WorldWideScience

Sample records for breakpoints demarcating sites

  1. Distinct retroelement classes define evolutionary breakpoints demarcating sites of evolutionary novelty

    Directory of Open Access Journals (Sweden)

    Green Eric D

    2009-07-01

    Full Text Available Abstract Background Large-scale genome rearrangements brought about by chromosome breaks underlie numerous inherited diseases, initiate or promote many cancers and are also associated with karyotype diversification during species evolution. Recent research has shown that these breakpoints are nonrandomly distributed throughout the mammalian genome and many, termed "evolutionary breakpoints" (EB, are specific genomic locations that are "reused" during karyotypic evolution. When the phylogenetic trajectory of orthologous chromosome segments is considered, many of these EB are coincident with ancient centromere activity as well as new centromere formation. While EB have been characterized as repeat-rich regions, it has not been determined whether specific sequences have been retained during evolution that would indicate previous centromere activity or a propensity for new centromere formation. Likewise, the conservation of specific sequence motifs or classes at EBs among divergent mammalian taxa has not been determined. Results To define conserved sequence features of EBs associated with centromere evolution, we performed comparative sequence analysis of more than 4.8 Mb within the tammar wallaby, Macropus eugenii, derived from centromeric regions (CEN, euchromatic regions (EU, and an evolutionary breakpoint (EB that has undergone convergent breakpoint reuse and past centromere activity in marsupials. We found a dramatic enrichment for long interspersed nucleotide elements (LINE1s and endogenous retroviruses (ERVs and a depletion of short interspersed nucleotide elements (SINEs shared between CEN and EBs. We analyzed the orthologous human EB (14q32.33, known to be associated with translocations in many cancers including multiple myelomas and plasma cell leukemias, and found a conserved distribution of similar repetitive elements. Conclusion Our data indicate that EBs tracked within the class Mammalia harbor sequence features retained since the

  2. Chromosomal instability in Afrotheria: fragile sites, evolutionary breakpoints and phylogenetic inference from genome sequence assemblies

    Directory of Open Access Journals (Sweden)

    Ruiz-Herrera Aurora

    2007-10-01

    Full Text Available Abstract Background Extant placental mammals are divided into four major clades (Laurasiatheria, Supraprimates, Xenarthra and Afrotheria. Given that Afrotheria is generally thought to root the eutherian tree in phylogenetic analysis of large nuclear gene data sets, the study of the organization of the genomes of afrotherian species provides new insights into the dynamics of mammalian chromosomal evolution. Here we test if there are chromosomal bands with a high tendency to break and reorganize in Afrotheria, and by analyzing the expression of aphidicolin-induced common fragile sites in three afrotherian species, whether these are coincidental with recognized evolutionary breakpoints. Results We described 29 fragile sites in the aardvark (OAF genome, 27 in the golden mole (CAS, and 35 in the elephant-shrew (EED genome. We show that fragile sites are conserved among afrotherian species and these are correlated with evolutionary breakpoints when compared to the human (HSA genome. Inddition, by computationally scanning the newly released opossum (Monodelphis domestica and chicken sequence assemblies for use as outgroups to Placentalia, we validate the HSA 3/21/5 chromosomal synteny as a rare genomic change that defines the monophyly of this ancient African clade of mammals. On the other hand, support for HSA 1/19p, which is also thought to underpin Afrotheria, is currently ambiguous. Conclusion We provide evidence that (i the evolutionary breakpoints that characterise human syntenies detected in the basal Afrotheria correspond at the chromosomal band level with fragile sites, (ii that HSA 3p/21 was in the amniote ancestor (i.e., common to turtles, lepidosaurs, crocodilians, birds and mammals and was subsequently disrupted in the lineage leading to marsupials. Its expansion to include HSA 5 in Afrotheria is unique and (iii that its fragmentation to HSA 3p/21 + HSA 5/21 in elephant and manatee was due to a fission within HSA 21 that is probably shared

  3. Over half of breakpoints in gene pairs involved in cancer-specific recurrent translocations are mapped to human chromosomal fragile sites

    Directory of Open Access Journals (Sweden)

    Pierce Levi CT

    2009-01-01

    Full Text Available Abstract Background Gene rearrangements such as chromosomal translocations have been shown to contribute to cancer development. Human chromosomal fragile sites are regions of the genome especially prone to breakage, and have been implicated in various chromosome abnormalities found in cancer. However, there has been no comprehensive and quantitative examination of the location of fragile sites in relation to all chromosomal aberrations. Results Using up-to-date databases containing all cancer-specific recurrent translocations, we have examined 444 unique pairs of genes involved in these translocations to determine the correlation of translocation breakpoints and fragile sites in the gene pairs. We found that over half (52% of translocation breakpoints in at least one gene of these gene pairs are mapped to fragile sites. Among these, we examined the DNA sequences within and flanking three randomly selected pairs of translocation-prone genes, and found that they exhibit characteristic features of fragile DNA, with frequent AT-rich flexibility islands and the potential of forming highly stable secondary structures. Conclusion Our study is the first to examine gene pairs involved in all recurrent chromosomal translocations observed in tumor cells, and to correlate the location of more than half of breakpoints to positions of known fragile sites. These results provide strong evidence to support a causative role for fragile sites in the generation of cancer-specific chromosomal rearrangements.

  4. Physical linkage of the fragile site FRA11B and a Jacobsen syndrome chromosome deletion breakpoint in 11q23.3.

    Science.gov (United States)

    Jones, C; Slijepcevic, P; Marsh, S; Baker, E; Langdon, W Y; Richards, R I; Tunnacliffe, A

    1994-12-01

    Autosomal fragile sites, unlike their X-linked counterparts, are not known to be associated with disease. However, one case report has highlighted a possible relationship between the inheritance of a rare folate-sensitive fragile site in band 11q23.3 (FRA11B) and the chromosome 11q23-->qter deletion in Jacobsen (11q-) syndrome. The mother and brother of the reported Jacobsen syndrome child are FRA11B carriers, suggesting that in vivo breakage at the fragile site during early development could have given rise to the chromosome deletion. We have tested this hypothesis by high resolution physical mapping of FRA11B and of the deletion chromosome breakpoint in the Jacobsen syndrome patient. A detailed restriction map of 600 kb of human chromosome band 11q23.3 has been assembled which covers the PBGD, CBL2 and THY1 genes. FISH experiments with YACs and cosmids from this region have localised FRA11B to an interval of approximately 100 kb containing the 5' end of the CBL2 gene, which includes a CCG trinucleotide repeat. This class of repeat is expanded in the four cloned examples of fragile site and therefore the CBL2 repeat is a candidate for the location of FRA11B. Further, it is shown that the chromosomal deletion breakpoint of the Jacobsen syndrome child maps within the same interval as the fragile site. The breakpoint has apparently been repaired and stabilised by the de novo addition of a telomere. These data are consistent with a role for an inherited fragile site in the aetiology of a chromosome deletion syndrome.

  5. Molecular variation at the In(2L)t proximal breakpoint site in natural populations of Drosophilia melanogaster and D. simulans

    National Research Council Canada - National Science Library

    Peter Andolfatto; Martin Kreitman

    2000-01-01

      A previous study of nucleotide polymorphism in a Costa Rican population of Drosophila melanogaster found evidence for a nonneutral deficiency in the number of haplotypes near the proximal breakpoint of In(2L...

  6. Demarcation of secondary hyperalgesia zones

    DEFF Research Database (Denmark)

    Ringsted, Thomas K; Enghuus, Casper; Petersen, Morten A

    2015-01-01

    BACKGROUND: Secondary hyperalgesia is increased sensitivity in normal tissue near an injury, and it is a measure of central sensitization reflecting injury-related effects on the CNS. Secondary hyperalgesia areas (SHAs), usually assessed by polyamide monofilaments, are important outcomes in studies...... of analgesic drug effects in humans. However, since the methods applied in demarcating the secondary hyperalgesia zone seem inconsistent across studies, we examined the effect of a standardized approach upon the measurement of SHA following a first degree burn injury (BI). NEW METHOD: The study was a two......-observer, test-retest study with the two sessions separated by 6wk. An observer-blinded design adjusted to examine day-to-day and observer-to-observer variability in SHA was used. In 23 healthy volunteers (12 females/11 males) a BI was induced by a contact thermode (47.0°C, 420s, 2.5×5.0cm(2)). The SHA...

  7. 7 CFR 1755.504 - Demarcation point.

    Science.gov (United States)

    2010-01-01

    .... The National Electrical Code ® and NEC ® are registered trademarks of the National Fire Protection... § 1755.504 Demarcation point. (a) The demarcation point (DP) provides the physical and electrical... Agriculture, 1400 Independence Avenue, SW., STOP 1598, Washington, DC 20250-1598, or at the National Archives...

  8. Molecular characterization of the breakpoints of an inversion fixed between Drosophila melanogaster and D. subobscura

    Energy Technology Data Exchange (ETDEWEB)

    Cirera, S.; Martin-Campos, J.M.; Segarra, C. [Universitat de Barcelone (Spain)] [and others

    1995-01-01

    The two breakpoints of a chromosomal inversion fixed since the split of Drosophila melanogaster and D. subobscura lineages have been isolated and sequenced in both species. The regions spanning the break-points initially were identified by the presence of two signals after interspecific in situ hybridization on polytene chromosomes. Interspecific comparison of the sequenced regions allowed us to delineate the location of the breakpoints. Close to one of these breakpoints a new transcription unit (bcn92) has been identified in both species. The inversion fixed between D. melanogaster and D. subobscura does not seem to have broken any transcription unit. Neither complete nor defective transposable elements were found in the regions encompassing the breakpoints. Short thymine-rich sequences (30-50 hp long) have been found bordering the breakpoint regions. Although alternating Pur-Pyr sequences were detected, these putative target sites for topoisomerase II were not differentially clustered in the breakpoints. 22 refs., 6 figs.

  9. Aluminum break-point contacts

    NARCIS (Netherlands)

    Heinemann, Martina; Groot, R.A. de

    1997-01-01

    Ab initio molecular dynamics is used to study the contribution of a single Al atom to an aluminum breakpoint contact during the final stages of breaking and the initial stages of the formation of such a contact. A hysteresis effect is found in excellent agreement with experiment and the form of the

  10. Syllable Boundary Demarcation in Hualapai and Havasupai.

    Science.gov (United States)

    Berardo, Marcellino

    This investigation focuses on syllable boundary demarcation in Hualapai and Havasupai, both native American Indian languages spoken in Northern Arizona. In an attempt to understand better the nature of the syllable, allophonic variation with respect to syllable position is examined. Cross-linguistic evidence suggests that sounds may take on…

  11. Geminates’ demarcating function from Latin to Italian

    Directory of Open Access Journals (Sweden)

    Sophie SAFFI

    2013-01-01

    Full Text Available This article aims to show that from a diachronic or synchronic point of view, in Romance languages, especially Italian, geminates, complementary phenomenon of the intensity stress, are involved in the construction of the word with a demarcating function. They separate the components of the word when it is necessary for the proper conduct of the construction of meaning.

  12. Localization of Jacobsen syndrome breakpoints on a 40-Mb physical map of distal chromosome 11q.

    Science.gov (United States)

    Tunnacliffe, A; Jones, C; Le Paslier, D; Todd, R; Cherif, D; Birdsall, M; Devenish, L; Yousry, C; Cotter, F E; James, M R

    1999-01-01

    Jacobsen syndrome is a haploinsufficiency disorder caused, most frequently by terminal deletion of part of the long arm of chromosome 11, with breakpoints in 11q23.3-11q24.2. Inheritance of an expanded p(CCG)n trinucleotide repeat at the folate-sensitive fragile site FRA11B has been implicated in the generation of the chromosome breakpoint in several Jacobsen syndrome patients. The majority of such breakpoints, however, map distal to this fragile site and are not linked with its expression. To characterize these distal breakpoints and ultimately to further investigate the mechanisms of chromosome breakage, a 40-Mb YAC contig covering the distal long arm of chromosome 11 was assembled. The utility of the YAC contig was demonstrated in three ways: (1) by rapidly mapping the breakpoints from two new Jacobsen syndrome patients using FISH; (2) by demonstrating conversion to high resolution PAC contigs after direct screening of PAC library filters with a YAC clone containing a Jacobsen syndrome breakpoint; and (3) by placing 23 Jacobsen syndrome breakpoints on the physical map. This analysis has suggested the existence of at least two new Jacobsen syndrome breakpoint cluster regions in distal chromosome 11.

  13. Localization of Jacobsen Syndrome Breakpoints on a 40-Mb Physical Map of Distal Chromosome 11q

    OpenAIRE

    Tunnacliffe, Alan; Jones, Christopher; Le Paslier, Denis; Todd, Roger; Cherif, Dora; Birdsall, Michelle; Devenish, Louise; Yousry, Cherine; Cotter, Finbarr E.; James, Michael R.

    1999-01-01

    Jacobsen syndrome is a haploinsufficiency disorder caused, most frequently by terminal deletion of part of the long arm of chromosome 11, with breakpoints in 11q23.3–11q24.2. Inheritance of an expanded p(CCG)n trinucleotide repeat at the folate-sensitive fragile site FRA11B has been implicated in the generation of the chromosome breakpoint in several Jacobsen syndrome patients. The majority of such breakpoints, however, map distal to this fragile site and are not linked with its expression. T...

  14. Divide-and-conquer approach for the exemplar breakpoint distance

    National Research Council Canada - National Science Library

    Nguyen, C Thach; Tay, Y C; Zhang, Louxin

    2005-01-01

    .... Unfortunately, the problem is NP-hard even for the breakpoint distance. This paper proposes a divide-and-conquer approach for calculating the exemplar breakpoint distance between two genomes with multiple gene families...

  15. Breakpoint Distance and PQ-Trees

    Science.gov (United States)

    Jiang, Haitao; Chauve, Cedric; Zhu, Binhai

    The PQ-tree is a fundamental data structure that can encode large sets of permutations. It has recently been used in comparative genomics to model ancestral genomes with some uncertainty: given a phylogeny for some species, extant genomes are represented by permutations on the leaves of the tree, and each internal node in the phylogenetic tree represents an extinct ancestral genome, represented by a PQ-tree. An open problem related to this approach is then to quantify the evolution between genomes represented by PQ-trees. In this paper we present results for two problems of PQ-tree comparison motivated by this application. First, we show that the problem of comparing two PQ-trees by computing the minimum breakpoint distance among all pairs of permutations generated respectively by the two considered PQ-trees is NP-complete for unsigned permutations. Next, we consider a generalization of the classical Breakpoint Median problem, where an ancestral genome is represented by a PQ-tree and p permutations are given, with p ≥ 1, and we want to compute a permutation generated by the PQ-tree that minimizes the sum of the breakpoint distances to the p permutations. We show that this problem is Fixed-Parameter Tractable with respect to the breakpoint distance value. This last result applies both on signed and unsigned permutations, and to uni-chromosomal and multi-chromosomal permutations.

  16. Preferential Breakpoints in the Recovery of Broken Dicentric Chromosomes in Drosophila melanogaster

    Science.gov (United States)

    Hill, Hunter; Golic, Kent G.

    2015-01-01

    We designed a system to determine whether dicentric chromosomes in Drosophila melanogaster break at random or at preferred sites. Sister chromatid exchange in a Ring-X chromosome produced dicentric chromosomes with two bridging arms connecting segregating centromeres as cells divide. This double bridge can break in mitosis. A genetic screen recovered chromosomes that were linearized by breakage in the male germline. Because the screen required viability of males with this X chromosome, the breakpoints in each arm of the double bridge must be closely matched to produce a nearly euploid chromosome. We expected that most linear chromosomes would be broken in heterochromatin because there are no vital genes in heterochromatin, and breakpoint distribution would be relatively unconstrained. Surprisingly, approximately half the breakpoints are found in euchromatin, and the breakpoints are clustered in just a few regions of the chromosome that closely match regions identified as intercalary heterochromatin. The results support the Laird hypothesis that intercalary heterochromatin can explain fragile sites in mitotic chromosomes, including fragile X. Opened rings also were recovered after male larvae were exposed to X-rays. This method was much less efficient and produced chromosomes with a strikingly different array of breakpoints, with almost all located in heterochromatin. A series of circularly permuted linear X chromosomes was generated that may be useful for investigating aspects of chromosome behavior, such as crossover distribution and interference in meiosis, or questions of nuclear organization and function. PMID:26294667

  17. Establishment of valnemulin susceptibility breakpoint against Clostridium perfringens in rabbits.

    Science.gov (United States)

    Tao, Meng-Ting; Zhou, Yu-Feng; Sun, Jian; Liu, Ya-Hong; Liao, Xiao-Ping

    2017-12-01

    Susceptibility breakpoints provide fundamental information for rational administration of antibiotics. The present investigation reports the first valnemulin susceptibility breakpoint (MICvalnemulin might be useful in resistance surveillance of pleuromutilins and development of clinical breakpoints. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Multiple Break-Points Detection in Array CGH Data via the Cross-Entropy Method.

    Science.gov (United States)

    Priyadarshana, W J R M; Sofronov, Georgy

    2015-01-01

    Array comparative genome hybridization (aCGH) is a widely used methodology to detect copy number variations of a genome in high resolution. Knowing the number of break-points and their corresponding locations in genomic sequences serves different biological needs. Primarily, it helps to identify disease-causing genes that have functional importance in characterizing genome wide diseases. For human autosomes the normal copy number is two, whereas at the sites of oncogenes it increases (gain of DNA) and at the tumour suppressor genes it decreases (loss of DNA). The majority of the current detection methods are deterministic in their set-up and use dynamic programming or different smoothing techniques to obtain the estimates of copy number variations. These approaches limit the search space of the problem due to different assumptions considered in the methods and do not represent the true nature of the uncertainty associated with the unknown break-points in genomic sequences. We propose the Cross-Entropy method, which is a model-based stochastic optimization technique as an exact search method, to estimate both the number and locations of the break-points in aCGH data. We model the continuous scale log-ratio data obtained by the aCGH technique as a multiple break-point problem. The proposed methodology is compared with well established publicly available methods using both artificially generated data and real data. Results show that the proposed procedure is an effective way of estimating number and especially the locations of break-points with high level of precision. Availability: The methods described in this article are implemented in the new R package breakpoint and it is available from the Comprehensive R Archive Network at http://CRAN.R-project.org/package=breakpoint.

  19. Fast semi-automated lesion demarcation in stroke.

    Science.gov (United States)

    de Haan, Bianca; Clas, Philipp; Juenger, Hendrik; Wilke, Marko; Karnath, Hans-Otto

    2015-01-01

    Lesion-behaviour mapping analyses require the demarcation of the brain lesion on each (usually transverse) slice of the individual stroke patient's brain image. To date, this is generally thought to be most precise when done manually, which is, however, both time-consuming and potentially observer-dependent. Fully automated lesion demarcation methods have been developed to address these issues, but these are often not practicable in acute stroke research where for each patient only a single image modality is available and the available image modality differs over patients. In the current study, we evaluated a semi-automated lesion demarcation approach, the so-called Clusterize algorithm, in acute stroke patients scanned in a range of common image modalities. Our results suggest that, compared to the standard of manual lesion demarcation, the semi-automated Clusterize algorithm is capable of significantly speeding up lesion demarcation in the most commonly used image modalities, without loss of either lesion demarcation precision or lesion demarcation reproducibility. For the three investigated acute datasets (CT, DWI, T2FLAIR), containing a total of 44 patient images obtained in a regular clinical setting at patient admission, the reduction in processing time was on average 17.8 min per patient and this advantage increased with increasing lesion volume (up to 60 min per patient for the largest lesion volumes in our datasets). Additionally, our results suggest that performance of the Clusterize algorithm in a chronic dataset with 11 T1 images was comparable to its performance in the acute datasets. We thus advocate the use of the Clusterize algorithm, integrated into a simple, freely available SPM toolbox, for the precise, reliable and fast preparation of imaging data for lesion-behaviour mapping analyses.

  20. Fast semi-automated lesion demarcation in stroke

    Directory of Open Access Journals (Sweden)

    Bianca de Haan

    2015-01-01

    Full Text Available Lesion–behaviour mapping analyses require the demarcation of the brain lesion on each (usually transverse slice of the individual stroke patient's brain image. To date, this is generally thought to be most precise when done manually, which is, however, both time-consuming and potentially observer-dependent. Fully automated lesion demarcation methods have been developed to address these issues, but these are often not practicable in acute stroke research where for each patient only a single image modality is available and the available image modality differs over patients. In the current study, we evaluated a semi-automated lesion demarcation approach, the so-called Clusterize algorithm, in acute stroke patients scanned in a range of common image modalities. Our results suggest that, compared to the standard of manual lesion demarcation, the semi-automated Clusterize algorithm is capable of significantly speeding up lesion demarcation in the most commonly used image modalities, without loss of either lesion demarcation precision or lesion demarcation reproducibility. For the three investigated acute datasets (CT, DWI, T2FLAIR, containing a total of 44 patient images obtained in a regular clinical setting at patient admission, the reduction in processing time was on average 17.8 min per patient and this advantage increased with increasing lesion volume (up to 60 min per patient for the largest lesion volumes in our datasets. Additionally, our results suggest that performance of the Clusterize algorithm in a chronic dataset with 11 T1 images was comparable to its performance in the acute datasets. We thus advocate the use of the Clusterize algorithm, integrated into a simple, freely available SPM toolbox, for the precise, reliable and fast preparation of imaging data for lesion–behaviour mapping analyses.

  1. Fast semi-automated lesion demarcation in stroke

    Science.gov (United States)

    de Haan, Bianca; Clas, Philipp; Juenger, Hendrik; Wilke, Marko; Karnath, Hans-Otto

    2015-01-01

    Lesion–behaviour mapping analyses require the demarcation of the brain lesion on each (usually transverse) slice of the individual stroke patient's brain image. To date, this is generally thought to be most precise when done manually, which is, however, both time-consuming and potentially observer-dependent. Fully automated lesion demarcation methods have been developed to address these issues, but these are often not practicable in acute stroke research where for each patient only a single image modality is available and the available image modality differs over patients. In the current study, we evaluated a semi-automated lesion demarcation approach, the so-called Clusterize algorithm, in acute stroke patients scanned in a range of common image modalities. Our results suggest that, compared to the standard of manual lesion demarcation, the semi-automated Clusterize algorithm is capable of significantly speeding up lesion demarcation in the most commonly used image modalities, without loss of either lesion demarcation precision or lesion demarcation reproducibility. For the three investigated acute datasets (CT, DWI, T2FLAIR), containing a total of 44 patient images obtained in a regular clinical setting at patient admission, the reduction in processing time was on average 17.8 min per patient and this advantage increased with increasing lesion volume (up to 60 min per patient for the largest lesion volumes in our datasets). Additionally, our results suggest that performance of the Clusterize algorithm in a chronic dataset with 11 T1 images was comparable to its performance in the acute datasets. We thus advocate the use of the Clusterize algorithm, integrated into a simple, freely available SPM toolbox, for the precise, reliable and fast preparation of imaging data for lesion–behaviour mapping analyses. PMID:26413473

  2. The human minisatellite consensus at breakpoints of oncogene translocations

    Energy Technology Data Exchange (ETDEWEB)

    Krowczynska, A.; Krontiris, T.G. (New England Medical Center Hospitals, Boston, MA (United States) Tufts Univ. School of Medicine, Boston, MA (United States)); Rudders, R.A. (New England Medical Center Hospitals, Boston, MA (United States))

    1990-03-11

    A reexamination of human minisatellite (hypervariable) regions following the cloning and sequencing of the new minisatellite, VTR1. 1, revealed that many of these structures possessed a strongly conserved copy of the chi-like octamer, GC(A/T)GG(A/T)GG. In oncogene translocations apparently created by aberrant VDJ recombinase activity, this VTR octamer was often found within a few bases of the breakpoint. Three bcl2 rearrangements which occurred within 2 bp of one another were located precisely adjacent to this consensus; it defined the 5{prime} border of that oncogene's major breakpoint cluster. Several c-myc translocations also occurred within 2 bp of this sequence. While the appearance of a chi-like element in polymorphic minisatellite sequences is consistent with a role promoting either recombination or replication slippage, the existence of such elements at sites of somatic translocations suggests chi function in site-specific recombination, perhaps as a subsidiary recognition signal in immunoglobulin gene rearrangement. The authors discuss the implications of these observations for mechanisms by which oncogene translocations and minisatellite sequences are generated.

  3. A New Criterion for Demarcating Life from Non-Life

    NARCIS (Netherlands)

    Hateren, J.H. van

    2013-01-01

    Criteria for demarcating life from non-life are important for deciding whether new candidate systems, either discovered extraterrestrially or constructed in the laboratory, are genuinely alive or not. They are also important for understanding the origin of life and its evolution. Current criteria

  4. Municipal Boundary Demarcation in South Africa: Processes and ...

    African Journals Online (AJOL)

    User

    1Chief Directorate: National Geo-spatial Information, Department of Rural Development and Land. Reform, South ... 1. Introduction. The Municipal Demarcation Board (MDB) is mandated to dissolve the spatial layout of the .... falling within the Ubuhlebezwe Municipality and have expressed that their sense of belonging is ...

  5. Municipal Boundary Demarcation in South Africa: Processes and ...

    African Journals Online (AJOL)

    After democracy in 1994, South Africa underwent a period of reform in order to address inequalities and effect broad social change. As part of this, the Municipal Demarcation Board began determining the locations of local government boundaries in 1998. The traditional communal lands and rural villages were often split by ...

  6. Scaffold Filling under the Breakpoint Distance

    Science.gov (United States)

    Jiang, Haitao; Zheng, Chunfang; Sankoff, David; Zhu, Binhai

    Motivated by the trend of genome sequencing without completing the sequence of the whole genomes, Muñoz et al. recently studied the problem of filling an incomplete multichromosomal genome (or scaffold) I with respect to a complete target genome G such that the resulting genomic distance between I' and G is minimized, where I' is the corresponding filled scaffold. We call this problem the one-sided scaffold filling problem. In this paper, we follow Muñoz et al. to investigate the scaffold filling problem under the breakpoint distance for the simplest unichromosomal genomes. When the input genome contains no gene repetition (i.e., is a fragment of a permutation), we show that the two-sided scaffold filling problem is polynomially solvable. However, when the input genome contains some genes which appear twice, even the one-sided scaffold filling problem becomes NP-complete. Finally, using the ideas for solving the two-sided scaffold filling problem under the breakpoint distance we show that the two-sided scaffold filling problem under the genomic/rearrangement distance is also polynomially solvable.

  7. Significance of density and demarcation of calcifications in calcifying tendinitis

    Energy Technology Data Exchange (ETDEWEB)

    Uhthoff, H.K.; Sarkar, K.; Hammond, I.

    1982-04-01

    Calcification of tendons can be either degenerative and progressive in nature or reactive and selfhealing. Radiologic examinations permit to distinguish between both kinds. The reactive calcification, known also as calcifying tendinitis, passes through two main phases, the formative and the resorptive phase. Since treatment is different for each phase, their roentgenologic distinction is important. Dense, well demarcated and homogenous calcifications indicate the presence of a formative phase whereas less dense, ill defined and fluffy deposits point toward an ongoing resorption.

