gov (United States)

    U.S. Environmental Protection Agency — This asset includes Superfund site-specific sampling information including location of samples, types of samples, and analytical chemistry characteristics of...

  7. SITE COMPREHENSIVE LISTING (CERCLIS) (Superfund) - NPL Sites

    Data.gov (United States)

    U.S. Environmental Protection Agency — National Priorities List (NPL) Sites - The Comprehensive Environmental Response, Compensation and Liability Information System (CERCLIS) (Superfund) Public Access...

  8. Environmental assessment: Deaf Smith County site, Texas

    Energy Technology Data Exchange (ETDEWEB)

    1986-05-01

    In February 1983, the US Department of Energy (DOE) identified a location in Deaf Smith County, Texas, as one of nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high-level radioactive waste. To determine their suitability, the Deaf Smith County site and the eight other potentially sites have been evaluated in accordance with the DOE's General Guidelines for the Recommendation of Sites for the Nuclear Waste Repositories. The Deaf Smith County site is in the Permian Basin, which is one of five distinct geohydrologic settings considered for the first repository. On the basis of the evaluations reported in this EA, the DOE has found that the Deaf Smith County site is not disqualified under the guidelines. On the basis of these findings, the DOE is nominating the Deaf Smith County site as one of the five sites suitable for characterization. 591 refs., 147 figs., 173 tabs.

  9. Environmental assessment: Deaf Smith County site, Texas

    International Nuclear Information System (INIS)

    1986-05-01

    In February 1983, the US Department of Energy (DOE) identified a location in Deaf Smith County, Texas, as one of nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high-level radioactive waste. To determine their suitability, the Deaf Smith County site and the eight other potentially sites have been evaluated in accordance with the DOE's General Guidelines for the Recommendation of Sites for the Nuclear Waste Repositories. The Deaf Smith County site is in the Permian Basin, which is one of five distinct geohydrologic settings considered for the first repository. On the basis of the evaluations reported in this EA, the DOE has found that the Deaf Smith County site is not disqualified under the guidelines. On the basis of these findings, the DOE is nominating the Deaf Smith County site as one of the five sites suitable for characterization. 591 refs., 147 figs., 173 tabs

  10. Magnetic resonance imaging detection of prostate cancer in men with previous negative prostate biopsy.

    Science.gov (United States)

    Truong, Matthew; Frye, Thomas P

    2017-06-01

    Use of transrectal ultrasound guided systematic prostate biopsy has poor diagnostic accuracy for prostate cancer (PCa) detection. Recently multiparametric MRI (mpMRI) of the prostate and MR/US fusion biopsy has been gaining popularity for men who have previously undergone a negative biopsy. We performed PubMed ® and Web of Science ® searches to identify studies on this subject, particularly focusing on studies consisting of patients who have had at least one previously negative biopsy. Across the literature, when a suspicious lesion is found on mpMRI, MR/US fusion biopsy has consistently demonstrated higher detection rate for any PCa and clinically significant PCa (csPCa) compared to the traditional repeat systematic biopsy (SB) approach. Furthermore, anteriorly located tumors are frequently identified using MR targeted biopsy (TB), suggesting that an MR guided approach allows for increased accuracy for detecting tumors commonly missed by systematic biopsies. We conclude that men with a prior negative biopsy and continued suspicion of PCa should strongly be encouraged to get a prostate mpMRI prior to a repeat biopsy.

  11. 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.``

  12. Site specific information in site selection

    International Nuclear Information System (INIS)

    Aeikaes, T.; Hautojaervi, A.

    1998-01-01

    The programme for the siting of a deep repository for final disposal of spent nuclear fuel was started already in 1983 and is carried out today by Posiva Oy which continues the work started by Teollisuuden Voima Oy. The programme aims at site selection by the end of the year 2000. The programme has progressed in successive interim stages with defined goals. After an early phase for site identification, five sites were selected in 1987 for preliminary site characterisation. Three of these were selected and judged to be best suited for the more detailed characterisation in 1992. An additional new site was included into the programme based on a separate feasibility study in the beginning of 1997. Since the year 1983 several safety assessments together with technical plans of the facility have been completed. When approaching the site selection the needs for more detailed consideration of the site specific properties in the safety assessment have been increased. The Finnish regulator STUK has published a proposal for general safety requirements for the final disposal of spent nuclear fuel in Finland. This set of requirements has been projected to be used in conjunction of the decision making by the end 2000. Based on the site evaluation all sites can provide a stable environment and there is evidence that the requirements for the longevity of the canister can be fulfilled at each site. In this manner the four candidate sites do not differ too much from each other. The main difference between the sites is in the salinity of the deep groundwater. The significance of differences in the salinity for the long-term safety cannot be defined yet. The differences may contribute to the discussion of the longevity of the bentonite buffer and also to the modelling of the groundwater flow and transport. The use of the geosphere as a transport barrier is basically culminated on the questions about sparse but fast flow routes and 'how bad channeling can be'. To answer these questions

  13. 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.