  8. Structure and consequences of IGH switch breakpoints in Burkitt lymphoma

    NARCIS (Netherlands)

    Guikema, Jeroen E. J.; Schuuring, Ed; Kluin, Philip M.

    2008-01-01

    The t(8;14) MYC/IGH breakpoint is the hallmark translocation of human Burkitt lymphoma (BL). The translocation breakpoint most often involves the immunoglobulin heavy-chain switch regions and is thought to be brought about by an aberrant class switch recombination (CSR) event. During CSR in normal

  9. Kalman Filter Track Fits and Track Breakpoint Analysis

    CERN Document Server

    Astier, Pierre; Cousins, R D; Letessier-Selvon, A A; Popov, B A; Vinogradova, T G; Astier, Pierre; Cardini, Alessandro; Cousins, Robert D.; Letessier-Selvon, Antoine; Popov, Boris A.; Vinogradova, Tatiana

    2000-01-01

    We give an overview of track fitting using the Kalman filter method in the NOMAD detector at CERN, and emphasize how the wealth of by-product information can be used to analyze track breakpoints (discontinuities in track parameters caused by scattering, decay, etc.). After reviewing how this information has been previously exploited by others, we describe extensions which add power to breakpoint detection and characterization. We show how complete fits to the entire track, with breakpoint parameters added, can be easily obtained from the information from unbroken fits. Tests inspired by the Fisher F-test can then be used to judge breakpoints. Signed quantities (such as change in momentum at the breakpoint) can supplement unsigned quantities such as the various chisquares. We illustrate the method with electrons from real data, and with Monte Carlo simulations of pion decays.

  10. Cat eye syndrome chromosome breakpoint clustering: identification of two intervals also associated with 22q11 deletion syndrome breakpoints.

    Science.gov (United States)

    McTaggart, K E; Budarf, M L; Driscoll, D A; Emanuel, B S; Ferreira, P; McDermid, H E

    1998-01-01

    The supernumerary cat eye syndrome (CES) chromosome is dicentric, containing two copies of 22pter-->q11.2. We have found that the duplication breakpoints are clustered in two intervals. The more proximal, most common interval is the 450-650 kb region between D22S427 and D22S36, which corresponds to the proximal deletion breakpoint interval found in the 22q11 deletion syndrome (DiGeorge/velocardiofacial syndrome). The more distal duplication breakpoint interval falls between CRKL and D22S112, which overlaps with the common distal deletion interval of the 22q11 deletion syndrome. We have therefore classified CES chromosomes into two types based on the location of the two breakpoints required to generate them. The smaller type I CES chromosomes are symmetrical, with both breakpoints located within the proximal interval. The larger type II CES chromosomes are either asymmetrical, with one breakpoint located in each of the two intervals, or symmetrical, with both breakpoints located in the distal interval. The co-localization of the breakpoints of these different syndromes, plus the presence of low-copy repeats adjacent to each interval, suggests the existence of several specific regions of chromosomal instability in 22q11.2 which are involved in the production of both deletions and duplications. Since the phenotype associated with the larger duplication does not appear to be more severe than that of the smaller duplication, determination of the type of CES chromosome does not currently have prognostic value.

  11. Most Jacobsen syndrome deletion breakpoints occur distal to FRA11B.

    Science.gov (United States)

    Michaelis, R C; Velagaleti, G V; Jones, C; Pivnick, E K; Phelan, M C; Boyd, E; Tarleton, J; Wilroy, R S; Tunnacliffe, A; Tharapel, A T

    1998-03-19

    Recent studies have identified a (CCG)n repeat in the 5' untranslated region of the CBL2 protooncogene (11q23.3) and have demonstrated that expansion of this repeat causes expression of the folate-sensitive fragile site FRA11B. It has also been demonstrated that FRA11B is the site of breakage in some cases of Jacobsen syndrome (JS) involving terminal deletions of chromosome 11q. We report on 2 patients with JS and a 46,XX,del(11)(q23.3) karyotype. In both cases, microsatellite and fluorescence in situ hybridization analyses indicated that the deletion breakpoint was approximately 1.5-3 Mb telomeric to FRA11B. There was no evidence of expansion of the CBL2 (CCG)n repeat in the parents of either patient. The deleted chromosome was of paternal origin in both cases, although it was of maternal origin in the cases reported to be caused by FRA11B. These findings and those in previously reported patients suggest that the breakpoint for most 11q deletions in JS patients is telomeric to FRA11B, which raises the possibility that there may be other fragile sites in 11q23.3 in addition to FRA11B. These findings also support previous evidence that there may be a propensity for breakpoints to differ depending on the parental origin of the deleted chromosome.

  12. Isolation of a cosmid clone corresponding to an inv(21) breakpoint of a patient with transient abnormal myelopoiesis

    Energy Technology Data Exchange (ETDEWEB)

    Ohta, Tohru, Nakano, Motoi, Tsujita, Takahiro [Nagasaki Univ. School of Medicine, Nagasaki (Japan)] [and others

    1996-03-01

    Transient abnormal myelopoiesis (TAM) is a leukemoid reaction occurring occasionally in Down syndrome (DS) newborn infants. It has been hypothesized that {open_quotes}disomic homozygosity{close_quotes} in 21-trisomic cells plays an important role in the genesis of TAM, and the putative TAM gene was suggested to be mapped at a 21q11 region. We encountered a DS-associated TAM infant with a 47, XY, inv(21) (q11.1q22.13), +inv(21) (q11.1q22.13) karyotype. On the basis of another presumption that in this patient the putative TAM gene is disrupted by the break, we tried to isolate a breakpoint DNA. FISH analysis with cosmid clones corresponding to various sequence-tagged-site (STS) markers mapped at around 21q11.1-q11.2, we confirmed that the proximal breakpoint of the inv (21) was located between two STSs, G51E07 and D21S215, the latter locus being consistent with the previous tentative mapping. After construction of a cosmid contig encompassing between the two markers, we have isolated a cosmid clone corresponding to the proximal breakpoint of the inversion. This breakpoint was located near a previously identified duplicated region that is homologous to the sequence at 21q22.1. The isolated cosmid clone is useful for analysis of other TAM patients and for a search for a transcript at or flanking the breakpoint. 27 refs., 4 figs.

  13. Characterization of the breakpoints of a polymorphic inversion complex detects strict and broad breakpoint reuse at the molecular level.

    Science.gov (United States)

    Puerma, Eva; Orengo, Dorcas J; Salguero, David; Papaceit, Montserrat; Segarra, Carmen; Aguadé, Montserrat

    2014-09-01

    Inversions are an integral part of structural variation within species, and they play a leading role in genome reorganization across species. Work at both the cytological and genome sequence levels has revealed heterogeneity in the distribution of inversion breakpoints, with some regions being recurrently used. Breakpoint reuse at the molecular level has mostly been assessed for fixed inversions through genome sequence comparison, and therefore rather broadly. Here, we have identified and sequenced the breakpoints of two polymorphic inversions-E1 and E2 that share a breakpoint-in the extant Est and E1 + 2 chromosomal arrangements of Drosophila subobscura. The breakpoints are two medium-sized repeated motifs that mediated the inversions by two different mechanisms: E1 via staggered breaks and subsequent repair and E2 via repeat-mediated ectopic recombination. The fine delimitation of the shared breakpoint revealed its strict reuse at the molecular level regardless of which was the intermediate arrangement. The occurrence of other rearrangements in the most proximal and distal extended breakpoint regions reveals the broad reuse of these regions. This differential degree of fragility might be related to their sharing the presence outside the inverted region of snoRNA-encoding genes. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  14. Molecular population genetics of inversion breakpoint regions in Drosophila pseudoobscura.

    Science.gov (United States)

    Wallace, Andre G; Detweiler, Don; Schaeffer, Stephen W

    2013-07-08

    Paracentric inversions in populations can have a profound effect on the pattern and organization of nucleotide variability along a chromosome. Regions near inversion breakpoints are expected to have greater levels of differentiation because of reduced genetic exchange between different gene arrangements whereas central regions in the inverted segments are predicted to have lower levels of nucleotide differentiation due to greater levels of genetic flux among different karyotypes. We used the inversion polymorphism on the third chromosome of Drosophila pseudoobscura to test these predictions with an analysis of nucleotide diversity of 18 genetic markers near and away from inversion breakpoints. We tested hypotheses about how the presence of different chromosomal arrangements affects the pattern and organization of nucleotide variation. Overall, markers in the distal segment of the chromosome had greater levels of nucleotide heterozygosity than markers within the proximal segment of the chromosome. In addition, our results rejected the hypothesis that the breakpoints of derived inversions will have lower levels of nucleotide variability than breakpoints of ancestral inversions, even when strains with gene conversion events were removed. High levels of linkage disequilibrium were observed within all 11 breakpoint regions as well as between the ends of most proximal and distal breakpoints. The central region of the chromosome had the greatest levels of linkage disequilibrium compared with the proximal and distal regions because this is the region that experiences the highest level of recombination suppression. These data do not fully support the idea that genetic exchange is the sole force that influences genetic variation on inverted chromosomes.

  15. The demarcation of permanent preservation areas along rivers

    Directory of Open Access Journals (Sweden)

    João de Deus Medeiros

    2013-06-01

    Full Text Available Through the analysis of the new Brazilian Forest Code (Law 4,771/65 legislative reform, this paper shows the evolution of legal protection to the riparian system (marginal strips, defined as vegetation strings along rivers and other water bodies, which vary according to the water body width. The demarcation of permanent preservation areas along rivers is a complex process which has led to doubts and conflicts. Riparian systems are spaces aimed at the agricultural expansion and, thus, they’re under pressure. The analysis showed that the limitation posed by the new rule agrees with the principle of reasonableness. The new Brazilian Forest Code review, which is currently included in the National Congress agenda, will be able to positively contribute to achieve the possible and desired balance between respect to the natural environment and expansion of land uses.

  16. Comparison of antimicrobial pharmacokinetic/pharmacodynamic breakpoints with EUCAST and CLSI clinical breakpoints for Gram-positive bacteria.

    Science.gov (United States)

    Asín, Eduardo; Isla, Arantxazu; Canut, Andrés; Rodríguez Gascón, Alicia

    2012-10-01

    This study compared the susceptibility breakpoints based on pharmacokinetic/pharmacodynamic (PK/PD) models and Monte Carlo simulation with those defined by the Clinical and Laboratory Standards Institute (CLSI) and the European Committee on Antimicrobial Susceptibility Testing (EUCAST) for antibiotics used for the treatment of infections caused by Gram-positive bacteria. A secondary objective was to evaluate the probability of achieving the PK/PD target associated with the success of antimicrobial therapy. A 10,000-subject Monte Carlo simulation was executed to evaluate 13 antimicrobials (47 intravenous dosing regimens). Susceptibility data were extracted from the British Society for Antimicrobial Chemotherapy database for bacteraemia isolates. The probability of target attainment and the cumulative fraction of response (CFR) were calculated. No antibiotic was predicted to be effective (CFR≥90%) against all microorganisms. The PK/PD susceptibility breakpoints were also estimated and were compared with CLSI and EUCAST breakpoints. The percentages of strains affected by breakpoint discrepancies were calculated. In the case of β-lactams, breakpoint discrepancies affected CLSI and EUCAST. If this occurs, an isolate will be considered susceptible based on CLSI and EUCAST breakpoints although the PK/PD analysis predicts failure, which may explain treatment failures reported in the literature. This study reinforces the idea of considering not only the antimicrobial activity but also the dosing regimen to increase the probability of clinical success of an antimicrobial treatment. Copyright © 2012 Elsevier B.V. and the International Society of Chemotherapy. All rights reserved.

  17. DNA Probe Pooling for Rapid Delineation of Chromosomal Breakpoints

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Chun-Mei; Kwan, Johnson; Baumgartner, Adolf; Weier, Jingly F.; Wang, Mei; Escudero, Tomas; Munne' , Santiago; Zitzelsberger, Horst F.; Weier, Heinz-Ulrich

    2009-01-30

    Structural chromosome aberrations are hallmarks of many human genetic diseases. The precise mapping of translocation breakpoints in tumors is important for identification of genes with altered levels of expression, prediction of tumor progression, therapy response, or length of disease-free survival as well as the preparation of probes for detection of tumor cells in peripheral blood. Similarly, in vitro fertilization (IVF) and preimplantation genetic diagnosis (PGD) for carriers of balanced, reciprocal translocations benefit from accurate breakpoint maps in the preparation of patient-specific DNA probes followed by a selection of normal or balanced oocytes or embryos. We expedited the process of breakpoint mapping and preparation of case-specific probes by utilizing physically mapped bacterial artificial chromosome (BAC) clones. Historically, breakpoint mapping is based on the definition of the smallest interval between proximal and distal probes. Thus, many of the DNA probes prepared for multi-clone and multi-color mapping experiments do not generate additional information. Our pooling protocol described here with examples from thyroid cancer research and PGD accelerates the delineation of translocation breakpoints without sacrificing resolution. The turnaround time from clone selection to mapping results using tumor or IVF patient samples can be as short as three to four days.

  18. Preoperative iodine staining may complicate the demarcation of esophageal carcinoma.

    Science.gov (United States)

    Asada-Hirayama, Itsuko; Ono, Satoshi; Kodashima, Shinya; Niimi, Keiko; Mochizuki, Satoshi; Yamamichi, Nobutake; Fujishiro, Mitsuhiro; Matsusaka, Keisuke; Fukayama, Masashi; Koike, Kazuhiko

    2013-07-01

    A 53-year-old man was suspected of having an esophageal neoplasm. An endoscopic examination including Lugol chromoendoscopy suggested an esophageal squamous cell neoplasm limited to the lamina propria. A targeted biopsy showed atypical squamous cells, and an endoscopic submucosal dissection was performed 22 days after the previous endoscopy. Although a single 40 mm unstained area was observed by preoperative Lugol chromoendoscopy, intraoperative endoscopy revealed a 25 mm iodine-unstained area, with small unstained areas scattered on the oral side. We included the small unstained areas in the extent of the resection through assessment by preoperative endoscopy. Histopathologically, the tumor extent appeared to coincide with the preoperative assessment. Tumor cells were found in the basal-parabasal layers of the mucosa, in which small unstained areas were scattered, although the superficial layers exhibited well-differentiated cells containing glycogen in the cytoplasm. Although Lugol chromoendoscopy, which can induce chemical esophagitis, is widely used, re-epithelialization after mucosal damage by preoperative iodine staining may complicate the intraoperative demarcation of tumors.

  19. BreakPoint Surveyor: a pipeline for structural variant visualization.

    Science.gov (United States)

    Wyczalkowski, Matthew A; Wylie, Kristine M; Cao, Song; McLellan, Michael D; Flynn, Jennifer; Huang, Mo; Ye, Kai; Fan, Xian; Chen, Ken; Wendl, Michael C; Ding, Li

    2017-10-01

    BreakPoint Surveyor (BPS) is a computational pipeline for the discovery, characterization, and visualization of complex genomic rearrangements, such as viral genome integration, in paired-end sequence data. BPS facilitates interpretation of structural variants by merging structural variant breakpoint predictions, gene exon structure, read depth, and RNA-sequencing expression into a single comprehensive figure. Source code and sample data freely available for download at https://github.com/ding-lab/BreakPointSurveyor, distributed under the GNU GPLv3 license, implemented in R, Python and BASH scripts, and supported on Unix/Linux/OS X operating systems. lding@wustl.edu. Supplementary data are available at Bioinformatics online.

  20. Towns in the Alps: Urbanization Processes, Economic Structure, and Demarcation of European Functional Urban Areas (EFUAs) in the Alps

    National Research Council Canada - National Science Library

    Manfred Perlik; Paul Messerli; Werner Bätzing

    2001-01-01

    .... Instead, it is necessary to demarcate urbanized zones according to functional criteria. This article presents a demarcation of urbanized zones in the Alps based on the French method of European functional urban areas (EFUAs...

  1. Breakpoint or Binder : Religious Engagement in Dutch Civil Society

    NARCIS (Netherlands)

    dr. Gürkan Çelik

    2013-01-01

    Civil society as a social sphere is constantly subjected to change. Using the Dutch context, this article addresses the question whether religiously inspired engagement is a binder or a breakpoint in modern societies. The author examines how religiously inspired people in the Netherlands involve

  2. Reassessment of breakpoints in chromosome 11p15

    NARCIS (Netherlands)

    Henry, I.; van Heyningen, V.; Puech, A.; Scrable, H.; Augereau, P.; Boehm, T.; Rabbitts, T.; Mannens, M.; Rochefort, H.; Jones, C.

    1993-01-01

    Specific tumor-associated rearrangements involving the regions 11p13 and 11p15 have been extensively documented. However, cytogenetic definition of the breakpoints occurring at the boundaries of these two regions was not precise enough to correlate with the molecular data. Using probes corresponding

  3. SVA retrotransposon insertion-associated deletion represents a novel mutational mechanism underlying large genomic copy number changes with non-recurrent breakpoints.

    Science.gov (United States)

    Vogt, Julia; Bengesser, Kathrin; Claes, Kathleen B M; Wimmer, Katharina; Mautner, Victor-Felix; van Minkelen, Rick; Legius, Eric; Brems, Hilde; Upadhyaya, Meena; Högel, Josef; Lazaro, Conxi; Rosenbaum, Thorsten; Bammert, Simone; Messiaen, Ludwine; Cooper, David N; Kehrer-Sawatzki, Hildegard

    2014-06-02

    Genomic disorders are caused by copy number changes that may exhibit recurrent breakpoints processed by nonallelic homologous recombination. However, region-specific disease-associated copy number changes have also been observed which exhibit non-recurrent breakpoints. The mechanisms underlying these non-recurrent copy number changes have not yet been fully elucidated. We analyze large NF1 deletions with non-recurrent breakpoints as a model to investigate the full spectrum of causative mechanisms, and observe that they are mediated by various DNA double strand break repair mechanisms, as well as aberrant replication. Further, two of the 17 NF1 deletions with non-recurrent breakpoints, identified in unrelated patients, occur in association with the concomitant insertion of SINE/variable number of tandem repeats/Alu (SVA) retrotransposons at the deletion breakpoints. The respective breakpoints are refractory to analysis by standard breakpoint-spanning PCRs and are only identified by means of optimized PCR protocols designed to amplify across GC-rich sequences. The SVA elements are integrated within SUZ12P intron 8 in both patients, and were mediated by target-primed reverse transcription of SVA mRNA intermediates derived from retrotranspositionally active source elements. Both SVA insertions occurred during early postzygotic development and are uniquely associated with large deletions of 1 Mb and 867 kb, respectively, at the insertion sites. Since active SVA elements are abundant in the human genome and the retrotranspositional activity of many SVA source elements is high, SVA insertion-associated large genomic deletions encompassing many hundreds of kilobases could constitute a novel and as yet under-appreciated mechanism underlying large-scale copy number changes in the human genome.

  4. Antimicrobial susceptibility of 6 antimicrobial agents in Helicobacter pylori clinical isolates by using EUCAST breakpoints compared with previously used breakpoints.

    Science.gov (United States)

    Alarcón, Teresa; Urruzuno, Pedro; Martínez, Maria Josefa; Domingo, Diego; Llorca, Laura; Correa, Ana; López-Brea, Manuel

    2017-05-01

    The aim of this study was to determine the differences in percentage resistance in H. pylori clinical isolates using EUCAST breakpoints compared with previously used breakpoints. MIC value distribution in H. pylori clinical isolates was also studied. Susceptibility to amoxicillin, tetracycline, metronidazole, clarithromycin, rifampicin and levofloxacin was performed by E-test in 824 H. pylori clinical isolates. EUCAST and previous breakpoints defined resistance as follows: MIC >0.12mg/L and ≥2mg/L for amoxicillin, >8mg/L and ≥8mg/L for metronidazole, >0.5mg/L and ≥1mg/L for clarithromycin, >1mg/L and ≥32mg/L for rifampicin, and >1mg/L and ≥4mg/L for tetracycline and >1mg/L levofloxacin. Overall resistance rate by EUCAST and by previous breakpoints was 8.5% and 3.2% for amoxicillin, 0.6% and 0.1% for tetracycline, 39.2% and 39.7% for metronidazole, 51.2% and 51.2% for clarithromycin, 32% and 3.1% for rifampicin, and 6.7% and 6.7% for levofloxacin. When using the different breakpoints for antimicrobial susceptibility testing, similar results were found with most antibiotics tested (tetracycline, metronidazole, clarithromycin, and levofloxacin), except for amoxicillin and rifampicin. Copyright © 2016 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

  5. COLREGS Demarcation Lines for the United States as of July 2014

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — U.S. collision regulation boundaries are lines of demarcation delineating those waters upon which mariners shall comply with the International Regulations for...

  6. The impact of revised CLSI cefazolin breakpoints on the clinical outcomes of Escherichia coli bacteremia.

    Science.gov (United States)

    Wang, Kung-Ching; Liu, Meei-Fang; Lin, Chin-Fu; Shi, Zhi-Yuan

    2016-10-01

    The susceptibility breakpoints of cephalosporins for Enterobacteriaceae were revised by the Clinical and Laboratory Standards Institute (CLSI) in 2010 and 2011. The clinical outcome and susceptibility data were analyzed to evaluate the impact of revised CLSI cefazolin breakpoints on the treatment of Escherichia coli bacteremia. Forty-three bacteremic Escherichia coli isolates from Taichung Veterans General Hospital, Taichung, Taiwan, during the period from January 2013 to December 2013, were selected to analyze the minimum inhibitory concentration (MIC) distributions of cefazolin and the correlated clinical responses to cefazolin therapy. The modal cefazolin MIC among the 43 isolates was 1 μg/mL and accounted for 18 (42%) isolates. The cumulative percentage for MICs ≤ 2 μg/mL was 79%. The conventional dosing regimens achieved clinical cure in 33 (97%) of 34 patients with bacteremia due to E. coli with a cefazolin MIC ≤ 2 μg/mL, in all of the six patients with a cefazolin MIC of 4 μg/mL, and all of the three patients with a cefazolin MIC of 8 μg/mL. The microbiological data support the revised CLSI breakpoints of cefazolin. The conventional cefazolin dosing regimens can still achieve satisfactory clinical cure rates for bacteremia of E. coli with a cefazolin MIC ≤ 2 μg/mL in patients without severe septic shock. Before the approval of the efficacy of cefazolin for the treatment of E. coli isolates with a cefazolin MIC of 4 μg/mL, it is prudent to use cefazolin only when a high drug level can be achieved in the infection site, such as the urinary tract. Copyright © 2015. Published by Elsevier B.V.

  7. Testing Chromosomal Phylogenies and Inversion Breakpoint Reuse in Drosophila

    Science.gov (United States)

    González, Josefa; Casals, Ferran; Ruiz, Alfredo

    2007-01-01

    A combination of cytogenetic and bioinformatic procedures was used to test the chromosomal phylogeny relating Drosophila buzzatii with D. repleta. Chromosomes X and 2, harboring most of the inversions fixed between these two species, were analyzed. First, chromosomal segments conserved during the divergence of the two species were identified by comparative in situ hybridization to the D. repleta chromosomes of 180 BAC clones from a BAC-based physical map of the D. buzzatii genome. These conserved segments were precisely delimited with the aid of clones containing inversion breakpoints. Then GRIMM software was used to estimate the minimum number of rearrangements necessary to transform one genome into the other and identify all possible rearrangement scenarios. Finally, the most plausible inversion trajectory was tested by hybridizing 12 breakpoint-bearing BAC clones to the chromosomes of seven other species in the repleta group. The results show that chromosomes X and 2 of D. buzzatii and D. repleta differ by 12 paracentric inversions. Nine of them are fixed in chromosome 2 and entail two breakpoint reuses. Our results also show that the cytological relationship between D. repleta and D. mercatorum is closer than that between D. repleta and D. peninsularis, and we propose that the phylogenetic relationships in this lineage of the repleta group be reconsidered. We also estimated the rate of rearrangement between D. repleta and D. buzzatii and conclude that rates within the genus Drosophila vary substantially between lineages, even within a single species group. PMID:17028333

  8. Antimicrobial Susceptibility Breakpoints and First-Step parC Mutations in Streptococcus pneumoniae: Redefining Fluoroquinolone Resistance

    OpenAIRE

    Lim, Sue; Bast, Darrin; McGeer, Allison; de Azavedo, Joyce; Low, Donald E.

    2003-01-01

    Clinical antimicrobial susceptibility breakpoints are used to predict the clinical outcome of antimicrobial treatment. In contrast, microbiologic breakpoints are used to identify isolates that may be categorized as susceptible when applying clinical breakpoints but harbor resistance mechanisms that result in their reduced susceptibility to the agent being tested. Currently, the National Committee for Clinical Laboratory Standards (NCCLS) guidelines utilize clinical breakpoints to characterize...

  9. Molecular cloning and analysis of breakpoints on ring chromosome 17 in a patient with autism.

    Science.gov (United States)

    Vazna, Alzbeta; Havlovicova, Marketa; Sedlacek, Zdenek

    2008-01-15

    The breakpoint junction on a ring chromosome 17 in a girl with autism, mental retardation, mild dysmorphism and neurofibromatosis was identified and analysed at the nucleotide level. The extent of the deleted segments was about 1.9 Mb on 17p and about 1.0 Mb on 17q. The structure of the junction between the 17p and 17q arms, especially the lack of significant homology between the juxtaposed genomic regions and the presence of short microhomology at the junction site, indicated non-homologous end joining as the most likely mechanism leading to the rearrangement. In addition to the 17p-17q junction itself, a de novo 1 kb deletion in a distance of 400 bp from the junction was identified, which arose most likely as a part of the rearrangement. The defect directly inactivated 3 genes, and the deleted terminal chromosome segments harboured 27 and 14 protein-coding genes from 17p and 17q, respectively. Several of the genes affected by the rearrangement are candidates for the symptoms observed in the patient. Additional rearrangements similar to the 1 kb deletion observed in our patient may remain undetected but can participate in the phenotype of patients with chromosomal aberrations. They can also be the reason for repeated failures to clone breakpoint junctions in other patients described in the literature.

  10. A molecular perspective on a complex polymorphic inversion system with cytological evidence of multiply reused breakpoints.

    Science.gov (United States)

    Orengo, D J; Puerma, E; Papaceit, M; Segarra, C; Aguadé, M

    2015-06-01

    Genome sequence comparison across the Drosophila genus revealed that some fixed inversion breakpoints had been multiply reused at this long timescale. Cytological studies of Drosophila inversion polymorphism had previously shown that, also at this shorter timescale, some breakpoints had been multiply reused. The paucity of molecularly characterized polymorphic inversion breakpoints has so far precluded contrasting whether cytologically shared breakpoints of these relatively young inversions are actually reused at the molecular level. The E chromosome of Drosophila subobscura stands out because it presents several inversion complexes. This is the case of the E1+2+9+3 arrangement that originated from the ancestral Est arrangement through the sequential accumulation of four inversions (E1, E2, E9 and E3) sharing some breakpoints. We recently identified the breakpoints of inversions E1 and E2, which allowed establishing reuse at the molecular level of the cytologically shared breakpoint of these inversions. Here, we identified and sequenced the breakpoints of inversions E9 and E3, because they share breakpoints at sections 58D and 64C with those of inversions E1 and E2. This has allowed establishing that E9 and E3 originated through the staggered-break mechanism. Most importantly, sequence comparison has revealed the multiple reuse at the molecular level of the proximal breakpoint (section 58D), which would have been used at least by inversions E2, E9 and E3. In contrast, the distal breakpoint (section 64C) might have been only reused once by inversions E1 and E2, because the distal E3 breakpoint is displaced >70 kb from the other breakpoint limits.

  11. Anatomic demarcation by positional variation in fibroblast gene expression programs.

    Directory of Open Access Journals (Sweden)

    John L Rinn

    2006-07-01

    Full Text Available Fibroblasts are ubiquitous mesenchymal cells with many vital functions during development, tissue repair, and disease. Fibroblasts from different anatomic sites have distinct and characteristic gene expression patterns, but the principles that govern their molecular specialization are poorly understood. Spatial organization of cellular differentiation may be achieved by unique specification of each cell type; alternatively, organization may arise by cells interpreting their position along a coordinate system. Here we test these models by analyzing the genome-wide gene expression profiles of primary fibroblast populations from 43 unique anatomical sites spanning the human body. Large-scale differences in the gene expression programs were related to three anatomic divisions: anterior-posterior (rostral-caudal, proximal-distal, and dermal versus nondermal. A set of 337 genes that varied according to these positional divisions was able to group all 47 samples by their anatomic sites of origin. Genes involved in pattern formation, cell-cell signaling, and matrix remodeling were enriched among this minimal set of positional identifier genes. Many important features of the embryonic pattern of HOX gene expression were retained in fibroblasts and were confirmed both in vitro and in vivo. Together, these findings suggest that site-specific variations in fibroblast gene expression programs are not idiosyncratic but rather are systematically related to their positional identities relative to major anatomic axes.

  12. Improved Approximation for Breakpoint Graph Decomposition and Sorting by Reversals

    DEFF Research Database (Denmark)

    Rizzi, Romeo; Caprara, Alberto

    2002-01-01

    Sorting by Reversals (SBR) is one of the most widely studied models of genome rearrangements in computational molecular biology. At present, 3/2 is the best known approximation ratio achievable in polynomial time for SBR. A very closely related problem, called Breakpoint Graph Decomposition (BGD......! instances of SBR on permutations with n elements. Our result uses the best known approximation algorithms for Stable Set on graphs with maximum degree 4 as well as for Set Packing where the maximum size of a set is 6. Any improvement in the ratio achieved by these approximation algorithms will yield...

  13. Implementation of Objective PASC-Derived Taxon Demarcation Criteria for Official Classification of Filoviruses

    Directory of Open Access Journals (Sweden)

    Yīmíng Bào

    2017-05-01

    Full Text Available The mononegaviral family Filoviridae has eight members assigned to three genera and seven species. Until now, genus and species demarcation were based on arbitrarily chosen filovirus genome sequence divergence values (≈50% for genera, ≈30% for species and arbitrarily chosen phenotypic virus or virion characteristics. Here we report filovirus genome sequence-based taxon demarcation criteria using the publicly accessible PAirwise Sequencing Comparison (PASC tool of the US National Center for Biotechnology Information (Bethesda, MD, USA. Comparison of all available filovirus genomes in GenBank using PASC revealed optimal genus demarcation at the 55–58% sequence diversity threshold range for genera and at the 23–36% sequence diversity threshold range for species. Because these thresholds do not change the current official filovirus classification, these values are now implemented as filovirus taxon demarcation criteria that may solely be used for filovirus classification in case additional data are absent. A near-complete, coding-complete, or complete filovirus genome sequence will now be required to allow official classification of any novel “filovirus.” Classification of filoviruses into existing taxa or determining the need for novel taxa is now straightforward and could even become automated using a presented algorithm/flowchart rooted in RefSeq (type sequences.

  14. Rethinking the deMaRcation of Malachi 2:17-3:5

    African Journals Online (AJOL)

    the implications this new demarcation of Mal. 2:17-3:7a and Mal. 3:7b-12. • have should be considered. BiBliogRaPhY. ACHTEMEIER, E. 1986. Nahum – Malachi. atlanta: John knox. (interpretation). BALDWIN, J.G.. 1972. Haggai, Zechariah, Malachi. An Introduction and Commentary. leicester: inter-Varsity Press. (totc).

  15. Measuring the depth of crosslinking demarcation line in vivo: Comparison of methods and devices.

    Science.gov (United States)

    Thorsrud, Andreas; Sandvik, Gunhild F; Hagem, Anne M; Drolsum, Liv

    2017-02-01

    To assess the interrelationship of different methods of measuring the demarcation line depth after corneal collagen crosslinking (CXL). University eye clinic, Oslo, Norway. Prospective case series. Eyes having CXL for progressive keratoconus were evaluated 1 month after CXL by in vitro confocal microscopy (IVCM), optical coherence tomography (OCT), and Scheimpflug imaging. When applying IVCM, the depth of the CXL demarcation line was measured with 2 methods; that is, IVCM keratocyte disappearance and IVCM intensity increase. With OCT, the evaluations were made by measuring the depth of the corneal stromal demarcation line. Scheimpflug imaging was used with 2 depth-measuring methods; that is manual Scheimpflug and objective Scheimpflug intensity change. The demarcation line depths in the central cornea were compared by the intraclass correlation coefficient (ICC) and pairwise comparison of the measured treated depth. If acceptable correlations (ICC > 0.7) were found, Bland-Altman analysis was performed. Twenty eyes of 20 patients were evaluated. Acceptable correlations were found between depth measurements using OCT-IVCM keratocyte disappearance (ICC = 0.80), OCT-IVCM intensity increase (ICC = 0.75), and IVCM intensity increase-IVCM keratocyte disappearance (ICC = 0.91). The Bland-Altman plots of these 3 pairs showed sufficient levels of agreement. Using pairwise comparison of these pairs, the measured depths were in the same level by the OCT-IVCM intensity increase only (P = .529). Scheimpflug images were inaccurate for measuring the CXL demarcation line depth. The 2 confocal microscopy methods and OCT images showed good correlation. Of these 3 pairs, only measurements with OCT and IVCM intensity increase depths were in the same level. Copyright © 2017 ASCRS and ESCRS. Published by Elsevier Inc. All rights reserved.

  16. Molecular sublocalization and characterization of the 11; 22 translocation breakpoint in a malignant rhabdoid tumor

    Energy Technology Data Exchange (ETDEWEB)

    Newsham, I.; Daub, D.; Besnard-Guerin, C.; Cavenee, W. (Univ. of California, San Diego, CA (United States))

    1994-02-01

    Malignant rhabdoid tumors are extremely aggressive soft-tissue sarcomas that tend to be widely metastatic at diagnosis. These tumors were first described as variants of the kidney neoplasm Wilms' tumor, although tumors of similar clinicopathologic features have been cited in a variety of extrarenal sites. Here, the authors have characterized the chromosomal translocation t(11;22)(p15.5;q11.23) from a retroperitoneal rhabdoid tumor. Somatic cell hybrids with segregated copies of the derivative 11 and derivative 22 chromosomes allowed sublocalization of the chromosome 11 breakpoint to a 1- to 2-Mb region between the proximal marker D11S12 and the distal locus tyrosine hydroxylase (TH). Translocation-associated aberrant fragments were identified by pulsed-field gel electrophoresis, with the smallest resulting from BssHII digestion as detected with a probe for TH. These data indicate that the locus or loci disrupted by this genetic abnormality might lie less than 60 kb proximal to this marker and place it in the chromosomal vicinity of genes involved in the etiologies of rhabdomyosarcoma, Wilms' tumor, and the congenital overgrowth disorder, Beckwith-Wiedemann syndrome. Analysis of two other tumor-associated loci, EWS1 and NF2, that have been mapped to the general region of 22q11.2 indicated that they were not involved in this translocation breakpoint. Isolation of the genes present at this translocation junction on both chromosomes 11 and 22 may yield important clinicopathologic and genetic markers for this enigmatic tumor as well as other pediatric diseases. 45 refs., 3 figs.

  17. European gene mapping project (EUROGEM) : Breakpoint panels for human chromosomes based on the CEPH reference families

    NARCIS (Netherlands)

    Attwood, J; Bryant, SP; Bains, R; Povey, R; Povey, S; Rebello, M; Kapsetaki, M; Moschonas, NK; Grzeschik, KH; Otto, M; Dixon, M; Sudworth, HE; Kooy, RF; Wright, A; Teague, P; Terrenato, L; Vergnaud, G; Monfouilloux, S; Weissenbach, J; Alibert, O; Dib, C; Faure, S; Bakker, E; Pearson, NM; Vossen, RHAM; Gal, A; MuellerMyhsok, B; Cann, HM; Spurr, NK

    1996-01-01

    Meiotic breakpoint panels for human chromosomes 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 14, 15, 17; 18, 20 and X were constructed from genotypes from the CEPH reference families. Each recombinant chromosome included has a breakpoint well-supported with reference to defined quantitative criteria. The panels

  18. Identification of novel cancer fusion genes using chromosome breakpoint screening.

    Science.gov (United States)

    Hua, Kate; Lin, Chin-Hui; Chen, Ya-Lun; Lin, Chi-Hung; Ping, Yueh-Hsin; Jou, Yuh-Shan; Chen, Chian-Feng

    2017-04-01

    Gene fusion due to rearrangement or translocation of chromosomes is a powerful mutational mechanism during tumorigenesis. Several new high-resolution technologies have recently been developed to evaluate large numbers of small aberrations as candidate loci for fusion gene screening. In our previous whole-genome screening study using 500K SNP arrays, we identified more than 700 homozygous deletions (HDs) and amplicons in 23 cancer cell lines. To explore novel fusion genes in cancer, we established stringent criteria for defining HD and amplicon breakpoints. Then genomic PCR and sequencing analyses identified a fusion gene, FNDC3B-PRKCI, that resulted from chromosome intra-rearrangement. Western blotting and 3'-RACE analyses revealed that the chimeric transcript was an in-frame fusion between FNDC3B and PRKCI. Finally, cell migration and colony formation assays suggested that FNDC3B-PRKCI is a potential oncogene.

  19. Characterization of breakpoint regions of large structural autosomal mosaic events.

    Science.gov (United States)

    Machiela, Mitchell J; Jessop, Lea; Zhou, Weiyin; Yeager, Meredith; Chanock, Stephen J

    2017-11-15

    Recent studies have reported a higher than anticipated frequency of large clonal autosomal mosaic events >2 Mb in size in the aging population. Mosaic events are detected from analyses of intensity parameters of linear stretches with deviations in heterozygous probes of single nucleotide polymorphism microarrays. The non-random distribution of detected mosaic events throughout the genome suggests common mechanisms could influence the formation of mosaic events. Here we use publicly available data tracks from the University of California Santa Cruz Genome Browser to investigate the genomic characteristics of the regions at the terminal ends of two frequent types of large structural mosaic events: telomeric neutral events and interstitial losses. We observed breakpoints are more likely to occur in regions enriched for open chromatin, increased gene density, elevated meiotic recombination rates and in the proximity of repetitive elements. These observations suggest that detected mosaic event breakpoints are preferentially recovered in genomic regions that are observed to be active and thus more accessible to environmental exposures and events related to gene transcription. We propose that errors in DNA repair pathways, such as non-homologous end joining and homologous recombination, may be important cellular mechanisms that lead to the formation of large structural mosaic events such as interstitial losses and copy neutral events that include telomeres. Further studies using next generation sequencing technologies should be instrumental in mapping the specific junctions of mosaic events to the nucleotide and provide insights into the molecular mechanisms responsible for clonal somatic structural events. Published by Oxford University Press 2017. This work is written by US Government employees and is in the public domain in the US.

  20. On Computing Breakpoint Distances for Genomes with Duplicate Genes.

    Science.gov (United States)

    Shao, Mingfu; Moret, Bernard M E

    2017-06-01

    A fundamental problem in comparative genomics is to compute the distance between two genomes in terms of its higher level organization (given by genes or syntenic blocks). For two genomes without duplicate genes, we can easily define (and almost always efficiently compute) a variety of distance measures, but the problem is NP-hard under most models when genomes contain duplicate genes. To tackle duplicate genes, three formulations (exemplar, maximum matching, and any matching) have been proposed, all of which aim to build a matching between homologous genes so as to minimize some distance measure. Of the many distance measures, the breakpoint distance (the number of nonconserved adjacencies) was the first one to be studied and remains of significant interest because of its simplicity and model-free property. The three breakpoint distance problems corresponding to the three formulations have been widely studied. Although we provided last year a solution for the exemplar problem that runs very fast on full genomes, computing optimal solutions for the other two problems has remained challenging. In this article, we describe very fast, exact algorithms for these two problems. Our algorithms rely on a compact integer-linear program that we further simplify by developing an algorithm to remove variables, based on new results on the structure of adjacencies and matchings. Through extensive experiments using both simulations and biological data sets, we show that our algorithms run very fast (in seconds) on mammalian genomes and scale well beyond. We also apply these algorithms (as well as the classic orthology tool MSOAR) to create orthology assignment, then compare their quality in terms of both accuracy and coverage. We find that our algorithm for the "any matching" formulation significantly outperforms other methods in terms of accuracy while achieving nearly maximum coverage.

  1. "Bewitching" or confusing methaphysics? The demarcation between science and metaphysics according to Karl Popper

    Directory of Open Access Journals (Sweden)

    M. Elaine Botha

    1986-03-01

    Full Text Available The problems of both classical and modern theory of knowledge, according to Popper, reside in the problem of demarcation: a problem closely re­ lated to the problem of induction. The paper argues the view that Popper's view of metaphysics is ambiguous, requiring another criterion to distinguish between "good " and "bad " metaphysics. The sources of the problem are pinpointed, and Popper's distinction between three types of theory outlined. The article then explores the distinction between types of theories and the issues of falsification, testability and refutation, before going on to a consideration of the relationship between science and metaphysics, and w eighing up the issue of good ancid metaphysics. From this emerges clearly that the second "criterionot demarcation" is needed to make precisely this distinction; also in view of Popper's u n ­ clear, even ambiguous, view of metaphysics.

  2. Structure and population genetics of the breakpoints of a polymorphic inversion in Drosophila subobscura.

    Science.gov (United States)

    Papaceit, Montserrat; Segarra, Carmen; Aguadé, Montserrat

    2013-01-01

    Drosophila subobscura is a paleartic species of the obscura group with a rich chromosomal polymorphism. To further our understanding on the origin of inversions and on how they regain variation, we have identified and sequenced the two breakpoints of a polymorphic inversion of D. subobscura--inversion 3 of the O chromosome--in a population sample. The breakpoints could be identified as two rather short fragments (∼300 bp and 60 bp long) with no similarity to any known transposable element family or repetitive sequence. The presence of the ∼300-bp fragment at the two breakpoints of inverted chromosomes implies its duplication, an indication of the inversion origin via staggered double-strand breaks. Present results and previous findings support that the mode of origin of inversions is neither related to the inversion age nor species-group specific. The breakpoint regions do not consistently exhibit the lower level of variation within and stronger genetic differentiation between arrangements than more internal regions that would be expected, even in moderately small inversions, if gene conversion were greatly restricted at inversion breakpoints. Comparison of the proximal breakpoint region in species of the obscura group shows that this breakpoint lies in a small high-turnover fragment within a long collinear region (∼300 kb). © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

  3. Demarcation of Prime Farmland Protection Areas around a Metropolis Based on High-Resolution Satellite Imagery.

    Science.gov (United States)

    Xia, Nan; Wang, YaJun; Xu, Hao; Sun, YueFan; Yuan, Yi; Cheng, Liang; Jiang, PengHui; Li, ManChun

    2016-12-21

    Prime farmland (PF) is defined as high-quality farmland and a prime farmland protection area (PFPA, including related roads, waters and facilities) is a region designated for the special protection of PF. However, rapid urbanization in China has led to a tremendous farmland loss and to the degradation of farmland quality. Based on remote sensing and geographic information system technology, this study developed a semiautomatic procedure for designating PFPAs using high-resolution satellite imagery (HRSI), which involved object-based image analysis, farmland composite evaluation, and spatial analysis. It was found that the HRSIs can provide elaborate land-use information, and the PFPA demarcation showed strong correlation with the farmland area and patch distance. For the benefit of spatial planning and management, different demarcation rules should be applied for suburban and exurban areas around a metropolis. Finally, the overall accuracy of HRSI classification was about 80% for the study area, and high-quality farmlands from evaluation results were selected as PFs. About 95% of the PFs were demarcated within the PFPAs. The results of this study will be useful for PFPA planning and the methods outlined could help in the automatic designation of PFPAs from the perspective of the spatial science.

  4. Segmental Duplication, Microinversion, and Gene Loss Associated with a Complex Inversion Breakpoint Region in Drosophila

    Science.gov (United States)

    Calvete, Oriol; González, Josefa; Betrán, Esther; Ruiz, Alfredo

    2012-01-01

    Chromosomal inversions are usually portrayed as simple two-breakpoint rearrangements changing gene order but not gene number or structure. However, increasing evidence suggests that inversion breakpoints may often have a complex structure and entail gene duplications with potential functional consequences. Here, we used a combination of different techniques to investigate the breakpoint structure and the functional consequences of a complex rearrangement fixed in Drosophila buzzatii and comprising two tandemly arranged inversions sharing the middle breakpoint: 2m and 2n. By comparing the sequence in the breakpoint regions between D. buzzatii (inverted chromosome) and D. mojavensis (noninverted chromosome), we corroborate the breakpoint reuse at the molecular level and infer that inversion 2m was associated with a duplication of a ∼13 kb segment and likely generated by staggered breaks plus repair by nonhomologous end joining. The duplicated segment contained the gene CG4673, involved in nuclear transport, and its two nested genes CG5071 and CG5079. Interestingly, we found that other than the inversion and the associated duplication, both breakpoints suffered additional rearrangements, that is, the proximal breakpoint experienced a microinversion event associated at both ends with a 121-bp long duplication that contains a promoter. As a consequence of all these different rearrangements, CG5079 has been lost from the genome, CG5071 is now a single copy nonnested gene, and CG4673 has a transcript ∼9 kb shorter and seems to have acquired a more complex gene regulation. Our results illustrate the complex effects of chromosomal rearrangements and highlight the need of complementing genomic approaches with detailed sequence-level and functional analyses of breakpoint regions if we are to fully understand genome structure, function, and evolutionary dynamics. PMID:22328714

  5. Impact of CLSI Breakpoint Changes on Microbiology Laboratories and Antimicrobial Stewardship Programs.

    Science.gov (United States)

    Heil, Emily L; Johnson, J Kristie

    2016-04-01

    In 2010, the Clinical and Laboratory Standards Institute (CLSI) lowered the MIC breakpoints for many beta-lactam antibiotics to enhance detection of known resistance amongEnterobacteriaceae The decision to implement these new breakpoints, including the changes announced in both 2010 and 2014, can have a significant impact on both microbiology laboratories and antimicrobial stewardship programs. In this commentary, we discuss the changes and how implementation of these updated CLSI breakpoints requires partnership between antimicrobial stewardship programs and the microbiology laboratory, including data on the impact that the changes had on antibiotic usage at our own institution. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  6. Co-localisation of CCG repeats and chromosome deletion breakpoints in Jacobsen syndrome: evidence for a common mechanism of chromosome breakage.

    Science.gov (United States)

    Jones, C; Müllenbach, R; Grossfeld, P; Auer, R; Favier, R; Chien, K; James, M; Tunnacliffe, A; Cotter, F

    2000-05-01

    Folate-sensitive fragile sites are associated with the expansion and hypermethylation of CCG-repeats. The fragile site in 11q23.3, FRA11B, has been shown to cause chromosome deletions in vivo, its expression being associated with Jacobsen (11q-) syndrome. However, the majority of Jacobsen deletions are distal to FRA11B and are not related to its expression. To test the hypothesis that other unidentified fragile sites might be located in 11q23.3-24 and may cause these deletions, we have identified and characterised CCG-trinucleotide repeats within a 40 Mb YAC contig spanning distal chromosome 11q. Only eight CCG-repeats were identified within the entire YAC contig (not including FRA11B ), six of which map to the region of 11q23.3-24 that includes Jacobsen deletions. We have previously collated the deletion mapping data of 24 Jacobsen patients with the physical map of chromosome 11q, and accurately localised six breakpoints to short intervals corresponding to individual YAC clones. We now show that in each of these cases, YAC clones found to contain a deletion breakpoint also contain a CCG-repeat. The improved analysis of one of these deletions, together with those of several new Jacobsen cases, further strengthens this association by localising five breakpoints to individual PAC clones containing CCG-repeats. These data provide strong evidence for the non-random clustering of chromosome deletion breakpoints with CCG-repeats, and suggests that they may play an important role in a common mechanism of chromosome breakage.

  7. Tourette syndrome in a pedigree with a 7;18 translocation: Identification of a YAC spanning the translocation breakpoint at 18q22.3

    Energy Technology Data Exchange (ETDEWEB)

    Boghosian-Sell, L.; Overhauser, J. [Thomas Jefferson Univ., Philadelphia, PA (United States); Comings, D.E. [City of Hope Medical Center, Duarte, CA (United States)

    1996-11-01

    Tourette syndrome is a neuropsychiatric disorder characterized by the presence of multiple, involuntary motor and vocal tics. Associated pathologies include attention deficit disorder and obsessive-compulsive disorder (OCD). Extensive linkage analysis based on an autosomal dominant mode of transmission with reduced penetrance has failed to show linkage with polymorphic markers, suggesting either locus heterogeneity or a polygenic origin for Tourette syndrome. An individual diagnosed with Tourette syndrome has been described carrying a constitutional chromosome translocation. Other family members carrying the translocation exhibit features seen in Tourette syndrome including motor tics, vocal tics, and OCD. Since the disruption of specific genes by a chromosomal rearrangement can elicit a particular phenotype, we have undertaken the physical mapping of the 7;18 translocation such that genes mapping at the site of the breakpoint can be identified and evaluated for a possible involvement in Tourette syndrome. Using somatic cell hybrids retaining either the der(7) or the der(18), a more precise localization of the breakpoints on chromosomes 7 and 18 have been determined. Furthermore, physical mapping has identified two YAC clones that span the translocation breakpoint on chromosome 18 as determined by FISH. These YAC clones will be useful for the eventual identification of genes that map to chromosomes 7 and 18 at the site of the translocation. 41 refs., 3 figs., 1 tab.

  8. Breakpoint localization of the marker chromosome associated with the cat eye syndrome.

    Science.gov (United States)

    Duncan, A M; Hough, C A; White, B N; McDermid, H E

    1986-01-01

    We investigated the breakpoints involved in the generation of the supernumerary bisatellited chromosome associated with the Cat Eye syndrome. In situ hybridization of DNA probes from band 22q11 revealed that, for two individuals with the Cat Eye syndrome, both breakpoints for the bisatellited chromosome were distal to the DNA sequence corresponding to probe D22S9 and proximal to the immunoglobulin C lambda genes and to at least one subgroup of the V lambda genes. PMID:3088989

  9. Breakpoint localization of the marker chromosome associated with the cat eye syndrome.

    OpenAIRE

    Duncan, A M; Hough, C A; White, B N; McDermid, H E

    1986-01-01

    We investigated the breakpoints involved in the generation of the supernumerary bisatellited chromosome associated with the Cat Eye syndrome. In situ hybridization of DNA probes from band 22q11 revealed that, for two individuals with the Cat Eye syndrome, both breakpoints for the bisatellited chromosome were distal to the DNA sequence corresponding to probe D22S9 and proximal to the immunoglobulin C lambda genes and to at least one subgroup of the V lambda genes.

  10. Pharmacodynamics of Doxycycline and Tetracycline against Staphylococcus pseudintermedius: Proposal of Canine-Specific Breakpoints for Doxycycline

    Science.gov (United States)

    Papich, Mark G.; Turnidge, John; Guardabassi, Luca

    2013-01-01

    Doxycycline is a tetracycline that has been licensed for veterinary use in some countries, but no clinical breakpoints are available for veterinary pathogens. The objectives of this study were (i) to establish breakpoints for doxycycline and (ii) to evaluate the use of tetracycline as a surrogate to predict the doxycycline susceptibility of Staphylococcus pseudintermedius isolates. MICs and inhibition zone diameters were determined for 168 canine S. pseudintermedius isolates according to Clinical and Laboratory Standards Institute (CLSI) standards. Tetracycline resistance genes were detected by PCR, and time-kill curves were determined for representative strains. In vitro pharmacodynamic and target animal pharmacokinetic data were analyzed by Monte Carlo simulation (MCS) for the development of MIC interpretive criteria. Optimal zone diameter breakpoints were defined using the standard error rate-bounded method. The two drugs displayed bacteriostatic activity and bimodal MIC distributions. Doxycycline was more active than tetracycline in non-wild-type strains. MCS and target attainment analysis indicated a certainty of ≥90% for attaining an area under the curve (AUC)/MIC ratio of >25 with a standard dosage of doxycycline (5 mg/kg of body weight every 12 h) for strains with MICs of ≤0.125 μg/ml. Tetracycline predicted doxycycline susceptibility, but current tetracycline breakpoints were inappropriate for the interpretation of doxycycline susceptibility results. Accordingly, canine-specific doxycycline MIC breakpoints (susceptible, ≤0.125 μg/ml; intermediate, 0.25 μg/ml; resistant, ≥0.5 μg/ml) and zone diameter breakpoints (susceptible, ≥25 mm; intermediate, 21 to 24 mm; resistant, ≤20 mm) and surrogate tetracycline MIC breakpoints (susceptible, ≤0.25 μg/ml; intermediate, 0.5 μg/ml; resistant, ≥1 μg/ml) and zone diameter breakpoints (susceptible, ≥23 mm; intermediate, 18 to 22 mm; resistant, ≤17 mm) were proposed based on the data generated

  11. Targeted next-generation sequencing at copy-number breakpoints for personalized analysis of rearranged ends in solid tumors.