  14. Identifying homelessness using health information exchange data.

    Science.gov (United States)

    Zech, John; Husk, Gregg; Moore, Thomas; Kuperman, Gilad J; Shapiro, Jason S

    2015-05-01

    Homeless patients experience poor health outcomes and consume a disproportionate amount of health care resources compared with domiciled patients. There is increasing interest in the federal government in providing care coordination for homeless patients, which will require a systematic way of identifying these individuals. We analyzed address data from Healthix, a New York City-based health information exchange, to identify patterns that could indicate homelessness. Patients were categorized as likely to be homeless if they registered with the address of a hospital, homeless shelter, place of worship, or an address containing a keyword synonymous with "homelessness." We identified 78,460 out of 7,854,927 Healthix patients (1%) as likely to have been homeless over the study period of September 30, 2008 to July 19, 2013. We found that registration practices for these patients varied widely across sites. The use of health information exchange data enabled us to identify a large number of patients likely to be homeless and to observe the wide variation in registration practices for homeless patients within and across sites. Consideration of these results may suggest a way to improve the quality of record matching for homeless patients. Validation of these results is necessary to confirm the homeless status of identified individuals. Ultimately, creating a standardized and structured field to record a patient's housing status may be a preferable approach. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  15. Yucca Mountain site characterization project: Site atlas 1997. Part 1

    International Nuclear Information System (INIS)

    1997-01-01

    The US Department of Energy (DOE) is conducting site characterization studies at Yucca Mountain, Nevada, to determine if the site is suitable for an underground repository for the permanent disposal of high-level radioactive waste. The Yucca Mountain Project (YMP) Site Atlas is a tool used to cartographically display some of the Geographic Information System (GIS) data in the form of thematic map products. Essentially, the Site Atlas is a compilation of map products that are designed to illustrate the location and extent of site characterization studies. Additionally, the Site Atlas provides maps showing project administrative boundaries and basemaps in the vicinity of the project. The data are current through September 1997. The Atlas is divided into two parts: Part 1 contains GIS maps and supporting characteristic data for geology; stratigraphy; tectonics; volcanism; hydrology; geochemistry; environmental issues; paleontology; repository design; YMP boreholes, trenches, pits, pavements, and exposures; basemap features; and surface-based testing activities, and Part 2 contains 1:6,000- and 1:12,000-scale orthophotography basemaps and orthophotography-based hypsography maps (topographic data). This data is shown at a 50% reduction. The maps and orthophotographs in this Site Atlas are provided to YMP participants as an informational source only and are not for making precise measurements. The Quality Assurance Requirements and Description statement on each map identifies the quality status of the thematic data presented. The Site Atlas is not a comprehensive guide; it does not include all scientific features or studies undertaken for the YMP. The features presented are a small subset of the total work being conducted for the project

  16. 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.

  17. Antimetabolites in cataract surgery to prevent failure of a previous trabeculectomy.

    Science.gov (United States)

    Thomas, Roger E; Crichton, Andrew; Thomas, Bennett C

    2014-07-28

    Patients having cataract surgery have often earlier undergone a trabeculectomy for glaucoma. However, cataract surgery may be associated with failure of the previous glaucoma surgery and antimetabolites may be used with cataract surgery to prevent such failure. There is no systematic review on whether antimetabolites with cataract surgery prevent failure of a previous trabeculectomy. To assess the effects of antimetabolites with cataract surgery on functioning of a previous trabeculectomy. We searched CENTRAL (which contains the Cochrane Eyes and Vision Group Trials Register) (2014, Issue 5), Ovid MEDLINE, Ovid MEDLINE In-Process and Other Non-Indexed Citations, Ovid MEDLINE Daily, Ovid OLDMEDLINE (January 1946 to June 2014), EMBASE (January 1980 to June 2014), Latin American and Caribbean Health Sciences Literature Database (LILACS) (January 1982 to June 2014), the metaRegister of Controlled Trials (mRCT) (www.controlled-trials.com), ClinicalTrials.gov (www.clinicaltrials.gov) and the World Health Organization (WHO) International Clinical Trials Registry Platform (ICTRP) (www.who.int/ictrp/search/en). We did not use any date or language restrictions in the electronic searches for trials. We last searched the electronic databases on 10 June 2014. We also searched the Science Citation Index database (July 2013) and reference lists of potentially relevant studies. Randomised controlled trials (RCTs) of antimetabolites with cataract surgery in people with a functioning trabeculectomy. Two review authors independently reviewed the titles and abstracts from the electronic searches. Two review authors independently assessed relevant full-text articles and entered data. We identified no RCTs to test the effectiveness of antimetabolites with cataract surgery in individuals with the intention of preventing failure of a previous trabeculectomy. There are no RCTs of antimetabolites with cataract surgery in people with a functioning trabeculectomy. Appropriately powered RCTs