    Directory of Open Access Journals (Sweden)

    Hyun-Kyoung Kim

    Full Text Available BACKGROUND: The concept of the utilization of rearranged ends for development of personalized biomarkers has attracted much attention owing to its clinical applicability. Although targeted next-generation sequencing (NGS for recurrent rearrangements has been successful in hematologic malignancies, its application to solid tumors is problematic due to the paucity of recurrent translocations. However, copy-number breakpoints (CNBs, which are abundant in solid tumors, can be utilized for identification of rearranged ends. METHOD: As a proof of concept, we performed targeted next-generation sequencing at copy-number breakpoints (TNGS-CNB in nine colon cancer cases including seven primary cancers and two cell lines, COLO205 and SW620. For deduction of CNBs, we developed a novel competitive single-nucleotide polymorphism (cSNP microarray method entailing CNB-region refinement by competitor DNA. RESULT: Using TNGS-CNB, 19 specific rearrangements out of 91 CNBs (20.9% were identified, and two polymerase chain reaction (PCR-amplifiable rearrangements were obtained in six cases (66.7%. And significantly, TNGS-CNB, with its high positive identification rate (82.6% of PCR-amplifiable rearrangements at candidate sites (19/23, just from filtering of aligned sequences, requires little effort for validation. CONCLUSION: Our results indicate that TNGS-CNB, with its utility for identification of rearrangements in solid tumors, can be successfully applied in the clinical laboratory for cancer-relapse and therapy-response monitoring.

  12. Identification of chromosome 7 inversion breakpoints in an autistic family narrows candidate region for autism susceptibility.

    Science.gov (United States)

    Cukier, Holly N; Skaar, David A; Rayner-Evans, Melissa Y; Konidari, Ioanna; Whitehead, Patrice L; Jaworski, James M; Cuccaro, Michael L; Pericak-Vance, Margaret A; Gilbert, John R

    2009-10-01

    Chromosomal breaks and rearrangements have been observed in conjunction with autism and autistic spectrum disorders. A chromosomal inversion has been previously reported in autistic siblings, spanning the region from approximately 7q22.1 to 7q31. This family is distinguished by having multiple individuals with autism and associated disabilities. The region containing the inversion has been strongly implicated in autism by multiple linkage studies, and has been particularly associated with language defects in autism as well as in other disorders with language components. Mapping of the inversion breakpoints by FISH has localized the inversion to the region spanning approximately 99-108.75 Mb of chromosome 7. The proximal breakpoint has the potential to disrupt either the coding sequence or regulatory regions of a number of cytochrome P450 genes while the distal region falls in a relative gene desert. Copy number variant analysis of the breakpoint regions detected no duplication or deletion that could clearly be associated with disease status. Association analysis in our autism data set using single nucleotide polymorphisms located near the breakpoints showed no significant association with proximal breakpoint markers, but has identified markers near the distal breakpoint ( approximately 108-110 Mb) with significant associations to autism. The chromosomal abnormality in this family strengthens the case for an autism susceptibility gene in the chromosome 7q22-31 region and targets a candidate region for further investigation.

  13. Impact of minimal inhibitory concentration breakpoints on local cumulative bacterial susceptibility data and antibiotic consumption.

    Science.gov (United States)

    Stokkou, Sofia; Tammer, Ina; Zibolka, Stefanie; Grabau, Christina; Geginat, Gernot

    2014-09-03

    The phenotypic antimicrobial susceptibility testing (AST) of bacteria depends on minimal inhibitory concentration breakpoints issued by national and international breakpoint committees. The current study was performed in order to test the influence of different AST standards on local cumulative AST data and on antibiotic consumption. Automated AST was performed with clinical isolates of Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, Staphylococcus aureus, coagulase-negative staphylococci, Enterococcus faecalis, and E. faecium. From each species 100 prospectively collected non-duplicate clinical isolates were tested and MIC data were interpreted according to the interpretation standards issued by DIN and EUCAST, respectively. In addition cumulative AST data from clinical isolates and antibiotic consumption were monitored before and after implementation of new EUCAST MIC breakpoints. The susceptibility rate of P. aeruginosa against piperacillin and gentamicin, and of C. freundii against piperacillin/tazobactam increased significantly, whereas the susceptibility rates of E. cloacae, S. marcescens, and M. morganii against ciprofloxacin decreased significantly after switching from DIN to EUCAST MIC breakpoints. These changes in the cumulative antibiotic resistance pattern were reflected by enhanced consumption of piperacillin/tazobactam after implementation of EUCAST MIC breakpoints. These data show that changes of AST breakpoints have a significant influence on local cumulative AST data and on antibiotic consumption.

  14. Demarcating Games and Play: Empathizing and systematizing as modes of being in the world

    DEFF Research Database (Denmark)

    Nielsen, Rune Kristian; Hammar, Emil

    This paper problematizes the assumption that the essence of ‘game’ and ‘play’ can somehow be distilled into a set of necessary and sufficient conditions for a phenomenon to be demarcated as ‘game’ and ‘play’. This is the notion that it is possible to come up with a definition of the necessary and...... means a proportional decrease in the other. This position is put to the point by putting the empathizing-systematizing framework into context with FIFA13....

  15. Demarcation laser photocoagulation induced retinal necrosis and rupture resulting in large retinal tear formation.

    Science.gov (United States)

    Quezada, Carlos; Pieramici, Dante J; Matsui, Rodrigo; Rabena, Melvin; Graue, Federico

    2015-06-01

    Retinal tears after laser photocoagulation are a rare complication that occurs after intense laser. It is talked about among retina specialist occurring particularly at the end of a surgical case while applying endophotocoagulation; to the best our knowledge, there are no reports in the literature of a large retinal tear induced after attempted in-office demarcation laser photocoagulation (DLP) that simulated a giant retinal tear. DLP has been employed in the management of selected cases of macula sparring rhegmatogenous retinal detachment (RRD). Even though extension of the retinal detachment through the "laser barrier" is considered a failure of treatment, few complications have been described with the use of this less invasive retinal detachment repair technique. We describe a case of a high myopic woman who initially was treated with demarcation laser photocoagulation for an asymptomatic retinal detachment associated with a single horseshoe tear and a full thickness large retinal tear was created where the laser was placed. Intense laser photocoagulation resulted in abrupt laser induced retinal necrosis and rupture creating this large retinal break. Proper laser technique should reduce the risks associated with this procedure. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. Missing mediated interruptions in manual assembly: Critical aspects of breakpoint selection.

    Science.gov (United States)

    Kolbeinsson, Ari; Lindblom, Jessica; Thorvald, Peter

    2017-05-01

    The factory of the future aims to make manufacturing more effective and easily customisable, using advanced sensors and communications to support information management. In this paper, we examine how breakpoint selection during interruption management can fail, even when using recommendations for interruption management from existing research. We present an experiment based on prior work where mediated interruptions (i.e. smart interruptions that should interrupt at opportune moments) were missed by participants when sent at one of two pre-defined breakpoints. These breakpoints were selected based on existing research to minimise the cost of interruption, which can involve longer times to complete tasks as well as making errors on tasks. Missing mediated interruptions in this way was unexpected, and the prior study was not configured to measure this effect, which has led to the experiment detailed here. We strive to explore whether there is a risk of missing notifications when mediated interruptions are used, and how this is affected by breakpoint selection. This was investigated through an experiment that uses tasks and environments that simulate a manufacturing assembly facility. The results indicate that the effect exists, i.e. that participants miss significantly more notifications when interrupted at fine breakpoints than when interrupted at coarse breakpoints. An embodied cognition perspective was used for analysis of the tasks to understand the cause of the effect. This analysis shows that an overlap between "action" and "anticipation of action" can account for why participants miss notifications at fine breakpoints. Based on these findings, recommendations were developed for designing interruption systems that minimise the costs (errors and time) imposed by interruptions during assembly tasks in manufacturing. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Cloning and characterization of the t(15;17) translocation breakpoint region in acute promyelocytic leukemia.

    Science.gov (United States)

    Lemons, R S; Eilender, D; Waldmann, R A; Rebentisch, M; Frej, A K; Ledbetter, D H; Willman, C; McConnell, T; O'Connell, P

    1990-07-01

    A reciprocal chromosomal translocation, t(15;17)(q22;q11.2-12), is characteristic of acute promyelocytic leukemia (APL) of French-American-British (FAB) subtype M3, and is not associated with any other human malignancy. The non-random pattern of the APL translocations suggests that specific genes on chromosomes 15 and 17 are somehow altered or deregulated as a consequence of the rearrangement. Translocation breakpoints in APL patients provide physical landmarks that suggest an approach to isolating the APL gene(s). Genetic and physical maps constructed for the APL breakpoint region on chromosome 17 have indicated that two fully-linked DNA markers, defining loci for THRA1 and D17S80, map to opposite sides of an APL breakpoint yet reside on a common 350-kb Clal fragment. Cosmid-walking experiments to clone this APL breakpoint have revealed a 38-kilobase deletion on chromosome 17. Studies in additional APL patients have shown that the breakpoint region on chromosome 17 spans at least 80 kilobases.

  18. A novel approach for determining cancer genomic breakpoints in the presence of normal DNA.

    Directory of Open Access Journals (Sweden)

    Yu-Tsueng Liu

    2007-04-01

    Full Text Available CDKN2A (encodes p16(INK4A and p14(ARF deletion, which results in both Rb and p53 inactivation, is the most common chromosomal anomaly in human cancers. To precisely map the deletion breakpoints is important to understanding the molecular mechanism of genomic rearrangement and may also be useful for clinical applications. However, current methods for determining the breakpoint are either of low resolution or require the isolation of relatively pure cancer cells, which can be difficult for clinical samples that are typically contaminated with various amounts of normal host cells. To overcome this hurdle, we have developed a novel approach, designated Primer Approximation Multiplex PCR (PAMP, for enriching breakpoint sequences followed by genomic tiling array hybridization to locate the breakpoints. In a series of proof-of-concept experiments, we were able to identify cancer-derived CDKN2A genomic breakpoints when more than 99.9% of wild type genome was present in a model system. This design can be scaled up with bioinformatics support and can be applied to validate other candidate cancer-associated loci that are revealed by other more systemic but lower throughput assays.

  19. Evolutionary breakpoint analysis on Y chromosomes of higher primates provides insight into human Y evolution.

    Science.gov (United States)

    Wimmer, R; Kirsch, S; Rappold, G A; Schempp, W

    2005-01-01

    Comparative FISH mapping of PAC clones covering almost 3 Mb of the human AZFa region in Yq11.21 to metaphases of human and great apes unravels breakpoints that were involved in species-specific Y chromosome evolution. An astonishing clustering of evolutionary breakpoints was detected in the very proximal region on the long arm of the human Y chromosome in Yq11.21. These breakpoints were involved in deletions, one specific for the human and another for the orang-utan Y chromosome, in a duplicative translocation/transposition specific for bonobo and chimpanzee Y chromosomes and in a pericentric inversion specific for the gorilla Y chromosome. In addition, our comparative results allow the deduction of a model for the human Y chromosome evolution. Copyright (c) 2005 S. Karger AG, Basel.

  20. Reduced cross-linking demarcation line depth at the peripheral cornea after corneal collagen cross-linking.

    Science.gov (United States)

    Yam, Jason C S; Cheng, Arthur C K

    2013-01-01

    To compare the corneal collagen cross-linking (CXL) demarcation line depth between the central and peripheral cornea after cross-linking using anterior segment optical coherence tomography. Retrospective interventional case series of 38 eyes with keratoconus or postoperative LASIK ectasia treated with riboflavin ultraviolet A CXL (UV-X, IROC). CXL demarcation line depth, corneal thickness, and the ratio of the CXL demarcation line depth to the corneal thickness were measured using anterior segment optical coherence tomography at the central cornea and at 2 and 4 mm from the corneal center in four regions: temporal, nasal, superior, and inferior. The CXL demarcation line depths at the center and periphery were compared using the Friedman test. The CXL demarcation line was deepest in the central cornea (302 μm; range: 180 to 397 μm) and was reduced progressively toward the peripheral cornea, at nasal 2 mm (289.5 μm; range: 125 to 370 μm), at nasal 4 mm (206.5 μm; range: 100 to 307 μm), at temporal 2 mm (278.5 μm; range: 128 to 375 μm), and at temporal 4 mm (194 μm; range: 80 to 325 μm) (Pcornea (64.8%; range: 44% to 80%) and was decreased toward the periphery, at nasal 2 mm (53.8%; range: 30% to 74%), at nasal 4 mm (33.8%; range: 19% to 53%), at temporal 2 mm (54.1%; range: 29% to 77%), and at temporal 4 mm (34.1%; range: 15% to 54%) (P⩽.001). Both the CXL demarcation line depth and its proportion over the corneal thickness were greater at the central cornea than the peripheral cornea. Copyright 2013, SLACK Incorporated.

  1. Cosmology at the Crossroads of the Natural and Human Sciences: is demarcation possible?

    CERN Document Server

    Nesteruk, Alexei V

    2011-01-01

    The paper discusses the problem of demarcation between the dimensions of natural and the human sciences in contemporary cosmology. In spite of a common presumption that cosmology is a natural science, the specificity of its alleged subject matter, that is the universe as a whole, makes cosmology fundamentally different from other natural sciences. The reason is that in cosmology the subject of cosmological research and its "object" are in a certain sense inseparable. Any study of the universe involves two opposite perspectives which can be described as "a-cosmic" and "cosmic", egocentric and non-egocentric. Cosmology involves two languages, namely that of physical causality (pertaining to the natural sciences) and that of intentionality (pertaining to the human sciences). On the one hand the universe can be seen as a product of discursive reason, that is as an abstract "physical" entity unfolding in space and time. On the other hand the universe can be experienced through our participation in, or communion wi...

  2. Intracranial pressure following complete removal of a small demarcated brain tumor

    DEFF Research Database (Denmark)

    Andresen, Morten; Juhler, Marianne

    2014-01-01

    and therapeutic purposes. This study documents normal ICP in humans. METHODS: In this study the authors included adult patients scheduled for complete removal of a solitary, clearly demarcated, small brain tumor. The mean age of these patients was 67 years old (range 58-85 years old). Exclusion criteria were...... human brain decreases to negative values when assuming the upright position. If these results are later confirmed in a larger series, they might provide reference values for diagnosis and treatment in patients with CSF-related disorders. New normal values also have implications for future shunt design...... intended to create a study population with as normal brains as possible. A new telemetric ICP monitoring device was implanted at the end of surgery and monitoring was conducted 2 and 4 weeks postoperatively. RESULTS: In the supine position, mean ICP was 0.5 ± 4.0 mm Hg at 4 weeks postoperatively. Postural...

  3. The rise and fall of breakpoint reuse depending on genome resolution

    Science.gov (United States)

    2011-01-01

    Background During evolution, large-scale genome rearrangements of chromosomes shuffle the order of homologous genome sequences ("synteny blocks") across species. Some years ago, a controversy erupted in genome rearrangement studies over whether rearrangements recur, causing breakpoints to be reused. Methods We investigate this controversial issue using the synteny block's for human-mouse-rat reported by Bourque et al. and a series of synteny blocks we generated using Mauve at resolutions ranging from coarse to very fine-scale. We conducted analyses to test how resolution affects the traditional measure of the breakpoint reuse rate. Results We found that the inversion-based breakpoint reuse rate is low at fine-scale synteny block resolution and that it rises and eventually falls as synteny block resolution decreases. By analyzing the cycle structure of the breakpoint graph of human-mouse-rat synteny blocks for human-mouse and comparing with theoretically derived distributions for random genome rearrangements, we showed that the implied genome rearrangements at each level of resolution become more “random” as synteny block resolution diminishes. At highest synteny block resolutions the Hannenhalli-Pevzner inversion distance deviates from the Double Cut and Join distance, possibly due to small-scale transpositions or simply due to inclusion of erroneous synteny blocks. At synteny block resolutions as coarse as the Bourque et al. blocks, we show the breakpoint graph cycle structure has already converged to the pattern expected for a random distribution of synteny blocks. Conclusions The inferred breakpoint reuse rate depends on synteny block resolution in human-mouse genome comparisons. At fine-scale resolution, the cycle structure for the transformation appears less random compared to that for coarse resolution. Small synteny blocks may contain critical information for accurate reconstruction of genome rearrangement history and parameters. PMID:22151330

  4. Performance of Vitek 2 for antimicrobial susceptibility testing of Enterobacteriaceae with Vitek 2 (2009 FDA) and 2014 CLSI breakpoints.

    Science.gov (United States)

    Bobenchik, April M; Deak, Eszter; Hindler, Janet A; Charlton, Carmen L; Humphries, Romney M

    2015-03-01

    Vitek 2 (bioMérieux Inc., Durham, NC) is a widely used commercial antimicrobial susceptibility test system. We compared the MIC results obtained using the Vitek 2 AST-GN69 and AST-XN06 cards to those obtained by CLSI broth microdilution (BMD) for 255 isolates of Enterobacteriaceae, including 25 isolates of carbapenem-resistant Enterobacteriaceae. In total, 25 antimicrobial agents were examined. For 10 agents, the MIC data were evaluated using two sets of breakpoints: (i) the Vitek 2 breakpoints, which utilized the 2009 FDA breakpoints at the time of the study and are equivalent to the 2009 CLSI M100-S19 breakpoints, and (ii) the 2014 CLSI M100-S24 breakpoints. There was an overall 98.7% essential agreement (EA). The categorical agreement was 95.5% (CA) using the Vitek 2 breakpoints and 95.7% using the CLSI breakpoints. There was 1 very major error (VME) (0.05%) observed using the Vitek 2 breakpoints (cefazolin) and 8 VMEs (0.5%) using the CLSI breakpoints (2 each for aztreonam, cefepime, and ceftriaxone, and 1 for cefazolin and ceftazidime). Fifteen major errors (MEs) (0.4%) were noted using the Vitek 2 breakpoints and 8 (0.5%) using the CLSI breakpoints. Overall, the Vitek 2 performance was comparable to that of BMD for testing a limited number of Enterobacteriaceae commonly isolated by clinical laboratories. Ongoing studies are warranted to assess performance in isolates with emerging resistance. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  5. Evolutionary history of the third chromosome gene arrangements of Drosophila pseudoobscura inferred from inversion breakpoints.

    Science.gov (United States)

    Wallace, Andre G; Detweiler, Don; Schaeffer, Stephen W

    2011-08-01

    The third chromosome of Drosophila pseudoobscura is polymorphic for numerous gene arrangements that form classical clines in North America. The polytene salivary chromosomes isolated from natural populations revealed changes in gene order that allowed the different gene arrangements to be linked together by paracentric inversions representing one of the first cases where genetic data were used to construct a phylogeny. Although the inversion phylogeny can be used to determine the relationships among the gene arrangements, the cytogenetic data are unable to infer the ancestral arrangement or the age of the different chromosome types. These are both important properties if one is to infer the evolutionary forces responsible for the spread and maintenance of the chromosomes. Here, we employ the nucleotide sequences of 18 regions distributed across the third chromosome in 80-100 D. pseudoobscura strains to test whether five gene arrangements are of unique or multiple origin, what the ancestral arrangement was, and what are the ages of the different arrangements. Each strain carried one of six commonly found gene arrangements and the sequences were used to infer their evolutionary relationships. Breakpoint regions in the center of the chromosome supported monophyly of the gene arrangements, whereas regions at the ends of the chromosome gave phylogenies that provided less support for monophyly of the chromosomes either because the individual markers did not have enough phylogenetically informative sites or genetic exchange scrambled information among the gene arrangements. A data set where the genetic markers were concatenated strongly supported a unique origin of the different gene arrangements. The inversion polymorphism of D. pseudoobscura is estimated to be about a million years old. We have also shown that the generated phylogeny is consistent with the cytological phylogeny of this species. In addition, the data presented here support hypothetical as the ancestral

  6. Less medical intervention after sharp demarcation of grade 1-2 cervical intraepithelial neoplasia smears by neural network screening

    NARCIS (Netherlands)

    Kok, MR; Boon, ME; Schreiner-Kok, PG; Hermans, J; Grobbee, DE; Kok, LP

    2001-01-01

    BACKGROUND. Neural network technology has been used for the daily screening of cervical smears in The Netherlands since 1992. The authors believe this method might have the potential to demarcate diagnoses of Grade 1-2 cervical intraepithelial neoplasia (CIN 1-2). METHODS. Of 133,196 women who were

  7. The demarcation of Globodera rostochiensis and Globodera pallida infestations in fields for seed potatoes, using a Monte Carlo approach

    NARCIS (Netherlands)

    Schomaker, C.H.; Been, T.H.

    2010-01-01

    A Monte Carlo approach was utilized to calculate the size of the demarcation unit, necessary to cover infestations with Globodera rostochiensis and Globodera pallida (PCN), detected with the new EU-sampling method. Results from 90 sampled fields were used to obtain frequency distributions of the

  8. The Impact of the Issue of Demarcation on Pre-Service Teachers' Beliefs on the Nature of Science

    Science.gov (United States)

    Turgut, Halil; Akcay, Hakan; Irez, Serhat

    2010-01-01

    The arguments about the dimensions of nature of science and the strategies for teaching it are still controversial. In this research, as part of these arguments, a context based on the issue of demarcation of science from pseudoscience was offered and questioned for its effectiveness in nature of science teaching. The research was planned for an…

  9. Evaluation of canine-specific minocycline and doxycycline susceptibility breakpoints for meticillin-resistant Staphylococcus pseudintermedius isolates from dogs.

    Science.gov (United States)

    Hnot, Melanie L; Cole, Lynette K; Lorch, Gwendolen; Papich, Mark G; Rajala-Schultz, Paivi J; Daniels, Joshua B

    2015-10-01

    Using the US Clinical and Laboratory Standards Institute (CLSI) human tetracycline breakpoints to predict minocycline and doxycycline susceptibility of Staphylococcus pseudintermedius (SP) isolates from dogs is not appropriate because they are too high to meet pharmacokinetic/pharmacodynamic data using a standard dose. New breakpoints have been approved for doxycycline and proposed for minocycline. Revised breakpoints are four dilutions lower than tetracycline breakpoints, providing a more conservative standard for classification of isolates. The objectives of this study were to measure minimum inhibitory concentrations (MICs) of minocycline and doxycycline of 100 canine meticillin-resistant SP clinical isolates, compare their susceptibilities to minocycline and doxycycline based on current and revised standards, and document their tetracycline resistance genes. E-test strips were used to determine MICs. PCR was used to identify tet genes. Using the human tetracycline breakpoint of MIC ≤ 4 μg/mL, 76 isolates were susceptible to minocycline and 36 isolates were susceptible to doxycycline. In contrast, using the proposed minocycline breakpoint (MIC ≤ 0.25 μg/mL) and approved doxycycline breakpoint (MIC ≤ 0.125 μg/mL), 31 isolates were susceptible to both minocycline and doxycycline. Thirty-one isolates carried no tet genes, two had tet(K) and 67 had tet(M). Use of the human tetracycline breakpoints misclassified 45 and five of the isolates as susceptible to minocycline and doxycycline, respectively. PCR analysis revealed that 43 and five of the isolates classified as susceptible to minocycline and doxycycline, respectively, possessed the tetracycline resistance gene, tet(M), known to confer resistance to both drugs. These results underscore the importance of utilizing the proposed minocycline and approved doxycycline canine breakpoints in place of human tetracycline breakpoints. © 2015 ESVD and ACVD.

  10. Interphase FISH detection of BCL2 rearrangement in follicular lymphoma using breakpoint-flanking probes

    NARCIS (Netherlands)

    Vaandrager, J W; Schuuring, E; Raap, T; Philippo, K; Kleiverda, K; Kluin, P

    Rearrangement of the BCL2 gene is an important parameter for the differential diagnosis of non-Hodgkin lymphomas. Although a relatively large proportion of breakpoints is clustered, many are missed by standard PCR. A FISH assay is therefore desired. Up to now, a lack of probes flanking the BCL2 gene

  11. En Route towards European Clinical breakpoints for veterinary antimicrobial susceptibility testing

    NARCIS (Netherlands)

    Toutain, Pierre Louis; Bousquet-Mélou, Alain; Damborg, Peter; Ferran, Aude A.; Mevius, Dik; Pelligand, Ludovic; Veldman, Kees T.; Lees, Peter

    2017-01-01

    VetCAST is the EUCAST sub-committee for Veterinary Antimicrobial Susceptibility Testing. Its remit is to define clinical breakpoints (CBPs) for antimicrobial drugs (AMDs) used in veterinary medicine in Europe. This position paper outlines the procedures and reviews scientific options to solve

  12. Investigation of the breakpoint region in stacks with a finite number of intrinsic Josephson junctions

    DEFF Research Database (Denmark)

    Shukrinov, Yu M.; Mahfouzi, F.; Pedersen, Niels Falsig

    2007-01-01

    and the saturated value depend on the coupling between junctions. We explain the results by the parametric resonance at the breakpoint and excitation of the longitudinal plasma wave by the Josephson oscillations. A way for the diagnostics of the junctions in the stack is proposed....

  13. On the Xq13 breakpoint: clinical and cytogenetic observations in a patient with acute myelogenous leukemia.

    Science.gov (United States)

    Sessarego, M; Bianchi Scarrà, G; Giuntini, P; Ajmar, F

    1983-01-01

    Cytogenetic study in a case of acute myelogenous leukemia revealed the presence of two identical dicentric marker chromosomes derived from an X with Xq13 breakpoints. Clinical and cytochemical findings suggest that the patient was affected by idiopathic acquired sideroblastic anemia before the acute leukemia.

  14. Demarcation of local neighborhoods to study relations between contextual factors and health

    Directory of Open Access Journals (Sweden)

    Chor Dora

    2010-06-01

    Full Text Available Abstract Background Several studies have highlighted the importance of collective social factors for population health. One of the major challenges is an adequate definition of the spatial units of analysis which present properties potentially related to the target outcomes. Political and administrative divisions of urban areas are the most commonly used definition, although they suffer limitations in their ability to fully express the neighborhoods as social and spatial units. Objective This study presents a proposal for defining the boundaries of local neighborhoods in Rio de Janeiro city. Local neighborhoods are constructed by means of aggregation of contiguous census tracts which are homogeneous regarding socioeconomic indicators. Methodology Local neighborhoods were created using the SKATER method (TerraView software. Criteria used for socioeconomic homogeneity were based on four census tract indicators (income, education, persons per household, and percentage of population in the 0-4-year age bracket considering a minimum population of 5,000 people living in each local neighborhood. The process took into account the geographic boundaries between administrative neighborhoods (a political-administrative division larger than a local neighborhood, but smaller than a borough and natural geographic barriers. Results The original 8,145 census tracts were collapsed into 794 local neighborhoods, distributed along 158 administrative neighborhoods. Local neighborhoods contained a mean of 10 census tracts, and there were an average of five local neighborhoods per administrative neighborhood. The local neighborhood units demarcated in this study are less socioeconomically heterogeneous than the administrative neighborhoods and provide a means for decreasing the well-known statistical variability of indicators based on census tracts. The local neighborhoods were able to distinguish between different areas within administrative neighborhoods

  15. Data Mining Validation of Fluconazole Breakpoints Established by the European Committee on Antimicrobial Susceptibility Testing▿

    Science.gov (United States)

    Cuesta, Isabel; Bielza, Concha; Larrañaga, Pedro; Cuenca-Estrella, Manuel; Laguna, Fernando; Rodriguez-Pardo, Dolors; Almirante, Benito; Pahissa, Albert; Rodríguez-Tudela, Juan L.

    2009-01-01

    European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints classify Candida strains with a fluconazole MIC ≤ 2 mg/liter as susceptible, those with a fluconazole MIC of 4 mg/liter as representing intermediate susceptibility, and those with a fluconazole MIC > 4 mg/liter as resistant. Machine learning models are supported by complex statistical analyses assessing whether the results have statistical relevance. The aim of this work was to use supervised classification algorithms to analyze the clinical data used to produce EUCAST fluconazole breakpoints. Five supervised classifiers (J48, Correlation and Regression Trees [CART], OneR, Naïve Bayes, and Simple Logistic) were used to analyze two cohorts of patients with oropharyngeal candidosis and candidemia. The target variable was the outcome of the infections, and the predictor variables consisted of values for the MIC or the proportion between the dose administered and the MIC of the isolate (dose/MIC). Statistical power was assessed by determining values for sensitivity and specificity, the false-positive rate, the area under the receiver operating characteristic (ROC) curve, and the Matthews correlation coefficient (MCC). CART obtained the best statistical power for a MIC > 4 mg/liter for detecting failures (sensitivity, 87%; false-positive rate, 8%; area under the ROC curve, 0.89; MCC index, 0.80). For dose/MIC determinations, the target was >75, with a sensitivity of 91%, a false-positive rate of 10%, an area under the ROC curve of 0.90, and an MCC index of 0.80. Other classifiers gave similar breakpoints with lower statistical power. EUCAST fluconazole breakpoints have been validated by means of machine learning methods. These computer tools must be incorporated in the process for developing breakpoints to avoid researcher bias, thus enhancing the statistical power of the model. PMID:19433568

  16. Helicobacter pylori resistance to six antibiotics by two breakpoint systems and resistance evolution in Bulgaria.

    Science.gov (United States)

    Boyanova, Lyudmila; Gergova, Galina; Evstatiev, Ivailo; Spassova, Zoya; Kandilarov, Naiden; Yaneva, Penka; Markovska, Rumyana; Mitov, Ivan

    2016-01-01

    Helicobacter pylori resistance to antibiotics is the main cause for eradication failures. Antibiotic resistance in 299 H. pylori strains from 233 untreated adults, 26 treated adults, and 40 untreated children was assessed by E tests and, for metronidazole, by breakpoint susceptibility testing and two breakpoint systems. Using EUCAST breakpoints (EBPs) and previous breakpoints (PBPs), overall resistance rates were: amoxicillin 4.0 and 0.6%, metronidazole 33.8 and 33.8%, clarithromycin 28.1 and 27.4%, levofloxacin 19.4 and 19.4%, tetracycline 3.7 and 1.5%, respectively, and rifampin 8.3% (EBP). Multidrug resistance was detected in treated and untreated adults and an untreated child and included 17 (EBPs) and 15 strains (PBPs). Differences between susceptibility categories were found for amoxicillin (3.5% of strains), clarithromycin (0.7%), and tetracycline (2.2%). Using PBPs, from 2005-2007 to 2010-2015, overall primary clarithromycin resistance continued to increase (17.9-25.6%) as noted in our previous study. However, in 2010-2015, overall primary metronidazole (24.0-31.5%) and fluoroquinolone (7.6-18.3%) resistance rates also increased. Primary resistance rates in children and adults were comparable. Briefly, differences in resistance rates by the two breakpoint systems affected the results for three antibiotics. National antibiotic consumption was linked to macrolide resistance in adults. Current primary H. pylori resistance to three antibiotics increased in all untreated patients and in the untreated adults, with the sharpest rise for the fluoroquinolones. The presence of fivefold H. pylori resistance to metronidazole, clarithromycin, tetracycline, levofloxacin, and amoxicillin according to EBPs is alarming.

  17. DEMARCATE: Density-based magnetic resonance image clustering for assessing tumor heterogeneity in cancer

    Directory of Open Access Journals (Sweden)

    Abhijoy Saha

    2016-01-01

    Full Text Available Tumor heterogeneity is a crucial area of cancer research wherein inter- and intra-tumor differences are investigated to assess and monitor disease development and progression, especially in cancer. The proliferation of imaging and linked genomic data has enabled us to evaluate tumor heterogeneity on multiple levels. In this work, we examine magnetic resonance imaging (MRI in patients with brain cancer to assess image-based tumor heterogeneity. Standard approaches to this problem use scalar summary measures (e.g., intensity-based histogram statistics that do not adequately capture the complete and finer scale information in the voxel-level data. In this paper, we introduce a novel technique, DEMARCATE (DEnsity-based MAgnetic Resonance image Clustering for Assessing Tumor hEterogeneity to explore the entire tumor heterogeneity density profiles (THDPs obtained from the full tumor voxel space. THDPs are smoothed representations of the probability density function of the tumor images. We develop tools for analyzing such objects under the Fisher–Rao Riemannian framework that allows us to construct metrics for THDP comparisons across patients, which can be used in conjunction with standard clustering approaches. Our analyses of The Cancer Genome Atlas (TCGA based Glioblastoma dataset reveal two significant clusters of patients with marked differences in tumor morphology, genomic characteristics and prognostic clinical outcomes. In addition, we see enrichment of image-based clusters with known molecular subtypes of glioblastoma multiforme, which further validates our representation of tumor heterogeneity and subsequent clustering techniques.

  18. Public and private in the post-soviet area: the problem of demarcation

    Directory of Open Access Journals (Sweden)

    M. I. Zaidel

    2014-01-01

    Full Text Available The article focuses on the problem of determination of public and private in the post­soviet area. Formation of these spheres should be a logical conclusion of successful transformation and modernization process in ex­soviet republics and getting all spheres of civil life out of the state control. Historical specific is underlined; it is given the determination and main characteristics of public and private. It is given two main approaches’ ways of interpretation the phenomena and formation of public sphere according to H. Arendt and Ju. Hubermas. The specific of formation and demarcation of public and private spheres in the post­soviet area is analyzed. The boundaries between public and private spheres were deformed by the soviet state and communist society. As a result it was built hierarchical relations among the state, society and ruler; it is typical for power centralized societies. The determining factor of institutional heritage in the processes of state­making is underlined. The deformation of division of state, public and private spheres is caused by combining of traditional and modern institutes and practices; as a result social practices that are against of logic of modern society slow down the development of market­oriented economy and modernization of institutions.

  19. A new approach to assess COPD by identifying lung function break-points.

    Science.gov (United States)

    Eriksson, Göran; Jarenbäck, Linnea; Peterson, Stefan; Ankerst, Jaro; Bjermer, Leif; Tufvesson, Ellen

    2015-01-01

    COPD is a progressive disease, which can take different routes, leading to great heterogeneity. The aim of the post-hoc analysis reported here was to perform continuous analyses of advanced lung function measurements, using linear and nonlinear regressions. Fifty-one COPD patients with mild to very severe disease (Global Initiative for Chronic Obstructive Lung Disease [GOLD] Stages I-IV) and 41 healthy smokers were investigated post-bronchodilation by flow-volume spirometry, body plethysmography, diffusion capacity testing, and impulse oscillometry. The relationship between COPD severity, based on forced expiratory volume in 1 second (FEV1), and different lung function parameters was analyzed by flexible nonparametric method, linear regression, and segmented linear regression with break-points. Most lung function parameters were nonlinear in relation to spirometric severity. Parameters related to volume (residual volume, functional residual capacity, total lung capacity, diffusion capacity [diffusion capacity of the lung for carbon monoxide], diffusion capacity of the lung for carbon monoxide/alveolar volume) and reactance (reactance area and reactance at 5Hz) were segmented with break-points at 60%-70% of FEV1. FEV1/forced vital capacity (FVC) and resonance frequency had break-points around 80% of FEV1, while many resistance parameters had break-points below 40%. The slopes in percent predicted differed; resistance at 5 Hz minus resistance at 20 Hz had a linear slope change of -5.3 per unit FEV1, while residual volume had no slope change above and -3.3 change per unit FEV1 below its break-point of 61%. Continuous analyses of different lung function parameters over the spirometric COPD severity range gave valuable information additional to categorical analyses. Parameters related to volume, diffusion capacity, and reactance showed break-points around 65% of FEV1, indicating that air trapping starts to dominate in moderate COPD (FEV1 =50%-80%). This may have an

  20. Comprehensive characterization of evolutionary conserved breakpoints in four New World Monkey karyotypes compared to Chlorocebus aethiops and Homo sapiens.

    Science.gov (United States)

    Fan, Xiaobo; Supiwong, Weerayuth; Weise, Anja; Mrasek, Kristin; Kosyakova, Nadezda; Tanomtong, Alongkoad; Pinthong, Krit; Trifonov, Vladimir A; Cioffi, Marcelo de Bello; Grothmann, Pierre; Liehr, Thomas; Oliveira, Edivaldo H C de

    2015-11-01

    Comparative cytogenetic analysis in New World Monkeys (NWMs) using human multicolor banding (MCB) probe sets were not previously done. Here we report on an MCB based FISH-banding study complemented with selected locus-specific and heterochromatin specific probes in four NWMs and one Old World Monkey (OWM) species, i.e. in Alouatta caraya (ACA), Callithrix jacchus (CJA), Cebus apella (CAP), Saimiri sciureus (SSC), and Chlorocebus aethiops (CAE), respectively. 107 individual evolutionary conserved breakpoints (ECBs) among those species were identified and compared with those of other species in previous reports. Especially for chromosomal regions being syntenic to human chromosomes 6, 8, 9, 10, 11, 12 and 16 previously cryptic rearrangements could be observed. 50.4% (54/107) NWM-ECBs were colocalized with those of OWMs, 62.6% (62/99) NWM-ECBs were related with those of Hylobates lar (HLA) and 66.3% (71/107) NWM-ECBs corresponded with those known from other mammalians. Furthermore, human fragile sites were aligned with the ECBs found in the five studied species and interestingly 66.3% ECBs colocalized with those fragile sites (FS). Overall, this study presents detailed chromosomal maps of one OWM and four NWM species. This data will be helpful to further investigation on chromosome evolution in NWM and hominoids in general and is prerequisite for correct interpretation of future sequencing based genomic studies in those species.

  1. Comprehensive characterization of evolutionary conserved breakpoints in four New World Monkey karyotypes compared to Chlorocebus aethiops and Homo sapiens

    Directory of Open Access Journals (Sweden)

    Xiaobo Fan

    2015-11-01

    Full Text Available Comparative cytogenetic analysis in New World Monkeys (NWMs using human multicolor banding (MCB probe sets were not previously done. Here we report on an MCB based FISH-banding study complemented with selected locus-specific and heterochromatin specific probes in four NWMs and one Old World Monkey (OWM species, i.e. in Alouatta caraya (ACA, Callithrix jacchus (CJA, Cebus apella (CAP, Saimiri sciureus (SSC, and Chlorocebus aethiops (CAE, respectively. 107 individual evolutionary conserved breakpoints (ECBs among those species were identified and compared with those of other species in previous reports. Especially for chromosomal regions being syntenic to human chromosomes 6, 8, 9, 10, 11, 12 and 16 previously cryptic rearrangements could be observed. 50.4% (54/107 NWM-ECBs were colocalized with those of OWMs, 62.6% (62/99 NWM-ECBs were related with those of Hylobates lar (HLA and 66.3% (71/107 NWM-ECBs corresponded with those known from other mammalians. Furthermore, human fragile sites were aligned with the ECBs found in the five studied species and interestingly 66.3% ECBs colocalized with those fragile sites (FS. Overall, this study presents detailed chromosomal maps of one OWM and four NWM species. This data will be helpful to further investigation on chromosome evolution in NWM and hominoids in general and is prerequisite for correct interpretation of future sequencing based genomic studies in those species.

  2. Influence of sequence identity and unique breakpoints on the frequency of intersubtype HIV-1 recombination

    Directory of Open Access Journals (Sweden)

    Abreha Measho

    2006-12-01

    Full Text Available Abstract Background HIV-1 recombination between different subtypes has a major impact on the global epidemic. The generation of these intersubtype recombinants follows a defined set of events starting with dual infection of a host cell, heterodiploid virus production, strand transfers during reverse transcription, and then selection. In this study, recombination frequencies were measured in the C1-C4 regions of the envelope gene in the presence (using a multiple cycle infection system and absence (in vitro reverse transcription and single cycle infection systems of selection for replication-competent virus. Ugandan subtypes A and D HIV-1 env sequences (115-A, 120-A, 89-D, 122-D, 126-D were employed in all three assay systems. These subtypes co-circulate in East Africa and frequently recombine in this human population. Results Increased sequence identity between viruses or RNA templates resulted in increased recombination frequencies, with the exception of the 115-A virus or RNA template. Analyses of the recombination breakpoints and mechanistic studies revealed that the presence of a recombination hotspot in the C3/V4 env region, unique to 115-A as donor RNA, could account for the higher recombination frequencies with the 115-A virus/template. Single-cycle infections supported proportionally less recombination than the in vitro reverse transcription assay but both systems still had significantly higher recombination frequencies than observed in the multiple-cycle virus replication system. In the multiple cycle assay, increased replicative fitness of one HIV-1 over the other in a dual infection dramatically decreased recombination frequencies. Conclusion Sequence variation at specific sites between HIV-1 isolates can introduce unique recombination hotspots, which increase recombination frequencies and skew the general observation that decreased HIV-1 sequence identity reduces recombination rates. These findings also suggest that the majority of

  3. Tracking genome engineering outcome at individual DNA breakpoints.

    Science.gov (United States)

    Certo, Michael T; Ryu, Byoung Y; Annis, James E; Garibov, Mikhail; Jarjour, Jordan; Rawlings, David J; Scharenberg, Andrew M

    2011-07-10

    Site-specific genome engineering technologies are increasingly important tools in the postgenomic era, where biotechnological objectives often require organisms with precisely modified genomes. Rare-cutting endonucleases, through their capacity to create a targeted DNA strand break, are one of the most promising of these technologies. However, realizing the full potential of nuclease-induced genome engineering requires a detailed understanding of the variables that influence resolution of nuclease-induced DNA breaks. Here we present a genome engineering reporter system, designated 'traffic light', that supports rapid flow-cytometric analysis of repair pathway choice at individual DNA breaks, quantitative tracking of nuclease expression and donor template delivery, and high-throughput screens for factors that bias the engineering outcome. We applied the traffic light system to evaluate the efficiency and outcome of nuclease-induced genome engineering in human cell lines and identified strategies to facilitate isolation of cells in which a desired engineering outcome has occurred.

  4. En Route towards European Clinical breakpoints for veterinary antimicrobial susceptibility testing

    DEFF Research Database (Denmark)

    Toutain, Pierre Louis; Bousquet-Mélou, Alain; Damborg, Peter

    2017-01-01

    VetCAST is the EUCAST sub-committee for Veterinary Antimicrobial Susceptibility Testing. Its remit is to define clinical breakpoints (CBPs) for antimicrobial drugs (AMDs) used in veterinary medicine in Europe. This position paper outlines the procedures and reviews scientific options to solve...... challenges for the determination of specific CBPs for animal species, drug substances and disease conditions. VetCAST will adopt EUCAST approaches: the initial step will be data assessment; then procedures for decisions on the CBP; and finally the release of recommendations for CBP implementation......-clinical pharmacokinetic data [this PK/PD break-point is the highest possible MIC for which a given percentage of animals in the target population achieves a critical value for the selected PK/PD index (fAUC/MIC or fT > MIC)] and (iii) when possible, a clinical cut-off, that is the relationship between MIC and clinical...

  5. Highly complex genetic rearrangement involving at least seven breakpoints in a case of chronic myeloid leukemia.

    Science.gov (United States)

    Weinstein, M; Grossman, A; Dittmar, K; Weiss, R; Benn, P

    1990-08-01

    Cytogenetic analysis for an atypical case of chronic myeloid leukemia (CML) showed a complex karyotype with four chromosome breakpoints (5q12, 12q21, 12q24, and 22q11) and translocation products that included a typical Philadelphia chromosome but apparently normal chromosomes 9. Molecular genetic analyses using four breakpoint cluster region (bcr) probes indicated that three breaks were probably present on chromosome 22. Two apparently independent breaks appeared to exist within the bcr, one of which was probably associated with a deletion of some bcr sequences. By combining the molecular and cytogenetic data, we could infer a total of seven breaks. This case illustrates the extensive and complex types of genetic alteration that may be associated with a c-abl and bcr fusion.

  6. Diversity of breakpoints of variant Philadelphia chromosomes in chronic myeloid leukemia in Brazilian patients

    Directory of Open Access Journals (Sweden)

    Maria de Lourdes Lopes Ferrari Chauffaille

    2015-02-01

    Full Text Available Background: Chronic myeloid leukemia is a myeloproliferative disorder characterized by the Philadelphia chromosome or t(9;22(q34.1;q11.2, resulting in the break-point cluster regionAbelson tyrosine kinase fusion gene, which encodes a constitutively active tyrosine kinase protein. The Philadelphia chromosome is detected by karyotyping in around 90% of chronic myeloid leukemia patients, but 5-10% may have variant types. Variant Philadelphia chromosomes are characterized by the involvement of another chromosome in addition to chromosome 9 or 22. It can be a simple type of variant when one other chromosome is involved, or complex, in which two or more chromosomes take part in the translocation. Few studies have reported the incidence of variant Philadelphia chromosomes or the breakpoints involved among Brazilian chronic myeloid leukemia patients. Objective: The aim of this report is to describe the diversity of the variant Philadelphia chromosomes found and highlight some interesting breakpoint candidates for further studies. Methods: the Cytogenetics Section Database was searched for all cases with diagnoses of chronic myeloid leukemia during a 12-year period and all the variant Philadelphia chromosomes were listed. Results: Fifty (5.17% cases out of 1071 Philadelphia-positive chronic myeloid leukemia were variants. The most frequently involved chromosome was 17, followed by chromosomes: 1, 20, 6, 11, 2, 10, 12 and 15. Conclusion: Among all the breakpoints seen in this survey, six had previously been described: 11p15, 14q32, 15q11.2, 16p13.1, 17p13 and 17q21. The fact that some regions get more fre- quently involved in such rare rearrangements calls attention to possible predisposition that should be further studied. Nevertheless, the pathological implication of these variants remains unclear.

  7. Investigating the role of X chromosome breakpoints in premature ovarian failure

    Directory of Open Access Journals (Sweden)

    Baronchelli Simona

    2012-07-01

    Full Text Available Abstract The importance of the genetic factor in the aetiology of premature ovarian failure (POF is emphasized by the high percentage of familial cases and X chromosome abnormalities account for 10% of chromosomal aberrations. In this study, we report the detailed analysis of 4 chromosomal abnormalities involving the X chromosome and associated with POF that were detected during a screening of 269 affected women. Conventional and molecular cytogenetics were valuable tools for locating the breakpoint regions and thus the following karyotypes were defined: 46,X,der(Xt(X;19(p21.1;q13.42mat, 46,X,t(X;2(q21.33;q14.3dn, 46,X,der(Xt(X;Y(q26.2;q11.223mat and 46,X,t(X;13(q13.3;q31dn. A bioinformatic analysis of the breakpoint regions identified putative candidate genes for ovarian failure near the breakpoint regions on the X chromosome or on autosomes that were involved in the translocation event. HS6ST1, HS6ST2 and MATER genes were identified and their functions and a literature review revealed an interesting connection to the POF phenotype. Moreover, the 19q13.32 locus is associated with the age of onset of the natural menopause. These results support the position effect of the breakpoint on flanking genes, and cytogenetic techniques, in combination with bioinformatic analysis, may help to improve what is known about this puzzling disorder and its diagnostic potential.

  8. Susceptibility of extended-spectrum-beta-lactamase-producing Enterobacteriaceae according to the new CLSI breakpoints.

    Science.gov (United States)

    Wang, Peng; Hu, Fupin; Xiong, Zizhong; Ye, Xinyu; Zhu, Demei; Wang, Yun F; Wang, Minggui

    2011-09-01

    In 2010 the Clinical and Laboratory Standards Institute (CLSI) lowered the susceptibility breakpoints of some cephalosporins and aztreonam for Enterobacteriaceae and eliminated the need to perform screening for extended-spectrum β-lactamases (ESBLs) and confirmatory tests. The aim of this study was to determine how many ESBL-producing strains of three common species of Enterobacteriaceae test susceptible using the new breakpoints. As determined with the CLSI screening and confirmatory tests, 382 consecutive ESBL-producing strains were collected at Huashan Hospital between 2007 and 2008, including 158 strains of Escherichia coli, 164 of Klebsiella pneumoniae, and 60 of Proteus mirabilis. Susceptibility was determined by the CLSI agar dilution method. CTX-M-, TEM-, and SHV-specific genes were determined by PCR amplification and sequencing. bla(CTX-M) genes alone or in combination with bla(SHV) were present in 92.7% (354/382) of these ESBL-producing strains. Forty-two (25.6%) strains of K. pneumoniae harbored SHV-type ESBLs alone or in combination. No TEM ESBLs were found. Utilizing the new breakpoints, all 382 strains were resistant to cefazolin, cefotaxime, and ceftriaxone, while 85.0 to 96.7% of P. mirabilis strains tested susceptible to ceftazidime, cefepime, and aztreonam, 41.8 to 45.6% of E. coli strains appeared to be susceptible to ceftazidime and cefepime, and 20.1% of K. pneumoniae were susceptible to cefepime. In conclusion, all ESBL-producing strains of Enterobacteriaceae would be reported to be resistant to cefazolin, cefotaxime, and ceftriaxone by using the new CLSI breakpoints, but a substantial number of ESBL-containing P. mirabilis and E. coli strains would be reported to be susceptible to ceftazidime, cefepime, and aztreonam, which is likely due to the high prevalence of CTX-M type ESBLs.

  9. Remote sensing of the correlation between breakpoint oscillations and infragravity waves in the surf and swash zone

    Science.gov (United States)

    Moura, T.; Baldock, T. E.

    2017-04-01

    A novel remote sensing methodology to determine the dominant infragravity mechanism in the inner surf and swash zone in the field is presented. Video observations of the breakpoint motion are correlated with the shoreline motion and inner surf zone water levels to determine the relationship between the time-varying breakpoint oscillations and the shoreline motion. The results of 13 field data sets collected from three different beaches indicate that, inside the surf zone, the dominance of bound wave or breakpoint forcing is strongly dependent on the surf zone width and the type of short wave breaking. Infragravity generation by bound wave release was stronger for conditions with relatively narrow surf zones and plunging waves; breakpoint forcing was dominant for wider surf zones and spilling breaker conditions.

  10. Mutation analysis in Duchenne and Becker muscular dystrophy patients from Bulgaria shows a peculiar distribution of breakpoints by intron

    Energy Technology Data Exchange (ETDEWEB)

    Todorova, A.; Bronzova, J.; Kremensky, I. [Univ. Hospital of Obstetrics and Gynecology, Sofia (Bulgaria)] [and others

    1996-10-02

    For the first time in Bulgaria, a deletion/duplication screening was performed on a group of 84 unrelated Duchenne/Becker muscular dystrophy patients, and the breakpoint distribution in the dystrophin gene was analyzed. Intragenic deletions were detected in 67.8% of patients, and intragenic duplications in 2.4%. A peculiar distribution of deletion breakpoints was found. Only 13.2% of the deletion breakpoints fell in the {open_quotes}classical{close_quotes} hot spot in intron 44, whereas the majority (> 54%) were located within the segment encompassing introns 45-51, which includes intron 50, the richest in breakpoints (16%) in the Bulgarian sample. Comparison with data from Greece and Turkey points at the probable existence of a deletion hot spot within intron 50, which might be a characteristic of populations of the Balkan region. 17 refs., 2 figs.

  11. Accurate Breakpoint Mapping in Apparently Balanced Translocation Families with Discordant Phenotypes Using Whole Genome Mate-Pair Sequencing

    DEFF Research Database (Denmark)

    Aristidou, Constantia; Koufaris, Costas; Theodosiou, Athina

    2017-01-01

    -MPS) was applied to map the breakpoints in nine two-way ABT carriers from four families. Translocation breakpoints and patient-specific structural variants were validated by Sanger sequencing and quantitative Real Time PCR, respectively. Identical sequencing patterns and breakpoints were identified in affected......Familial apparently balanced translocations (ABTs) segregating with discordant phenotypes are extremely challenging for interpretation and counseling due to the scarcity of publications and lack of routine techniques for quick investigation. Recently, next generation sequencing has emerged...... as an efficacious methodology for precise detection of translocation breakpoints. However, studies so far have mainly focused on de novo translocations. The present study focuses specifically on familial cases in order to shed some light to this diagnostic dilemma. Whole-genome mate-pair sequencing (WG...

  12. SoftSearch: integration of multiple sequence features to identify breakpoints of structural variations.

    Directory of Open Access Journals (Sweden)

    Steven N Hart

    Full Text Available BACKGROUND: Structural variation (SV represents a significant, yet poorly understood contribution to an individual's genetic makeup. Advanced next-generation sequencing technologies are widely used to discover such variations, but there is no single detection tool that is considered a community standard. In an attempt to fulfil this need, we developed an algorithm, SoftSearch, for discovering structural variant breakpoints in Illumina paired-end next-generation sequencing data. SoftSearch combines multiple strategies for detecting SV including split-read, discordant read-pair, and unmated pairs. Co-localized split-reads and discordant read pairs are used to refine the breakpoints. RESULTS: We developed and validated SoftSearch using real and synthetic datasets. SoftSearch's key features are 1 not requiring secondary (or exhaustive primary alignment, 2 portability into established sequencing workflows, and 3 is applicable to any DNA-sequencing experiment (e.g. whole genome, exome, custom capture, etc.. SoftSearch identifies breakpoints from a small number of soft-clipped bases from split reads and a few discordant read-pairs which on their own would not be sufficient to make an SV call. CONCLUSIONS: We show that SoftSearch can identify more true SVs by combining multiple sequence features. SoftSearch was able to call clinically relevant SVs in the BRCA2 gene not reported by other tools while offering significantly improved overall performance.

  13. Correlation of intercentromeric distance, mosaicism, and sexual phenotype: molecular localization of breakpoints in isodicentric Y chromosomes.

    Science.gov (United States)

    Beaulieu Bergeron, Mélanie; Brochu, Pierre; Lemyre, Emmanuelle; Lemieux, Nicole

    2011-11-01

    Isodicentric chromosomes are among the structural abnormalities of the Y chromosome that are commonly identified in patients. The simultaneous 45,X cell line that is generated in cell division due to instability of the isodicentric Y chromosome [idic(Y)] has long been hypothesized to explain the variable sexual development of these patients, although gonads have been studied in only a subset of cases. We report here on the molecular localization of breakpoints in ten patients with an idic(Y). Breakpoints were mapped by FISH using BACs; gonads and fibroblasts were also analyzed when possible to evaluate the level of mosaicism. First, we demonstrate great tissue variability in the distribution of idic(Y). Second, palindromes and direct repeats were near the breakpoint of several idic(Y), suggesting that these sequences play a role in the formation of idic(Y). Finally, our data suggest that intercentromeric distance has a negative influence on the stability of idic(Y), as a greater proportion of cells with breakage or loss of the idic(Y) were found in idic(Y) with a greater intercentromeric distance. Females had a significantly greater intercentromeric distance on their idic(Y) than did males. In conclusion, our study indicates that the Y chromosome contains sequences that are more prone to formation of isodicentric chromosomes. We also demonstrate that patients with an intercentromeric distance greater than 20 Mb on their idic(Y) are at increased risk of having a female sexual phenotype. Copyright © 2011 Wiley Periodicals, Inc.