  18. Environmental assessment: Davis Canyon site, Utah

    International Nuclear Information System (INIS)

    1986-05-01

    In February 1983, the US Department of Energy (DOE) identified the Davis Canyon site in Utah as one of the nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high-level radioactive waste. To determine their suitability, the Davis Canyon site and the eight other potentially acceptable sites have been evaluated in accordance with the DOE's General Guidelines for the Recommendation of Sites for the Nuclear Waste Repositories. These evaluations were reported in draft environmental assessments (EAs), which were issued for public review and comment. After considering the comments received on the draft EAs, the DOE prepared the final EA. The Davis Canyon site is in the Paradox Basin, which is one of five distinct geohydrologic settings considered for the first repository. This setting contains one other potentially acceptable site -- the Lavender Canyon site. Although the Lavender Canyon site is suitable for site characterization, the DOE has concluded that the Davis Canyon site is the preferred site in the Paradox Basin. On the basis of the evaluations reported in this EA, the DOE has found that the Davis Canyon site is not disqualified under the guidelines. Furthermore, the DOE has fond that the site is suitable for site characterization because the evidence does not support a conclusion that the site will not be able to meet each of the qualifying conditions specified in the guidelines. On the basis of these findings, the DOE is nominating the Davis Canyon site as one of five sites suitable for characterization. 181 figs., 175 tabs

  19. Environmental assessment: Davis Canyon site, Utah

    Energy Technology Data Exchange (ETDEWEB)

    none,

    1986-05-01

    In February 1983, the US Department of Energy (DOE) identified the Davis Canyon site in Utah as one of the nine potentially acceptable sites for a mined geologic repository for spent nuclear fuel and high-level radioactive waste. To determine their suitability, the Davis Canyon site and the eight other potentially acceptable sites have been evaluated in accordance with the DOE's General Guidelines for the Recommendation of Sites for the Nuclear Waste Repositories. These evaluations were reported in draft environmental assessments (EAs), which were issued for public review and comment. After considering the comments received on the draft EAs, the DOE prepared the final EA. The Davis Canyon site is in the Paradox Basin, which is one of five distinct geohydrologic settings considered for the first repository. This setting contains one other potentially acceptable site -- the Lavender Canyon site. Although the Lavender Canyon site is suitable for site characterization, the DOE has concluded that the Davis Canyon site is the preferred site in the Paradox Basin. On the basis of the evaluations reported in this EA, the DOE has found that the Davis Canyon site is not disqualified under the guidelines. Furthermore, the DOE has fond that the site is suitable for site characterization because the evidence does not support a conclusion that the site will not be able to meet each of the qualifying conditions specified in the guidelines. On the basis of these findings, the DOE is nominating the Davis Canyon site as one of five sites suitable for characterization. 181 figs., 175 tabs.

  20. Assessing hypotheses about nesting site occupancy dynamics

    Science.gov (United States)

    Bled, Florent; Royle, J. Andrew; Cam, Emmanuelle

    2011-01-01

    Hypotheses about habitat selection developed in the evolutionary ecology framework assume that individuals, under some conditions, select breeding habitat based on expected fitness in different habitat. The relationship between habitat quality and fitness may be reflected by breeding success of individuals, which may in turn be used to assess habitat quality. Habitat quality may also be assessed via local density: if high-quality sites are preferentially used, high density may reflect high-quality habitat. Here we assessed whether site occupancy dynamics vary with site surrogates for habitat quality. We modeled nest site use probability in a seabird subcolony (the Black-legged Kittiwake, Rissa tridactyla) over a 20-year period. We estimated site persistence (an occupied site remains occupied from time t to t + 1) and colonization through two subprocesses: first colonization (site creation at the timescale of the study) and recolonization (a site is colonized again after being deserted). Our model explicitly incorporated site-specific and neighboring breeding success and conspecific density in the neighborhood. Our results provided evidence that reproductively "successful'' sites have a higher persistence probability than "unsuccessful'' ones. Analyses of site fidelity in marked birds and of survival probability showed that high site persistence predominantly reflects site fidelity, not immediate colonization by new owners after emigration or death of previous owners. There is a negative quadratic relationship between local density and persistence probability. First colonization probability decreases with density, whereas recolonization probability is constant. This highlights the importance of distinguishing initial colonization and recolonization to understand site occupancy. All dynamics varied positively with neighboring breeding success. We found evidence of a positive interaction between site-specific and neighboring breeding success. We addressed local