  14. Molecular characterization of the translocation breakpoints in the Down syndrome mouse model Ts65Dn.

    Science.gov (United States)

    Reinholdt, Laura G; Ding, Yueming; Gilbert, Griffith J; Gilbert, Griffith T; Czechanski, Anne; Solzak, Jeffrey P; Roper, Randall J; Johnson, Mark T; Donahue, Leah Rae; Lutz, Cathleen; Davisson, Muriel T

    2011-12-01

    Ts65Dn is a mouse model of Down syndrome: a syndrome that results from chromosome (Chr) 21 trisomy and is associated with congenital defects, cognitive impairment, and ultimately Alzheimer's disease. Ts65Dn mice have segmental trisomy for distal mouse Chr 16, a region sharing conserved synteny with human Chr 21. As a result, this strain harbors three copies of over half of the human Chr 21 orthologs. The trisomic segment of Chr 16 is present as a translocation chromosome (Mmu17(16)), with breakpoints that have not been defined previously. To molecularly characterize the Chrs 16 and 17 breakpoints on the translocation chromosome in Ts65Dn mice, we used a selective enrichment and high-throughput paired-end sequencing approach. Analysis of paired-end reads flanking the Chr 16, Chr 17 junction on Mmu17(16) and de novo assembly of the reads directly spanning the junction provided the precise locations of the Chrs 16 and 17 breakpoints at 84,351,351 and 9,426,822 bp, respectively. These data provide the basis for low-cost, highly efficient genotyping of Ts65Dn mice. More importantly, these data provide, for the first time, complete characterization of gene dosage in Ts65Dn mice.

  15. Effectiveness of breakpoint chlorination to reduce accelerated chemical chloramine decay in severely nitrified bulk waters.

    Science.gov (United States)

    Bal Krishna, K C; Sathasivan, Arumugam; Kastl, George

    2014-12-01

    Rectifying the accelerated chloramine decay after the onset of nitrification is a major challenge for water utilities that employ chloramine as a disinfectant. Recently, the evidence of soluble microbial products (SMPs) accelerating chloramine decay beyond traditionally known means was reported. After the onset of nitrification, with an intention to inactivate nitrifying bacteria and thus maintaining disinfectant residuals, breakpoint chlorination followed by re-chloramination is usually practiced by water utilities. However, what actually breakpoint chlorination does beyond known effects is not known, especially in light of the new finding of SMPs. In this study, experiments were conducted using severely nitrified chloraminated water samples (chloramine residuals 0.1 mg N L−1 and an order of magnitude higher chloramine decay rate compared to normal decay) obtained from two laboratory scale systems operated by feeding natural organic matter (NOM) containing and NOM free waters. Results showed that the accelerated decay of chloramine as a result of SMPs can be eliminated by spiking higher free chlorine residuals (about 0.92 ± 0.03 to 1.16 ± 0.12 mg Cl2 L−1) than the stoichiometric requirement for breakpoint chlorination and nitrite oxidation. Further, accelerated initial chlorine decay showed chlorine preferentially reacts with nitrite and ammonia before destroying SMPs. This study, clearly demonstrated there is an additional demand from SMPs that needs to be satisfied to effectively recover disinfection residuals in subsequent re-chloramination.

  16. A translocation breakpoint disrupts the ASPM gene in a patient with primary microcephaly.

    Science.gov (United States)

    Pichon, Bruno; Vankerckhove, Sophie; Bourrouillou, Georges; Duprez, Laurence; Abramowicz, Marc J

    2004-05-01

    Primary microcephaly (microcephalia vera) is a developmental abnormality resulting in a small brain, with mental retardation. It is usually transmitted as an autosomal recessive trait, and six loci have been reported to date. We analyzed a translocation breakpoint previously reported in a patient with apparently sporadic primary microcephaly, at 1q31, where locus MCPH5 maps. The patient was lost to follow-up, and we sampled a maternal aunt who carried the familial translocation. FISH analyses showed that the insert of BAC clone RP11-32D17 spanned the breakpoint. The breakpoint was further located within a fragment of this insert corresponding to intron 17 of the ASPM gene, resulting in a predicted transcript truncated of more than half of its coding sequence. It is very likely that the proband carried a second ASPM mutation in trans, but he was not available for sampling and hence we could not confirm this hypothesis. Our observation adds to the mutation spectrum of ASPM in primary microcephaly, and is to our knowledge the second example of a constitutional, reciprocal translocation responsible for a bona fide autosomal recessive phenotype.

  17. Impact of CLSI and EUCAST Cefepime breakpoint changes on the susceptibility reporting for Enterobacteriaceae.

    Science.gov (United States)

    Bork, Jacqueline T; Heil, Emily L; Leekha, Surbhi; Fowler, Randal C; Hanson, Nancy D; Majumdar, Anjali; Johnson, J Kristie

    2017-12-01

    We analyzed the effects of different cefepime MIC breakpoints on Enterobacteriaceae cefepime susceptibility and the presence of AmpC and extended-spectrum β-lactamase (ESBL) genes within the cefepime MIC interpretative categories. Using Enterobacteriaceae susceptibility data from 2013 comparisons of MIC breakpoints were performed using Pearson's chi-squared test. Molecular testing on a subset of isolates was done. Among 3784 non-duplicate clinical isolates, cefepime susceptibility decreased from 97.6% to 96.1% to 93.7% for CLSI 2013, CLSI 2014, and EUCAST 2011, respectively. In ceftriaxone non-susceptible isolates, cefepime susceptibility decreased from 79% to 66% (PCLSI 2013 and 2014, respectively, which was greater and statistically significant for Escherichia coli and Klebsiella spp. but not for Enterobacter spp. (P=0.06). Isolates with MIC ≤1μg/mL more often harbored AmpC (77%) than ESBL (18%) genes. Lower cefepime MIC breakpoints decrease cefepime susceptibility for isolates harboring ESBLs, while sparing the majority of those with AmpCs. Published by Elsevier Inc.

  18. Sequence characterisation of deletion breakpoints in the dystrophin gene by PCR

    Energy Technology Data Exchange (ETDEWEB)

    Abbs, S.; Sandhu, S.; Bobrow, M. [Guy`s Hospital, London (United Kingdom)

    1994-09-01

    Partial deletions of the dystrophin gene account for 65% of cases of Duchenne muscular dystrophy. A high proportion of these structural changes are generated by new mutational events, and lie predominantly within two `hotspot` regions, yet the underlying reasons for this are not known. We are characterizing and sequencing the regions surrounding deletion breakpoints in order to: (i) investigate the mechanisms of deletion mutation, and (ii) enable the design of PCR assays to specifically amplify mutant and normal sequences, allowing us to search for the presence of somatic mosaicism in appropriate family members. Using this approach we have been able to demonstrate the presence of somatic mosaicism in a maternal grandfather of a DMD-affected male, deleted for exons 49-50. Three deletions, namely of exons 48-49, 49-50, and 50, have been characterized using a PCR approach that avoids any cloning procedures. Breakpoints were initially localized to within regions of a few kilobases using Southern blot restriction analyses with exon-specific probes and PCR amplification of exonic and intronic loci. Sequencing was performed directly on PCR products: (i) mutant sequences were obtained from long-range or inverse-PCR across the deletion junction fragments, and (ii) normal sequences were obtained from the products of standard PCR, vectorette PCR, or inverse-PCR performed on YACs. Further characterization of intronic sequences will allow us to amplify and sequence across other deletion breakpoints and increase our knowledge of the mechanisms of mutation in the dystophin gene.

  19. Analysis of fine-scale mammalian evolutionary breakpoints provides new insight into their relation to genome organisation

    Directory of Open Access Journals (Sweden)

    Zaghloul Lamia

    2009-07-01

    Full Text Available Abstract Background The Intergenic Breakage Model, which is the current model of structural genome evolution, considers that evolutionary rearrangement breakages happen with a uniform propensity along the genome but are selected against in genes, their regulatory regions and in-between. However, a growing body of evidence shows that there exists regions along mammalian genomes that present a high susceptibility to breakage. We reconsidered this question taking advantage of a recently published methodology for the precise detection of rearrangement breakpoints based on pairwise genome comparisons. Results We applied this methodology between the genome of human and those of five sequenced eutherian mammals which allowed us to delineate evolutionary breakpoint regions along the human genome with a finer resolution (median size 26.6 kb than obtained before. We investigated the distribution of these breakpoints with respect to genome organisation into domains of different activity. In agreement with the Intergenic Breakage Model, we observed that breakpoints are under-represented in genes. Surprisingly however, the density of breakpoints in small intergenes (1 per Mb appears significantly higher than in gene deserts (0.1 per Mb. More generally, we found a heterogeneous distribution of breakpoints that follows the organisation of the genome into isochores (breakpoints are more frequent in GC-rich regions. We then discuss the hypothesis that regions with an enhanced susceptibility to breakage correspond to regions of high transcriptional activity and replication initiation. Conclusion We propose a model to describe the heterogeneous distribution of evolutionary breakpoints along human chromosomes that combines natural selection and a mutational bias linked to local open chromatin state.

  20. Gene alterations at Drosophila inversion breakpoints provide prima facie evidence for natural selection as an explanation for rapid chromosomal evolution

    Directory of Open Access Journals (Sweden)

    Guillén Yolanda

    2012-02-01

    Full Text Available Abstract Background Chromosomal inversions have been pervasive during the evolution of the genus Drosophila, but there is significant variation between lineages in the rate of rearrangement fixation. D. mojavensis, an ecological specialist adapted to a cactophilic niche under extreme desert conditions, is a chromosomally derived species with ten fixed inversions, five of them not present in any other species. Results In order to explore the causes of the rapid chromosomal evolution in D. mojavensis, we identified and characterized all breakpoints of seven inversions fixed in chromosome 2, the most dynamic one. One of the inversions presents unequivocal evidence for its generation by ectopic recombination between transposon copies and another two harbor inverted duplications of non-repetitive DNA at the two breakpoints and were likely generated by staggered single-strand breaks and repair by non-homologous end joining. Four out of 14 breakpoints lay in the intergenic region between preexisting duplicated genes, suggesting an adaptive advantage of separating previously tightly linked duplicates. Four out of 14 breakpoints are associated with transposed genes, suggesting these breakpoints are fragile regions. Finally two inversions contain novel genes at their breakpoints and another three show alterations of genes at breakpoints with potential adaptive significance. Conclusions D. mojavensis chromosomal inversions were generated by multiple mechanisms, an observation that does not provide support for increased mutation rate as explanation for rapid chromosomal evolution. On the other hand, we have found a number of gene alterations at the breakpoints with putative adaptive consequences that directly point to natural selection as the cause of D. mojavensis rapid chromosomal evolution.

  1. Gene alterations at Drosophila inversion breakpoints provide prima facie evidence for natural selection as an explanation for rapid chromosomal evolution.

    Science.gov (United States)

    Guillén, Yolanda; Ruiz, Alfredo

    2012-02-01

    Chromosomal inversions have been pervasive during the evolution of the genus Drosophila, but there is significant variation between lineages in the rate of rearrangement fixation. D. mojavensis, an ecological specialist adapted to a cactophilic niche under extreme desert conditions, is a chromosomally derived species with ten fixed inversions, five of them not present in any other species. In order to explore the causes of the rapid chromosomal evolution in D. mojavensis, we identified and characterized all breakpoints of seven inversions fixed in chromosome 2, the most dynamic one. One of the inversions presents unequivocal evidence for its generation by ectopic recombination between transposon copies and another two harbor inverted duplications of non-repetitive DNA at the two breakpoints and were likely generated by staggered single-strand breaks and repair by non-homologous end joining. Four out of 14 breakpoints lay in the intergenic region between preexisting duplicated genes, suggesting an adaptive advantage of separating previously tightly linked duplicates. Four out of 14 breakpoints are associated with transposed genes, suggesting these breakpoints are fragile regions. Finally two inversions contain novel genes at their breakpoints and another three show alterations of genes at breakpoints with potential adaptive significance. D. mojavensis chromosomal inversions were generated by multiple mechanisms, an observation that does not provide support for increased mutation rate as explanation for rapid chromosomal evolution. On the other hand, we have found a number of gene alterations at the breakpoints with putative adaptive consequences that directly point to natural selection as the cause of D. mojavensis rapid chromosomal evolution.

  2. In vitro antibacterial activity of doripenem against clinical isolates from French teaching hospitals: proposition of zone diameter breakpoints

    OpenAIRE

    Lascols, C.; Legrand, P.; Mérens, A.; Leclercq, R.; Armand-Lefevre, L.; Drugeon, H. B.; Kitzis, M. D.; Muller-Serieys, C.; Reverdy, M. E.; Roussel-Delvallez, M.; Moubareck, C.; Lemire, A.; Miara, A.; Gjoklaj, M.; Soussy, C.-J.

    2010-01-01

    Abstract The aims of the study were to determine the in vitro activity of doripenem, a new carbapenem, against a large number of bacterial pathogens and to propose zone diameter breakpoints for clinical categorization in France according to the European Committee on Antimicrobial Susceptibility Testing (EUCAST) minimum inhibitory concentration (MIC) breakpoints. The MICs of doripenem were determined by the broth microdilution method against 1,547 clinical isolates from eight French...

  3. In vitro antibacterial activity of ceftobiprole against clinical isolates from French teaching hospitals: proposition of zone diameter breakpoints

    OpenAIRE

    2011-01-01

    Abstract The aims of this study were to determine the in vitro activity profile of ceftobiprole, a pyrrolidinone cephalosporin, against a large number of bacterial pathogens and to propose zone diameter breakpoints for clinical categorisation according to the European Committee on Antimicrobial Susceptibility Testing (EUCAST) minimum inhibitory concentration (MIC) breakpoints. MICs of ceftobiprole were determined by broth microdilution against 1548 clinical isolates collected in ei...

  4. Gene alterations at Drosophila inversion breakpoints provide prima facie evidence for natural selection as an explanation for rapid chromosomal evolution

    Science.gov (United States)

    2012-01-01

    Background Chromosomal inversions have been pervasive during the evolution of the genus Drosophila, but there is significant variation between lineages in the rate of rearrangement fixation. D. mojavensis, an ecological specialist adapted to a cactophilic niche under extreme desert conditions, is a chromosomally derived species with ten fixed inversions, five of them not present in any other species. Results In order to explore the causes of the rapid chromosomal evolution in D. mojavensis, we identified and characterized all breakpoints of seven inversions fixed in chromosome 2, the most dynamic one. One of the inversions presents unequivocal evidence for its generation by ectopic recombination between transposon copies and another two harbor inverted duplications of non-repetitive DNA at the two breakpoints and were likely generated by staggered single-strand breaks and repair by non-homologous end joining. Four out of 14 breakpoints lay in the intergenic region between preexisting duplicated genes, suggesting an adaptive advantage of separating previously tightly linked duplicates. Four out of 14 breakpoints are associated with transposed genes, suggesting these breakpoints are fragile regions. Finally two inversions contain novel genes at their breakpoints and another three show alterations of genes at breakpoints with potential adaptive significance. Conclusions D. mojavensis chromosomal inversions were generated by multiple mechanisms, an observation that does not provide support for increased mutation rate as explanation for rapid chromosomal evolution. On the other hand, we have found a number of gene alterations at the breakpoints with putative adaptive consequences that directly point to natural selection as the cause of D. mojavensis rapid chromosomal evolution. PMID:22296923

  5. ERG and FLI1 binding sites demarcate targets for aberrant epigenetic regulation by AML1-ETO in acute myeloid leukemia

    NARCIS (Netherlands)

    Martens, Joost H. A.; Mandoli, Amit; Simmer, Femke; Wierenga, Bart-Jan; Saeed, Sadia; Singh, Abhishek A.; Altucci, Lucia; Vellenga, Edo; Stunnenberg, Hendrik G.

    2012-01-01

    ERG and FLI1 are closely related members of the ETS family of transcription factors and have been identified as essential factors for the function and maintenance of normal hematopoietic stem cells. Here genome-wide analysis revealed that both ERG and FLI1 occupy similar genomic regions as AML1-ETO

  6. Network as transconcept: elements for a conceptual demarcation in the field of public health.

    Science.gov (United States)

    Amaral, Carlos Eduardo Menezes; Bosi, Maria Lúcia Magalhães

    2016-08-22

    The main proposal to set up an articulated mode of operation of health services has been the concept of network, which has been appropriated in different ways in the field of public health, as it is used in other disciplinary fields or even taking it from common sense. Amid the diversity of uses and concepts, we recognize the need for rigorous conceptual demarcation about networks in the field of health. Such concern aims to preserve the strategic potential of this concept in the research and planning in the field, overcoming uncertainties and distortions still observed in its discourse-analytic circulation in public health. To this end, we will introduce the current uses of network in different disciplinary fields, emphasizing dialogues with the field of public health. With this, we intend to stimulate discussions about the development of empirical dimensions and analytical models that may allow us to understand the processes produced within and around health networks. RESUMO A principal proposta para configurar um modo articulado de funcionamento dos serviços de saúde tem sido o conceito de rede, que vem sendo apropriado de diferentes formas no campo da saúde coletiva, conforme seu emprego em outros campos disciplinares ou mesmo tomando-o do senso comum. Em meio à pluralidade de usos e concepções, reconhecemos a necessidade de rigorosa demarcação conceitual acerca de redes no campo da saúde. Tal preocupação visa a preservar o potencial estratégico desse conceito na investigação e planificação no campo, superando precariedades e distorções ainda observadas em sua circulação discursivo-analítica na saúde coletiva. Para tanto, apresentaremos os usos correntes de rede em diferentes campos disciplinares, destacando interlocuções com o campo da saúde coletiva. Com isso, pretendemos estimular o debate acerca do desenvolvimento de dimensões empíricas e modelos de análise que permitam compreender os processos produzidos no interior e ao redor

  7. Breakpoint mapping by next generation sequencing reveals causative gene disruption in patients carrying apparently balanced chromosome rearrangements with intellectual deficiency and/or congenital malformations.

    Science.gov (United States)

    Schluth-Bolard, Caroline; Labalme, Audrey; Cordier, Marie-Pierre; Till, Marianne; Nadeau, Gwenaël; Tevissen, Hélène; Lesca, Gaétan; Boutry-Kryza, Nadia; Rossignol, Sylvie; Rocas, Delphine; Dubruc, Estelle; Edery, Patrick; Sanlaville, Damien

    2013-03-01

    Apparently balanced chromosomal rearrangements (ABCR) are associated with an abnormal phenotype in 6% of cases. This may be due to cryptic genomic imbalances or to the disruption of genes at the breakpoint. However, breakpoint cloning using conventional methods (ie, fluorescent in situ hybridisation (FISH), Southern blot) is often laborious and time consuming. In this work, we used next generation sequencing (NGS) to locate breakpoints at the molecular level in four patients with multiple congenital abnormalities and/or intellectual deficiency (MCA/ID) who were carrying ABCR (one translocation, one complex chromosomal rearrangement and two inversions), which corresponded to nine breakpoints. Genomic imbalance was previously excluded by array comparative genomic hybridisation (CGH) in all four patients. Whole genome paired-end protocol was used to identify breakpoints. The results were verified by FISH and by PCR with Sanger sequencing. We were able to map all nine breakpoints. NGS revealed an additional breakpoint due to a cryptic inversion at a breakpoint junction in one patient. Nine of 10 breakpoints occurred in repetitive elements and five genes were disrupted in their intronic sequence (TCF4, SHANK2, PPFIA1, RAB19, KCNQ1). NGS is a powerful tool allowing rapid breakpoint cloning of ABCR at the molecular level. We showed that in three out of four patients, gene disruption could account for the phenotype, allowing adapted genetic counselling and stopping unnecessary investigations. We propose that patients carrying ABCR with an abnormal phenotype should be explored systematically by NGS once a genomic imbalance has been excluded by array CGH.

  8. Fluoroquinolone susceptibility testing of Salmonella enterica: detection of acquired resistance and selection of zone diameter breakpoints for levofloxacin and ofloxacin.

    Science.gov (United States)

    Sjölund-Karlsson, Maria; Howie, Rebecca L; Crump, John A; Whichard, Jean M

    2014-03-01

    Fluoroquinolones (e.g., ciprofloxacin) have become a mainstay for treating severe Salmonella infections in adults. Fluoroquinolone resistance in Salmonella is mostly due to mutations in the topoisomerase genes, but plasmid-mediated quinolone resistance (PMQR) mechanisms have also been described. In 2012, the Clinical and Laboratory Standards Institute (CLSI) revised the ciprofloxacin interpretive criteria (breakpoints) for disk diffusion and MIC test methods for Salmonella. In 2013, the CLSI published MIC breakpoints for Salmonella to levofloxacin and ofloxacin, but breakpoints for assigning disk diffusion results to susceptible (S), intermediate (I), and resistant (R) categories are still needed. In this study, the MICs and inhibition zone diameters for nalidixic acid, ciprofloxacin, levofloxacin, and ofloxacin were determined for 100 clinical isolates of nontyphi Salmonella with or without resistance mechanisms. We confirmed that the new levofloxacin MIC breakpoints resulted in the highest category agreement (94%) when plotted against the ciprofloxacin MICs and that the new ofloxacin MIC breakpoints resulted in 92% category agreement between ofloxacin and ciprofloxacin. By applying the new MIC breakpoints in the MIC zone scattergrams for levofloxacin and ofloxacin, the following disk diffusion breakpoints generated the least number of errors: ≥28 mm (S), 19 to 27 mm (I), and ≤18 mm (R) for levofloxacin and ≥25 mm (S), 16 to 24 mm (I), and ≤15 mm (R) for ofloxacin. Neither the levofloxacin nor the ofloxacin disk yielded good separation of isolates with and without resistance mechanisms. Further studies will be needed to develop a disk diffusion assay that efficiently detects all isolates with acquired resistance to fluoroquinolones.

  9. Detection of variations and identifying genomic breakpoints for large deletions in the LDLR by Ion Torrent semiconductor sequencing.

    Science.gov (United States)

    Faiz, Fathimath; Allcock, Richard J; Hooper, Amanda J; van Bockxmeer, Frank M

    2013-10-01

    The aims of this study were to 1) compare LDLR variant detection between Ion Torrent Personal Genome Machine (PGM) sequencing and conventional methods used for familial hypercholesterolaemia (FH) diagnosis i.e. exon-by-exon sequence analysis and multiplex ligation-dependent probe amplification (MLPA) and 2) identify genomic breakpoints for 12 cases of large deletions in LDLR previously identified by MLPA. Thirty FH patient samples were selected, 22 with mutations previously determined. Primers were designed and optimised to generate six amplicons covering the entire LDLR and sequenced on a PGM. An additional twelve samples carrying MLPA variants were sequenced on the PGM followed by Sanger sequencing to establish the breakpoints. A total of 2179 LDLR variants were identified in the 30 samples, with 383 variants in the region sequenced that was common to both PGM and Sanger methods. Three discrepancies were identified; two of these were identified by visual inspection of the BAM files, whilst the remaining discrepancy was likely an artefact of the PCR approach. Approximate genomic breakpoints for the 12 MLPA variants were identified using PGM sequencing, and Sanger sequencing of these regions established causative breakpoints. Eleven different rearrangements/mutational events were found, with eight out of eleven occurring in Alus. Two of the three samples with exons 2-6del had identical breakpoints. Two samples with exons 11-12del had unique breakpoints, indicating separate ancestral origin or mutational events. This study showed that Ion Torrent PGM sequencing is an accurate and efficient method to detect LDLR variants while providing additional information such as genomic breakpoints. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  10. Concurrent Breakpoints

    Science.gov (United States)

    2011-12-18

    motivated by recent testing techniques for concurrent programs, such as CalFuzzer [17, 39, 31, 18], AssetFuzzer [20], CTrigger [32], Penelope [40], and...40] F. Sorrentino, A. Farzan, and P. Madhusudan. Penelope : weaving threads to expose atomicity violations. In Eighteenth ACM SIGSOFT international

  11. Rapid mapping of chromosomal breakpoints: from blood to BAC in 20 days.

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Chun-Mei; Kwan, Johnson; Weier, Jingly F.; Baumgartner, Aldof; Wang, Mei; Escudero, Tomas; Munne, Santiago; Weier, Heinz-Ulrich

    2009-02-25

    Structural chromosome aberrations and associated segmental or chromosomal aneusomies are major causes of reproductive failure in humans. Despite the fact that carriers of reciprocal balanced translocation often have no other clinical symptoms or disease, impaired chromosome homologue pairing in meiosis and karyokinesis errors lead to over-representation of translocations carriers in the infertile population and in recurrent pregnancy loss patients. At present, clinicians have no means to select healthy germ cells or balanced zygotes in vivo, but in vitro fertilization (IVF) followed by preimplantation genetic diagnosis (PGD) offers translocation carriers a chance to select balanced or normal embryos for transfer. Although a combination of telomeric and centromeric probes can differentiate embryos that are unbalanced from normal or unbalanced ones, a seemingly random position of breakpoints in these IVF-patients poses a serious obstacle to differentiating between normal and balanced embryos, which for most translocation couples, is desirable. Using a carrier with reciprocal translocation t(4;13) as an example, we describe our state-of-the-art approach to the preparation of patient-specific DNA probes that span or 'extent' the breakpoints. With the techniques and resources described here, most breakpoints can be accurately mapped in a matter of days using carrier lymphocytes, and a few extra days are allowed for PGD-probe optimization. The optimized probes will then be suitable for interphase cell analysis, a prerequisite for PGD since blastomeres are biopsied from normally growing day 3 - embryos regardless of their position in the mitotic cell cycle. Furthermore, routine application of these rapid methods should make PGD even more affordable for translocation carriers enrolled in IVF programs.

  12. Breakpoint of a Y chromosome pericentric inversion in the DAZ gene area. A case report.

    Science.gov (United States)

    Causio, F; Canale, D; Schonauer, L M; Fischetto, R; Leonetti, T; Archidiacono, N

    2000-07-01

    The presence of a spermatogenesis locus (gene or gene complex) in the euchromatic region of the long arm of the Y chromosome (Yq11), defined as azoospermia factor on the basis of gross structural rearrangement, was detected. The gene family responsible for different spermatogenetic defects is "deleted in azoospermia" (DAZ). A 34-year-old man had oligozoospermia, and a cytogenetic analysis carried out on peripheral lymphocytes with G banding revealed a 46,X, inv(Y)(p11q11)karyotype. The relation between the chromosomal breakpoint and the DAZ gene was more precisely defined by a fluorescent in situ hybridization technique. We revealed two signals for the DAZ gene, weaker than normal, one on the short arm and the other on the long arm of the Y chromosome, indicating that the breakpoint was located at the DAZ gene level. This is the first report documenting a chromosomal pericentric inversion with disruption in the DAZ gene area. We hope to obtain information on whether the disruption affects a functional zone of the gene and correlates with oligospermia at the chromosomal level.

  13. ATM modulates the loading of recombination proteins onto a chromosomal translocation breakpoint hotspot.

    Directory of Open Access Journals (Sweden)

    Jiying Sun

    Full Text Available Chromosome translocations induced by DNA damaging agents, such as ionizing radiation and certain chemotherapies, alter genetic information resulting in malignant transformation. Abrogation or loss of the ataxia-telangiectasia mutated (ATM protein, a DNA damage signaling regulator, increases the incidence of chromosome translocations. However, how ATM protects cells from chromosome translocations is still unclear. Chromosome translocations involving the MLL gene on 11q23 are the most frequent chromosome abnormalities in secondary leukemias associated with chemotherapy employing etoposide, a topoisomerase II poison. Here we show that ATM deficiency results in the excessive binding of the DNA recombination protein RAD51 at the translocation breakpoint hotspot of 11q23 chromosome translocation after etoposide exposure. Binding of Replication protein A (RPA and the chromatin remodeler INO80, which facilitate RAD51 loading on damaged DNA, to the hotspot were also increased by ATM deficiency. Thus, in addition to activating DNA damage signaling, ATM may avert chromosome translocations by preventing excessive loading of recombinational repair proteins onto translocation breakpoint hotspots.

  14. Detection of Chromosomal Breakpoints in Patients with Developmental Delay and Speech Disorders

    Science.gov (United States)

    Utami, Kagistia H.; Hillmer, Axel M.; Aksoy, Irene; Chew, Elaine G. Y.; Teo, Audrey S. M.; Zhang, Zhenshui; Lee, Charlie W. H.; Chen, Pauline J.; Seng, Chan Chee; Ariyaratne, Pramila N.; Rouam, Sigrid L.; Soo, Lim Seong; Yousoof, Saira; Prokudin, Ivan; Peters, Gregory; Collins, Felicity; Wilson, Meredith; Kakakios, Alyson; Haddad, Georges; Menuet, Arnaud; Perche, Olivier; Tay, Stacey Kiat Hong; Sung, Ken W. K.; Ruan, Xiaoan; Ruan, Yijun; Liu, Edison T.; Briault, Sylvain; Jamieson, Robyn V.; Davila, Sonia; Cacheux, Valere

    2014-01-01

    Delineating candidate genes at the chromosomal breakpoint regions in the apparently balanced chromosome rearrangements (ABCR) has been shown to be more effective with the emergence of next-generation sequencing (NGS) technologies. We employed a large-insert (7–11 kb) paired-end tag sequencing technology (DNA-PET) to systematically analyze genome of four patients harbouring cytogenetically defined ABCR with neurodevelopmental symptoms, including developmental delay (DD) and speech disorders. We characterized structural variants (SVs) specific to each individual, including those matching the chromosomal breakpoints. Refinement of these regions by Sanger sequencing resulted in the identification of five disrupted genes in three individuals: guanine nucleotide binding protein, q polypeptide (GNAQ), RNA-binding protein, fox-1 homolog (RBFOX3), unc-5 homolog D (C.elegans) (UNC5D), transmembrane protein 47 (TMEM47), and X-linked inhibitor of apoptosis (XIAP). Among them, XIAP is the causative gene for the immunodeficiency phenotype seen in the patient. The remaining genes displayed specific expression in the fetal brain and have known biologically relevant functions in brain development, suggesting putative candidate genes for neurodevelopmental phenotypes. This study demonstrates the application of NGS technologies in mapping individual gene disruptions in ABCR as a resource for deciphering candidate genes in human neurodevelopmental disorders (NDDs). PMID:24603971

  15. Evolutionary breakpoints in the gibbon suggest association between cytosine methylation and karyotype evolution.

    Science.gov (United States)

    Carbone, Lucia; Harris, R Alan; Vessere, Gery M; Mootnick, Alan R; Humphray, Sean; Rogers, Jane; Kim, Sung K; Wall, Jeffrey D; Martin, David; Jurka, Jerzy; Milosavljevic, Aleksandar; de Jong, Pieter J

    2009-06-01

    Gibbon species have accumulated an unusually high number of chromosomal changes since diverging from the common hominoid ancestor 15-18 million years ago. The cause of this increased rate of chromosomal rearrangements is not known, nor is it known if genome architecture has a role. To address this question, we analyzed sequences spanning 57 breaks of synteny between northern white-cheeked gibbons (Nomascus l. leucogenys) and humans. We find that the breakpoint regions are enriched in segmental duplications and repeats, with Alu elements being the most abundant. Alus located near the gibbon breakpoints (other Alus. Bisulphite allelic sequencing reveals that these gibbon Alus have a lower average density of methylated cytosine that their human orthologues. The finding of higher CpG content and lower average CpG methylation suggests that the gibbon Alu elements are epigenetically distinct from their human orthologues. The association between undermethylation and chromosomal rearrangement in gibbons suggests a correlation between epigenetic state and structural genome variation in evolution.

  16. Evolutionary breakpoints in the gibbon suggest association between cytosine methylation and karyotype evolution.

    Directory of Open Access Journals (Sweden)

    Lucia Carbone

    2009-06-01

    Full Text Available Gibbon species have accumulated an unusually high number of chromosomal changes since diverging from the common hominoid ancestor 15-18 million years ago. The cause of this increased rate of chromosomal rearrangements is not known, nor is it known if genome architecture has a role. To address this question, we analyzed sequences spanning 57 breaks of synteny between northern white-cheeked gibbons (Nomascus l. leucogenys and humans. We find that the breakpoint regions are enriched in segmental duplications and repeats, with Alu elements being the most abundant. Alus located near the gibbon breakpoints (<150 bp have a higher CpG content than other Alus. Bisulphite allelic sequencing reveals that these gibbon Alus have a lower average density of methylated cytosine that their human orthologues. The finding of higher CpG content and lower average CpG methylation suggests that the gibbon Alu elements are epigenetically distinct from their human orthologues. The association between undermethylation and chromosomal rearrangement in gibbons suggests a correlation between epigenetic state and structural genome variation in evolution.

  17. Genomic instability in rat: Breakpoints induced by ionising radiation and interstitial telomeric-like sequences

    Energy Technology Data Exchange (ETDEWEB)

    Camats, Nuria [Institut de Biotecnologia i Biomedicina (IBB), Universitat Autonoma de Barcelona, 08193 Barcelona (Spain); Departament de Biologia Cel.lular, Fisiologia i Immunologia Universitat Autonoma de Barcelona, 08193 Barcelona (Spain); Ruiz-Herrera, Aurora [Departament de Biologia Cel.lular, Fisiologia i Immunologia Universitat Autonoma de Barcelona, 08193 Barcelona (Spain); Parrilla, Juan Jose [Servicio de Ginecologia y Obstetricia, Hospital Universitario Virgen de la Arrixaca, Ctra, Madrid-Cartagena, s/n, El Palmar, 30120 Murcia (Spain); Acien, Maribel [Servicio de Ginecologia y Obstetricia, Hospital Universitario Virgen de la Arrixaca, Ctra, Madrid-Cartagena, s/n, El Palmar, 30120 Murcia (Spain); Paya, Pilar [Servicio de Ginecologia y Obstetricia, Hospital Universitario Virgen de la Arrixaca, Ctra, Madrid-Cartagena, s/n, El Palmar, 30120 Murcia (Spain); Giulotto, Elena [Dipartimento di Genetica e Microbiologia Adriano Buzzati Traverso, Universita degli Studi di Pavia, 27100 Pavia (Italy); Egozcue, Josep [Departament de Biologia Cel.lular, Fisiologia i Immunologia Universitat Autonoma de Barcelona, 08193 Barcelona (Spain); Garcia, Francisca [Institut de Biotecnologia i Biomedicina (IBB), Universitat Autonoma de Barcelona, 08193 Barcelona (Spain); Garcia, Montserrat [Institut de Biotecnologia i Biomedicina (IBB), Universitat Autonoma de Barcelona, 08193 Barcelona (Spain) and Departament de Biologia Cellular, Fisiologia i Immunologia Universitat Autonoma de Barcelona, 08193 Barcelona (Spain)]. E-mail: Montserrat.Garcia.Caldes@uab.es

    2006-03-20

    The Norwegian rat (Rattus norvegicus) is the most widely studied experimental species in biomedical research although little is known about its chromosomal structure. The characterisation of possible unstable regions of the karyotype of this species would contribute to the better understanding of its genomic architecture. The cytogenetic effects of ionising radiation have been widely used for the study of genomic instability, and the importance of interstitial telomeric-like sequences (ITSs) in instability of the genome has also been reported in previous studies in vertebrates. In order to describe the unstable chromosomal regions of R. norvegicus, the distribution of breakpoints induced by X-irradiation and ITSs in its karyotype were analysed in this work. For the X-irradiation analysis, 52 foetuses (from 14 irradiated rats) were studied, 4803 metaphases were analysed, and a total of 456 breakpoints induced by X-rays were detected, located in 114 chromosomal bands, with 25 of them significantly affected by X-irradiation (hot spots). For the analysis of ITSs, three foetuses (from three rats) were studied, 305 metaphases were analysed and 121 ITSs were detected, widely distributed in the karyotype of this species. Seventy-six percent of all hot spots analysed in this study were co-localised with ITSs.

  18. The chimpanzee-specific pericentric inversions that distinguish humans and chimpanzees have identical breakpoints in Pan troglodytes and Pan paniscus.

    Science.gov (United States)

    Szamalek, Justyna M; Goidts, Violaine; Searle, Jeremy B; Cooper, David N; Hameister, Horst; Kehrer-Sawatzki, Hildegard

    2006-01-01

    Seven of nine pericentric inversions that distinguish human (HSA) and chimpanzee karyotypes are chimpanzee-specific. In this study we investigated whether the two extant chimpanzee species, Pan troglodytes (common chimpanzee) and Pan paniscus (bonobo), share exactly the same pericentric inversions. The methods applied were FISH with breakpoint-spanning BAC/PAC clones and PCR analyses of the breakpoint junction sequences. Our findings for the homologues to HSA 4, 5, 9, 12, 16, and 17 confirm for the first time at the sequence level that these pericentric inversions have identical breakpoints in the common chimpanzee and the bonobo. Therefore, these inversions predate the separation of the two chimpanzee species 0.86-2 Mya. Further, the inversions distinguishing human and chimpanzee karyotypes may be regarded as early acquisitions, such that they are likely to have been present at the time of human/chimpanzee divergence. According to the chromosomal speciation theory the inversions themselves could have promoted human speciation.

  19. Sequence analysis of the breakpoint regions of an X;5 translocation in a female with Duchenne muscular dystrophy

    Energy Technology Data Exchange (ETDEWEB)

    Bakel, I. van; Holt, S.; Craig, I. [Univ. of Oxford (United Kingdom)] [and others

    1995-08-01

    X;autosome translocations in females with Duchenne muscular dystrophy (DMD) provide an opportunity to study the mechanisms responsible for chromosomal rearrangements that occur in the germ line. We describe here a detailed molecular analysis of the translocation breakpoints of an X;autosome reciprocal translocation, t(X;5) (p21;q31.1), in a female with DMD. Cosmid clones that contained the X-chromosome breakpoint region were identified, and subclones that hybridized to the translocation junction fragment in restriction digests of the patient`s DNA were isolated and sequenced. Primers designed from the X-chromosomal sequence were used to obtain the junction fragments on the der(X) and the der(5) by inverse PCR. The resultant clones were also cloned and sequenced, and this information used to isolate the chromosome 5 breakpoint region. Comparison of the DNA sequences of the junction fragments with those of the breakpoint regions on chromosomes X and 5 revealed that the translocation arose by nonhomologous recombination with an imprecise reciprocal exchange. Four and six base pairs of unknown origin are inserted at the exchange points of the der(X) and der(5), respectively, and three nucleotides are deleted from the X-chromosome sequence. Two features were found that may have played a role in the generation of the translocation. These were (1) a repeat motif with an internal homopyrimidine stretch 10 bp upstream from the X-chromosome breakpoint and (2) a 9-bp sequence of 78% homology located near the breakpoints on chromosomes 5 and X. 32 refs., 4 figs., 2 tabs.

  20. Molecular analysis of deletions in the human beta-globin gene cluster: deletion junctions and locations of breakpoints.

    Science.gov (United States)

    Henthorn, P S; Smithies, O; Mager, D L

    1990-02-01

    DNA fragments that contain the deletion junction regions of four independent deletions involving the human beta-globin gene cluster have been isolated and cloned. The fragments were isolated from individuals with the conditions referred to as Sicilian (delta beta)zero-thalassemia, Turkish G gamma+(A gamma delta beta)zero-thalassemia, Black G gamma+(A gamma delta beta)zero-thalassemia, and HPFH-2. The sequences of the deletion junctions and of the normal DNA surrounding their 3' breakpoints were determined and compared to the previously determined sequences of normal DNA surrounding their 5' breakpoints. These comparisons show that the deletions were the result of nonhomologous recombinational events. Two of the deletion junctions contain "orphan" nucleotides, while the other two show very limited amounts of "junctional homology." Both types of junctions are common among recombination events in mammalian cells and we discuss a simple joining scheme that could account for the junctions reported here. Unlike other deletions in this cluster and in other gene clusters, none of the eight deletion breakpoints examined here occurred within Alu family repeats. To examine the significance of deletion breakpoints within various sequence categories, we analyzed the data from a well-defined set of deletions within this locus. In contrast to deletions in the alpha-globin gene cluster, the occurrence of breakpoints in Alu family repetitive sequences is not statistically significant within the beta-globin gene cluster. However, breakpoints do occur within transcriptional units of the beta-globin gene cluster more frequently than expected by chance alone. We conclude from our analysis that the mechanisms of DNA joining are not locus or location specific, but at least a portion of the mechanisms of chromosomal breakages do show locus specificity.

  1. DB2: a probabilistic approach for accurate detection of tandem duplication breakpoints using paired-end reads.

    Science.gov (United States)

    Yavaş, Gökhan; Koyutürk, Mehmet; Gould, Meetha P; McMahon, Sarah; LaFramboise, Thomas

    2014-03-05

    With the advent of paired-end high throughput sequencing, it is now possible to identify various types of structural variation on a genome-wide scale. Although many methods have been proposed for structural variation detection, most do not provide precise boundaries for identified variants. In this paper, we propose a new method, Distribution Based detection of Duplication Boundaries (DB2), for accurate detection of tandem duplication breakpoints, an important class of structural variation, with high precision and recall. Our computational experiments on simulated data show that DB2 outperforms state-of-the-art methods in terms of finding breakpoints of tandem duplications, with a higher positive predictive value (precision) in calling the duplications' presence. In particular, DB2's prediction of tandem duplications is correct 99% of the time even for very noisy data, while narrowing down the space of possible breakpoints within a margin of 15 to 20 bps on the average. Most of the existing methods provide boundaries in ranges that extend to hundreds of bases with lower precision values. Our method is also highly robust to varying properties of the sequencing library and to the sizes of the tandem duplications, as shown by its stable precision, recall and mean boundary mismatch performance. We demonstrate our method's efficacy using both simulated paired-end reads, and those generated from a melanoma sample and two ovarian cancer samples. Newly discovered tandem duplications are validated using PCR and Sanger sequencing. Our method, DB2, uses discordantly aligned reads, taking into account the distribution of fragment length to predict tandem duplications along with their breakpoints on a donor genome. The proposed method fine tunes the breakpoint calls by applying a novel probabilistic framework that incorporates the empirical fragment length distribution to score each feasible breakpoint. DB2 is implemented in Java programming language and is freely available

  2. SVA retrotransposon insertion-associated deletion represents a novel mutational mechanism underlying large genomic copy number changes with non-recurrent breakpoints

    NARCIS (Netherlands)

    J. Vogt (Julia); K. Bengesser (Kathrin); K.B.M. Claes (Kathleen B.M.); K. Wimmer (Katharina); V.-F. Mautner (Victor-Felix); R. van Minkelen (Rick); E. Legius (Eric); H. Brems (Hilde); M. Upadhyaya (Meena); J. Högel (Josef); C. Lazaro (Conxi); T. Rosenbaum (Thorsten); S. Bammert (Simone); L. Messiaen (Ludwine); D.N. Cooper (David); H. Kehrer-Sawatzki (Hildegard)

    2014-01-01

    textabstractBackground: Genomic disorders are caused by copy number changes that may exhibit recurrent breakpoints processed by nonallelic homologous recombination. However, region-specific disease-associated copy number changes have also been observed which exhibit non-recurrent breakpoints. The

  3. The Federation of Indian Organizations of the Negro River’s journey for traditional land demarcation in Brazil

    Directory of Open Access Journals (Sweden)

    Fernanda Martinez de Oliveira

    2011-07-01

    Full Text Available The article aims to present the fight for government recognition of indigenous collective rights to land ownership in the Upper Rio Negro region in Brazil. It contextualizes the historical aspects of the colonization process in the region and the efforts to create the  Federation of Indian Organizations of the Negro River (FOIRN. Focus of particular interest is how the organizational strategy adopted by the FOIRN has allowed the Indian population of the Upper Rio Negro to active participate in the land demarcation process, with their opinions heard and respected. The article was written with basis on information obtained from a variety of sources, such as documents, conversations and interviews with the main social actors involved in the area, carried out during a field visit to São Gabriel da Cachoeira in January 2010. 

  4. Sixty years old is the breakpoint of human frontal cortex aging.

    Science.gov (United States)

    Cabré, Rosanna; Naudí, Alba; Dominguez-Gonzalez, Mayelin; Ayala, Victòria; Jové, Mariona; Mota-Martorell, Natalia; Piñol-Ripoll, Gerard; Gil-Villar, Maria Pilar; Rué, Montserrat; Portero-Otín, Manuel; Ferrer, Isidre; Pamplona, Reinald

    2017-02-01

    Human brain aging is the physiological process which underlies as cause of cognitive decline in the elderly and the main risk factor for neurodegenerative diseases such as Alzheimer's disease. Human neurons are functional throughout a healthy adult lifespan, yet the mechanisms that maintain function and protect against neurodegenerative processes during aging are unknown. Here we show that protein oxidative and glycoxidative damage significantly increases during human brain aging, with a breakpoint at 60 years old. This trajectory is coincident with a decrease in the content of the mitochondrial respiratory chain complex I-IV. We suggest that the deterioration in oxidative stress homeostasis during aging induces an adaptive response of stress resistance mechanisms based on the sustained expression of REST, and increased or decreased expression of Akt and mTOR, respectively, over the adult lifespan in order to preserve cell neural survival and function. Copyright © 2016 Elsevier Inc. All rights reserved.

  5. Precise mapping of 17 deletion breakpoints within the central hotspot deletion region (introns 50 and 51) of the DMD gene.

    Science.gov (United States)

    Esposito, Gabriella; Tremolaterra, Maria Roberta; Marsocci, Evelina; Tandurella, Igor Cm; Fioretti, Tiziana; Savarese, Maria; Carsana, Antonella

    2017-12-01

    Exon deletions in the human DMD gene, which encodes the dystrophin protein, are the molecular defect in 50-70% of cases of Duchenne/Becker muscular dystrophies. Deletions are preferentially clustered in the 5' (exons 2-20) and the central (exons 45-53) region of DMD, likely because local DNA structure predisposes to specific breakage or recombination events. Notably, innovative therapeutic strategies may rescue dystrophin function by homology-based specific targeting of sequences within the central DMD hot spot deletion region. To further study molecular mechanisms that generate such frequent genome variations and to identify residual intronic sequences, we sequenced 17 deletion breakpoints within introns 50 and 51 of DMD and analyzed the surrounding genomic architecture. There was no breakpoint clustering within the introns nor extensive homology between sequences adjacent to each junction. However, at or near the breakpoint, we found microhomology, short tandem repeats, interspersed repeat elements and short sequence stretches that predispose to DNA deletion or bending. Identification of such structural elements contributes to elucidate general mechanisms generating deletion within the DMD gene. Moreover, precise mapping of deletion breakpoints and localization of repeated elements are of interest, because residual intronic sequences may be targeted by therapeutic strategies based on genome editing correction.

  6. Effect of chlorine demand on the ammonia breakpoint curve: model development, validation with nitrite, and application to municipal wastewater.

    Science.gov (United States)

    Chen, W L; Jensen, J N

    2001-01-01

    Chlorine added during wastewater disinfection may be consumed through reactions with chlorine-demanding chemical species. In this study, a mechanistically based kinetic model for chlorine demand in the presence of ammonia was developed and validated with laboratory studies on ammonia-nitrite systems, and then applied to breakpoint curves obtained with wastewater samples. The model is a modification of kinetic models for chlorine-ammonia systems to include hypochlorous acid-demand and monochloramine-demand reactions. The model accurately describes both laboratory-generated breakpoint curves with added nitrite and literature data. In a plant thought to be undergoing partial nitrification, breakpoint curves were consistent with high chlorine demand (i.e., small initial slopes and large doses to achieve the total chlorine maximum and breakpoint). A simplified kinetic model was also developed. Chlorine demand calculated from the simplified model was similar to chlorine demand from plant data. The simplified model was used to generate operating guidelines to calculate chlorine doses needed to overcome demand from nitrite or other sources.

  7. Optimum temperature of a northern population of Arctic charr (Salvelinus alpinus) using heart rate Arrhenius breakpoint analysis

    DEFF Research Database (Denmark)

    Hansen, Aslak Kappel; Byriel, David Bille; R. Jensen, Mads

    2017-01-01

    the optimum temperature (Topt) of nine adult Arctic charr (Salvelinus alpinus) from Qeqertarsuaq, Greenland, using maximum heart rate (fHmax) for investigating the optimal temperatures for activity. The Arrhenius breakpoint of maximum heart rate measurements occurred between 5.9 and 8.3 °C (average = 7.5 °C...

  8. A novel translocation breakpoint within the BPTF gene is associated with a pre-malignant phenotype.

    Directory of Open Access Journals (Sweden)

    Yosef Buganim

    Full Text Available Partial gain of chromosome arm 17q is an abundant aberrancy in various cancer types such as lung and prostate cancer with a prominent occurrence and prognostic significance in neuroblastoma--one of the most common embryonic tumors. The specific genetic element/s in 17q responsible for the cancer-promoting effect of these aberrancies is yet to be defined although many genes located in 17q have been proposed to play a role in malignancy. We report here the characterization of a naturally-occurring, non-reciprocal translocation der(Xt(X;17 in human lung embryonal-derived cells following continuous culturing. This aberrancy was strongly correlated with an increased proliferative capacity and with an acquired ability to form colonies in vitro. The breakpoint region was mapped by fluorescence in situ hybridization (FISH to the 17q24.3 locus. Further characterization by a custom-made comparative genome hybridization array (CGH localized the breakpoint within the Bromodomain PHD finger Transcription Factor gene (BPTF, a gene involved in transcriptional regulation and chromatin remodeling. Interestingly, this translocation led to elevation in the mRNA levels of the endogenous BPTF. Knock-down of BPTF restricted proliferation suggesting a role for BPTF in promoting cellular growth. Furthermore, the BPTF chromosomal region was found to be amplified in various human tumors, especially in neuroblastomas and lung cancers in which 55% and 27% of the samples showed gain of 17q24.3, respectively. Additionally, 42% percent of the cancer cell lines comprising the NCI-60 had an abnormal BPTF locus copy number. We suggest that deregulation of BPTF resulting from the translocation may confer the cells with the observed cancer-promoting phenotype and that our cellular model can serve to establish causality between 17q aberrations and carcinogenesis.

  9. Sustainable and effective control of trihalomethanes in the breakpoint chlorination of wastewater effluents.

    Science.gov (United States)

    Espigares, Elena; Moreno, Elena; Fernández-Crehuet, Milagros; Jiménez, Eladio; Espigares, Miguel

    2013-01-01

    The control of trihalomethanes (THMs) in waters subjected to chlorination is essential for protecting public health. However, the necessary means are not always available, especially in developing countries and regions. Under circumstances of scarce resources, one can utilize various means available for the control of THMs: a simple and affordable analytical method for testing of THMs, the study of the parameters tested routinely that could be used as indicators and the dose of chlorine used for the chlorination process. The objective of this work was to study the potential formation of THMs in wastewater effluents using a simple method of detection and various doses of chlorine in relation to the breakpoint and to validate some commonly determined parameters as indicators of THM formation. THM concentrations were measured using a simple spectrophotometric method based on the Fujiwara reaction. To determine the chlorine demand, a super-chlorination was performed and free and residual chlorine was measured; the mean value of chlorine demand was 166.6 mgCl2/L. The chlorination with concentrations well below the chlorine demand produces a significant reduction in microbial content. With regard to the formation of THMs the higher the dose of chlorine added, the higher the concentration of THMs. In relation to commonly determined parameters our data only provide a logarithmic linear regression between THMs and ammonium. According to our results, the breakpoint must be determined for the chlorination of sewage and their effluents, and chlorination should be performed with concentrations of chlorine at approximately 1/3 of the demand.

  10. Species-specific shifts in centromere sequence composition are coincident with breakpoint reuse in karyotypically divergent lineages

    Science.gov (United States)

    Bulazel, Kira V; Ferreri, Gianni C; Eldridge, Mark DB; O'Neill, Rachel J

    2007-01-01

    Background It has been hypothesized that rapid divergence in centromere sequences accompanies rapid karyotypic change during speciation. However, the reuse of breakpoints coincident with centromeres in the evolution of divergent karyotypes poses a potential paradox. In distantly related species where the same centromere breakpoints are used in the independent derivation of karyotypes, centromere-specific sequences may undergo convergent evolution rather than rapid sequence divergence. To determine whether centromere sequence composition follows the phylogenetic history of species evolution or patterns of convergent breakpoint reuse through chromosome evolution, we examined the phylogenetic trajectory of centromere sequences within a group of karyotypically diverse mammals, macropodine marsupials (wallabies, wallaroos and kangaroos). Results The evolution of three classes of centromere sequences across nine species within the genus Macropus (including Wallabia) were compared with the phylogenetic history of a mitochondrial gene, Cytochrome b (Cyt b), a nuclear gene, selenocysteine tRNA (TRSP), and the chromosomal histories of the syntenic blocks that define the different karyotype arrangements. Convergent contraction or expansion of predominant satellites is found to accompany specific karyotype rearrangements. The phylogenetic history of these centromere sequences includes the convergence of centromere composition in divergent species through convergent breakpoint reuse between syntenic blocks. Conclusion These data support the 'library hypothesis' of centromere evolution within this genus as each species possesses all three satellites yet each species has experienced differential expansion and contraction of individual classes. Thus, we have identified a correlation between the evolution of centromere satellite sequences, the reuse of syntenic breakpoints, and karyotype convergence in the context of a gene-based phylogeny. PMID:17708770

  11. Indigenous territorial rights as a human right; an analysis of the (auto demarcation of indigenous territories process in Venezuela (1999-2014

    Directory of Open Access Journals (Sweden)

    Linda Bustillos

    2016-04-01

    Full Text Available The 1999 Constitution of the Bolivarian Republic of Venezuela (CBRV recognizes Indigenous Rights; among them, the territorial claims. In agreement with what is stated in the article 119 of the Magna Carta, the right to the territory of these populations is exercised through the public policy of demarcation, which is understood as the process in which its territorial space is disclaimed, made by the State in participation with the peoples and communities to be demarcated, subsequently to entitle the collective ownership for these human beings groups. Fifteen years after the Constitution was approved, this process of delineation has been slow and misleading. This delay has caused that in the present, these human beings groups are being stalked by outside interests (illegal mining, development projects, irregular forces, among others who threaten their existence as distinct cultures; since the right to territory is a fundamental human right for their survival. This article is the result of a field research. In the first part, the study analyzes the Organic Law of Indigenous Peoples and Communities (LOPCI (2005 in Venezuela, with the purpose of clarifying at what stage the territorial demarcation process is paralyzed; and as a result, it describes how many communities and indigenous peoples have been demarcated and entitled from 2005 to 2014.

  12. Demarcation of homogeneous structural domains within a rock mass based on joint orientation and trace length

    Science.gov (United States)

    Song, Shengyuan; Wang, Qing; Chen, Jianping; Cao, Chen; Li, Yanyan; Zhou, Xin

    2015-11-01

    This paper presents a new method for determining the structural domain boundaries within the rock mass. This new method is based on a statistical comparison of data from pairs of sample regions. The stereonet is divided into 100 windows with approximately equal areas. The poles of joints occurring in each corresponding window on the two projection plots of the regions being compared are then merged and arranged in ascending order with respect to their trace lengths. Finally, the Wald-Wolfowitz runs test is used to identify the homogeneity of structural populations by analyzing the joint sequence. Based on a significance level of 0.01, the homogeneity of structural populations collected from four adjacent adits at the Songta dam site is determined using the proposed method. The results show that the boundaries of structural domain change with the sizes of the sampling domains being compared. The initial sampling domains should be selected according to the engineering geological conditions of the studied area. In addition, the clear advantage of the proposed method is that both joint orientation and trace length are considered.

  13. Quadriceps Muscles O2 Extraction and EMG Breakpoints during a Ramp Incremental Test

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    Danilo Iannetta

    2017-09-01

    Full Text Available Muscle deoxygenated breakpoint ([HHb]BP has been found to be associated with other indices of exercise tolerance in the vastus lateralis (VL muscle but not in the vastus medialis (VM and rectus femoris (RF.Purpose: To investigate whether the [HHb]BP occurs also in the VM and RF muscles and whether or not it is associated with other physiological indices of exercise tolerance, such as the EMG threshold (EMGt and the respiratory compensation point (RCP.Methods: Twelve young endurance trained participants performed maximal ramp incremental (RI cycling tests (25–30 W·min−1 increments. Muscle oxygen extraction and activity as well as ventilatory and gas exchange parameters were measured. After accounting for the mean response time, the oxygen uptake (V·O2 corresponding to the RCP, [HHb]BP, and the EMGt was determined.Results: Peak power output (POpeak was 359 ± 48 W. Maximal oxygen consumption (V·O2max was 3.87 ± 0.46 L·min−1. The V·O2 at the RCP was 3.39 ± 0.41 L·min−1. The V·O2 (L·min−1 corresponding to the [HHb]BP and EMGt were: 3.49 ± 0.46 and 3.40 ± 0.44; 3.44 ± 0.61 and 3.43 ± 0.49; 3.59 ± 0.52, and 3.48 ± 0.46 for VL, VM, and RF, respectively. Pearson's correlation between these thresholds ranged from 0.90 to 0.97 (P < 0.05. No difference was found for the absolute V·O2 and the normalized PO (% at which the thresholds occurred in all three muscles investigated (P > 0.05. Although in eight out of 12 participants, the [HHb]BP in the RF led to a steeper increase instead of leading to a plateau-like response as observed in the VL and VM, the V·O2 at the breakpoints still coincided with that at the RCP.Conclusions: This study demonstrated that local indices of exercise tolerance derived from different portions of the quadriceps are not different to the systemic index of the RCP.

  14. Impact of bacterial load on pharmacodynamics and susceptibility breakpoints for tigecycline and Klebsiella pneumoniae.

    Science.gov (United States)

    Tsala, Marilena; Vourli, Sophia; Daikos, George L; Tsakris, Athanassios; Zerva, Loukia; Mouton, Johan W; Meletiadis, Joseph

    2017-01-01

    In the absence of other therapeutic options, tigecycline is used to treat bloodstream infections and pneumonia caused by carbapenemase-producing Klebsiella pneumoniae (CP-Kp). In this study, the standard and high tigecycline dosing regimens were simulated and tested against different inocula of CP-Kp isolates in an in vitro pharmacokinetic (PK)/pharmacodynamic (PD) model. Four susceptible isolates (EUCAST MICs of 0.125-1 mg/L) and two intermediately susceptible CP-Kp clinical isolates (MICs of 2 mg/L) were tested at three different inocula (10(7), 10(5) and 10(3) cfu/mL), simulating tigecycline serum and lung fCmax concentrations of 0.15 and 1.5 mg/L, respectively, of 50 mg tigecycline every 12 h for 48 h. The exposure-effect relationships were described and the probability of target attainment was calculated for each inoculum in order to determine PK/PD susceptibility breakpoints. No cfu reduction was observed at serum concentrations. At lung concentrations and low inocula, a bacteriostatic and killing effect was found for isolates with MICs of 0.25 and 0.125 mg/L, respectively. The fAUC0-24/MIC (tAUC0-24/MIC) associated with half-maximal activity was 16 (150) with 10(3) cfu/mL, 28 (239) with 10(5) cfu/mL and 79 (590) with 10(7) cfu/mL. A PK/PD susceptibility breakpoint of ≤0.06 and ≤0.125 mg/L for bacteraemia with ≤10(1) cfu/mL and ≤0.25 and ≤0.5 mg/L for pneumonia with ≤10(3) cfu/g was determined for the standard tigecycline dose of 50 mg and the higher dose of 100 mg, respectively. Tigecycline monotherapy with either 50 or 100 mg would not be sufficient for most patients with bacteraemia, though the higher dose of 100 mg could be effective for patients with pneumonia with low bacterial load. © The Author 2016. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  15. Localization of the 17q breakpoint of a constitutional 1;17 translocation in a patient with neuroblastoma within a 25-kb segment located between the ACCN1 and TLK2 genes and near the distal breakpoints of two microdeletions in neurofibromatosis type 1 patients

    NARCIS (Netherlands)

    van Roy, Nadine; Vandesompele, Jo; Berx, Geert; Staes, Katrien; van Gele, Mireille; de Smet, Els; de Paepe, Anne; Laureys, Geneviève; van der Drift, Pauline; Versteeg, Rogier; van Roy, Frans; Speleman, Frank

    2002-01-01

    We have constructed a 1.4-Mb P1 artificial chromosome/bacterial artificial chromosome (PAC/BAC) contig spanning the 17q breakpoint of a constitutional translocation t(1;17)(p36.2;q11.2) in a patient with neuroblastoma. Three 17q breakpoint-overlapping cosmids were identified and sequenced. No coding

  16. Redefined genomic architecture in 15q24 directed by patient deletion/duplication breakpoint mapping.

    Science.gov (United States)

    El-Hattab, Ayman W; Smolarek, Teresa A; Walker, Martha E; Schorry, Elizabeth K; Immken, LaDonna L; Patel, Gayle; Abbott, Mary-Alice; Lanpher, Brendan C; Ou, Zhishuo; Kang, Sung-Hae L; Patel, Ankita; Scaglia, Fernando; Lupski, James R; Cheung, Sau Wai; Stankiewicz, Pawel

    2009-10-01

    We report four new patients with a submicroscopic deletion in 15q24 manifesting developmental delay, short stature, hypotonia, digital abnormalities, joint laxity, genital abnormalities, and characteristic facial features. These clinical features are shared with six recently reported patients with a 15q24 microdeletion, supporting the notion that this is a recognizable syndrome. We describe a case of an ~2.6 Mb microduplication involving a portion of the minimal deletion critical region in a 15-year-old male with short stature, mild mental retardation, attention deficit hyperactivity disorder, Asperger syndrome, decreased joint mobility, digital abnormalities, and characteristic facial features. Some of these features are shared with a recently reported case with a 15q24 microduplication involving the minimal deletion critical region. We also report two siblings and their mother with duplication adjacent and distal to this region exhibiting mild developmental delay, hypotonia, tapering fingers, characteristic facial features, and prominent ears. The deletion and duplication breakpoints were mapped by array comparative genomic hybridization and the genomic structure in 15q24 was analyzed further. Surprisingly, in addition to the previously recognized three low-copy repeat clusters (BP1, BP2, and BP3), we identified two other paralogous low-copy repeat clusters that likely mediated the formation of alternative sized 15q24 genomic rearrangements via non-allelic homologous recombination.

  17. Investigation of Breakpoint and Trend of Daily Air Temperature Range for Mashhad, Iran

    Directory of Open Access Journals (Sweden)

    shideh shams

    2017-01-01

    same temperatures. Third, a revision of internal consistence was done, verifying that daily Tmax always exceeds daily Tmin. Fourth, the temporal coherency was tested by checking if consecutive temperature records differ by more than 8 degrees. The homogeneity of the series was tested by means of the Standard Normal Homogeneity test, the Buishand range and the Pettitt tests, on yearly, seasonal and monthly time scales. Breakpoint can be detected by means of these methods. In addition, Von Neumann ratio test was used to explore the series’ randomness. Having investigated data’s randomness in this study, series’ trend was determined by the Kendal-Tau test. Furthermore, the slope of the series’ trend was calculated using the Sen’s slope method. Results Discussion: Results indicated a decreasing trend in DTR during last 60 years (1951-2010 in Mashhad climatological station. Moreover, the results revealed that the slope of yearly DTR was decreasing (-0.029 ⁰C per year, which indicates that minimum air temperature values raise more maximum air temperature values. A breakpoint was detected during 1985. During 1951-1985, the average amount of DTR was 14.6⁰C, while this parameter reduced to 12.9⁰C for the period 1985-2010. The Kendall-Tau test was used to obtain the significance of trend during 1951-2010, 1951-1985 and 1985-2010. The results showed that during 1951-2010, DTR significantly reduced at a rate of 0.29oC per decade. However, between 1951 and 1985, DTR trend increased at a rate of 0.61oC per decade, while DTR trend between 1985 and 2010 reduced at a rate of 0.19 ⁰C per decade, which was not significant (P-value=5%. In the seasonal DTR series, the highest trend’s slope was calculated for the summer data (-0.43 ⁰C in a decade, while the lowest one accrued in spring (-0.15⁰C in a decade. From 1951 to 1985, DTR had an increasing trend, due to minimum air temperature’s downward trend. But from the late 1980 to 2010, as it was expected, downward

  18. European Gene Mapping Project (EUROGEM): breakpoint panels for human chromosomes based on the CEPH reference families. Centre d'Etude du Polymorphisme Humain.

    Science.gov (United States)

    Cox, S A; Attwood, J; Bryant, S P; Bains, R; Povey, S; Rebello, M; Kapsetaki, M; Moschonas, N K; Grzeschik, K H; Otto, M; Dixon, M; Sudworth, H E; Kooy, R F; Wright, A; Teague, P; Terrenato, L; Vergnaud, G; Monfouilloux, S; Weissenbach, J; Alibert, O; Dib, C; Fauré, S; Bakker, E; Pearson, N M; Spurr, N K

    1996-11-01

    Meiotic breakpoint panels for human chromosomes 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 14, 15, 17, 18, 20 and X were constructed from genotypes from the CEPH reference families. Each recombinant chromosome included has a breakpoint well-supported with reference to defined quantitative criteria. The panels were constructed at both a low-resolution, useful for a first-pass localization, and high-resolution, for a more precise placement. The availability of such panels will reduce the number of genotyping experiments necessary to order new polymorphisms with respect to existing genetic markers. This paper shows only a representative sample of the breakpoints detected. The complete data are available on the World Wide Web (URL http:/(/)www.icnet.uk/axp/hgr/eurogem++ +/HTML/data.html) or by anonymous ftp (ftp.gene.ucl.ac.uk in/pub/eurogem/maps/breakpoints).

  19. Fine Mapping of Chromosome 17 Translocation Breakpoints ⩾900 Kb Upstream of SOX9 in Acampomelic Campomelic Dysplasia and a Mild, Familial Skeletal Dysplasia

    Science.gov (United States)

    Hill-Harfe, Katherine L.; Kaplan, Lee; Stalker, Heather J.; Zori, Roberto T.; Pop, Ramona; Scherer, Gerd; Wallace, Margaret R.

    2005-01-01

    Previously, our group reported a five-generation family in which a balanced t(13;17) translocation is associated with a spectrum of skeletal abnormalities, including Robin sequence, hypoplastic scapulae, and a missing pair of ribs. Using polymerase chain reaction (PCR) with chromosome-specific markers to analyze DNA from somatic cell hybrids containing the derivative translocation chromosomes, we narrowed the breakpoint on each chromosome. Subsequent sequencing of PCR products spanning the breakpoints identified the breaks precisely. The chromosome 17 breakpoint maps ∼932 kb upstream of the sex-determining region Y (SRY)–related high-mobility group box gene (SOX9) within a noncoding transcript represented by two IMAGE cDNA clones. A growing number of reports have implicated chromosome 17 breakpoints at a distance of up to 1 Mb from SOX9 in some cases of campomelic dysplasia (CD). Although this multigeneration family has a disorder that shares some features with CD, their phenotype is significantly milder than any reported cases of (nonmosaic) CD. Therefore, this case may represent an etiologically distinct skeletal dysplasia or may be an extremely mild familial example of CD, caused by the most proximal translocation breakpoint from SOX9 reported to date. In addition, we have refined the breakpoint in an acampomelic CD case described elsewhere and have found that it lies ∼900 kb upstream of SOX9. PMID:15717285

  20. 29 CFR Appendix D to Subpart R of... - Illustration of the Use of Control Lines To Demarcate Controlled Decking Zones (CDZs): Non...

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 8 2010-07-01 2010-07-01 false Illustration of the Use of Control Lines To Demarcate Controlled Decking Zones (CDZs): Non-mandatory Guidelines for Complying With § 1926.760(c)(3) D Appendix D... Steel Erection Pt. 1926, Subpt. R, App. D Appendix D to Subpart R of Part 1926—Illustration of the Use...

  1. Clinically and Microbiologically Derived Azithromycin Susceptibility Breakpoints for Salmonella enterica Serovars Typhi and Paratyphi A

    Science.gov (United States)

    Thieu, Nga Tran Vu; Dolecek, Christiane; Karkey, Abhilasha; Gupta, Ruchi; Turner, Paul; Dance, David; Maude, Rapeephan R.; Ha, Vinh; Tran, Chinh Nguyen; Thi, Phuong Le; Be, Bay Pham Van; Phi, La Tran Thi; Ngoc, Rang Nguyen; Ghose, Aniruddha; Dongol, Sabina; Campbell, James I.; Thanh, Duy Pham; Thanh, Tuyen Ha; Moore, Catrin E.; Sona, Soeng; Gaind, Rajni; Deb, Monorama; Anh, Ho Van; Van, Sach Nguyen; Tinh, Hien Tran; Day, Nicholas P. J.; Dondorp, Arjen; Thwaites, Guy; Faiz, Mohamed Abul; Phetsouvanh, Rattanaphone; Newton, Paul; Basnyat, Buddha; Farrar, Jeremy J.; Baker, Stephen

    2015-01-01

    Azithromycin is an effective treatment for uncomplicated infections with Salmonella enterica serovar Typhi and serovar Paratyphi A (enteric fever), but there are no clinically validated MIC and disk zone size interpretative guidelines. We studied individual patient data from three randomized controlled trials (RCTs) of antimicrobial treatment in enteric fever in Vietnam, with azithromycin used in one treatment arm, to determine the relationship between azithromycin treatment response and the azithromycin MIC of the infecting isolate. We additionally compared the azithromycin MIC and the disk susceptibility zone sizes of 1,640 S. Typhi and S. Paratyphi A clinical isolates collected from seven Asian countries. In the RCTs, 214 patients who were treated with azithromycin at a dose of 10 to 20 mg/ml for 5 to 7 days were analyzed. Treatment was successful in 195 of 214 (91%) patients, with no significant difference in response (cure rate, fever clearance time) with MICs ranging from 4 to 16 μg/ml. The proportion of Asian enteric fever isolates with an MIC of ≤16 μg/ml was 1,452/1,460 (99.5%; 95% confidence interval [CI], 98.9 to 99.7) for S. Typhi and 207/240 (86.3%; 95% CI, 81.2 to 90.3) (P azithromycin disk identified S. Typhi isolates with an MIC of ≤16 μg/ml with a sensitivity of 99.7%. An azithromycin MIC of ≤16 μg/ml or disk inhibition zone size of ≥13 mm enabled the detection of susceptible S. Typhi isolates that respond to azithromycin treatment. Further work is needed to define the response to treatment in S. Typhi isolates with an azithromycin MIC of >16 μg/ml and to determine MIC and disk breakpoints for S. Paratyphi A. PMID:25733500

  2. PDZK1 prevents neointima formation via suppression of breakpoint cluster region kinase in vascular smooth muscle.

    Science.gov (United States)

    Lee, Wan Ru; Sacharidou, Anastasia; Behling-Kelly, Erica; Oltmann, Sarah C; Zhu, Weifei; Ahmed, Mohamed; Gerard, Robert D; Hui, David Y; Abe, Jun-ichi; Shaul, Philip W; Mineo, Chieko

    2015-01-01

    Scavenger receptor class B, type I (SR-BI) and its adaptor protein PDZK1 mediate responses to HDL cholesterol in endothelium. Whether the receptor-adaptor protein tandem serves functions in other vascular cell types is unknown. The current work determined the roles of SR-BI and PDZK1 in vascular smooth muscle (VSM). To evaluate possible VSM functions of SR-BI and PDZK1 in vivo, neointima formation was assessed 21 days post-ligation in the carotid arteries of wild-type, SR-BI-/- or PDZK1-/- mice. Whereas neointima development was negligible in wild-type and SR-BI-/-, there was marked neointima formation in PDZK1-/- mice. PDZK1 expression was demonstrated in primary mouse VSM cells, and compared to wild-type cells, PDZK1-/- VSM displayed exaggerated proliferation and migration in response to platelet derived growth factor (PDGF). Tandem affinity purification-mass spectrometry revealed that PDZK1 interacts with breakpoint cluster region kinase (Bcr), which contains a C-terminal PDZ binding sequence and is known to enhance responses to PDGF in VSM. PDZK1 interaction with Bcr in VSM was demonstrated by pull-down and by coimmunoprecipitation, and the augmented proliferative response to PDGF in PDZK1-/- VSM was abrogated by Bcr depletion. Furthermore, compared with wild-type Bcr overexpression, the introduction of a Bcr mutant incapable of PDZK1 binding into VSM cells yielded an exaggerated proliferative response to PDGF. Thus, PDZK1 has novel SR-BI-independent function in VSM that affords protection from neointima formation, and this involves PDZK1 suppression of VSM cell proliferation via an inhibitory interaction with Bcr.

  3. Validation of a colistin plasma concentration breakpoint as a predictor of nephrotoxicity in patients treated with colistin methanesulfonate.

    Science.gov (United States)

    Horcajada, Juan P; Sorlí, Luisa; Luque, Sonia; Benito, Natividad; Segura, Concepción; Campillo, Nuria; Montero, Milagro; Esteve, Erika; Mirelis, Beatriz; Pomar, Virginia; Cuquet, Jordi; Martí, Carmina; Garro, Pau; Grau, Santiago

    2016-12-01

    Nephrotoxicity limits the effective use of colistin for the treatment of multidrug-resistant Gram-negative bacteria (MDR-GNB) infections. We previously defined a steady-state colistin plasma concentration (Css) of 2.42 mg/L that predicted nephrotoxicity at end of treatment (EOT). The objective of this study was to validate this breakpoint in a prospective cohort. This was a multicentre, prospective, observational study conducted at three hospitals with a cohort of patients treated for MDR-GNB infection with colistin methanesulfonate from September 2011 until January 2015. Nephrotoxicity was evaluated at Day 7 and at EOT using the RIFLE criteria. Css values were measured and analysed using HPLC. Taking the previously defined breakpoint for colistin concentration as a criterion, patients were divided into two groups (Css, ≤2.42 mg/L vs. >2.42 mg/L). Sixty-four patients were included. Seven patients (10.9%) had a Css > 2.42 mg/L and were compared with the remaining patients. Bivariate analysis showed that patients with a Css > 2.42 mg/L were older and had a significantly higher incidence of nephrotoxicity at Day 7 and EOT. Although not statistically significant, nephrotoxicity occurred earlier in these patients (6.2 days vs. 9.2 days in patients with lower Css; P = 0.091). Multivariate analysis of nephrotoxicity showed that Css > 2.42 mg/L was the only predictive factor. Nephrotoxicity was more frequent and occurred earlier in patients with colistin plasma concentrations higher than the previously defined breakpoint (2.42 mg/L). Colistin therapeutic drug monitoring should be routinely considered to avoid reaching this toxicity threshold and potential clinical consequences. Copyright © 2016 Elsevier B.V. and International Society of Chemotherapy. All rights reserved.

  4. Identification of novel deletion breakpoints bordered by segmental duplications in the NF1 locus using high resolution array‐CGH

    Science.gov (United States)

    Mantripragada, K K; Thuresson, A‐C; Piotrowski, A; de Ståhl, T Díaz; Menzel, U; Grigelionis, G; Ferner, R E; Griffiths, S; Bolund, L; Mautner, V; Nordling, M; Legius, E; Vetrie, D; Dahl, N; Messiaen, L; Upadhyaya, M; Bruder, C E G; Dumanski, J P

    2006-01-01

    Background Segmental duplications flanking the neurofibromatosis type 1 (NF1) gene locus on 17q11 mediate most gene deletions in NF1 patients. However, the large size of the gene and the complexity of the locus architecture pose difficulties in deletion analysis. We report the construction and application of the first NF1 locus specific microarray, covering 2.24 Mb of 17q11, using a non‐redundant approach for array design. The average resolution of analysis for the array is ∼12 kb per measurement point with an increased average resolution of 6.4 kb for the NF1 gene. Methods We performed a comprehensive array‐CGH analysis of 161 NF1 derived samples and identified heterozygous deletions of various sizes in 39 cases. The typical deletion was identified in 26 cases, whereas 13 samples showed atypical deletion profiles. Results The size of the atypical deletions, contained within the segment covered by the array, ranged from 6 kb to 1.6 Mb and their breakpoints could be accurately determined. Moreover, 10 atypical deletions were observed to share a common breakpoint either on the proximal or distal end of the deletion. The deletions identified by array‐CGH were independently confirmed using multiplex ligation‐dependent probe amplification. Bioinformatic analysis of the entire locus identified 33 segmental duplications. Conclusions We show that at least one of these segmental duplications, which borders the proximal breakpoint located within the NF1 intron 1 in five atypical deletions, might represent a novel hot spot for deletions. Our array constitutes a novel and reliable tool offering significantly improved diagnostics for this common disorder. PMID:15944227

  5. En Route towards European Clinical Breakpoints for Veterinary Antimicrobial Susceptibility Testing: A Position Paper Explaining the VetCAST Approach

    Directory of Open Access Journals (Sweden)

    Pierre-Louis Toutain

    2017-12-01

    Full Text Available VetCAST is the EUCAST sub-committee for Veterinary Antimicrobial Susceptibility Testing. Its remit is to define clinical breakpoints (CBPs for antimicrobial drugs (AMDs used in veterinary medicine in Europe. This position paper outlines the procedures and reviews scientific options to solve challenges for the determination of specific CBPs for animal species, drug substances and disease conditions. VetCAST will adopt EUCAST approaches: the initial step will be data assessment; then procedures for decisions on the CBP; and finally the release of recommendations for CBP implementation. The principal challenges anticipated by VetCAST are those associated with the differing modalities of AMD administration, including mass medication, specific long-acting product formulations or local administration. Specific challenges comprise mastitis treatment in dairy cattle, the range of species and within species breed considerations and several other variable factors not relevant to human medicine. Each CBP will be based on consideration of: (i an epidemiological cut-off value (ECOFF – the highest MIC that defines the upper end of the wild-type MIC distribution; (ii a PK/PD breakpoint obtained from pre-clinical pharmacokinetic data [this PK/PD break-point is the highest possible MIC for which a given percentage of animals in the target population achieves a critical value for the selected PK/PD index (fAUC/MIC or fT > MIC] and (iii when possible, a clinical cut-off, that is the relationship between MIC and clinical cure. For the latter, VetCAST acknowledges the paucity of such data in veterinary medicine. When a CBP cannot be established, VetCAST will recommend use of ECOFF as surrogate. For decision steps, VetCAST will follow EUCAST procedures involving transparency, consensus and independence. VetCAST will ensure freely available dissemination of information, concerning standards, guidelines, ECOFF, PK/PD breakpoints, CBPs and other relevant information

  6. Molecular characterization of two proximal deletion breakpoint regions in both Prader-Willi and Angelman syndrome patients

    Energy Technology Data Exchange (ETDEWEB)

    Christian, S.L.; Huang, B.; Ledbetter, D.H. [National Institutes of Health, Bethesda, MD (United States)] [and others

    1995-07-01

    Prader-Willi syndrome (PWS) and Angelman syndrome (AS) are distinct mental retardation syndromes caused by paternal and maternal deficiencies, respectively, in chromosome 15q11{minus}q13. Approximately 70% of these patients have a large deletion of {approximately}4 Mb extending from D15S9 (ML34) through D15S12 (IR10A). To further characterize the deletion breakpoints proximal to D15S9, three new polymorphic microsatellite markers were developed that showed observed heterozygosities of 60%-87%. D15S541 and D15S542 were isolated for YAC A124A3 containing the D15S18 (IR39) locus. D15S543 was isolated from a cosmid cloned from the proximal right end of YAC 254B5 containing the D15S9 (ML34) locus. Gene-centromere mapping of these markers, using a panel of ovarian teratomas of known meiotic origin, extended the genetic map of chromosome 15 by 2-3 cM toward the centromere. Analysis of the more proximal S541/S542 markers on 53 Prader-Willi and 33 Angelman deletion patients indicated two classes of patients: 44% (35/80) of the informative patients were deleted for these markers (class I), while 56% (45/80) were not deleted (class II), with no difference between PWS and AS. In contrast, D15S543 was deleted in all informative patients (13/48) or showed the presence of a single allele (in 35/48 patients), suggesting that this marker is deleted in the majority of PWS and AS cases. These results confirm the presence of two common proximal deletion breakpoint regions in both Prader-Willi and Angelman syndromes and are consistent with the same deletion mechanism being responsible for paternal and maternal deletions. One breakpoint region lies between D15S541/S542 and D15S543, with an additional breakpoint region being proximal to D15S541/S542. 46 refs., 2 figs., 3 tabs.

  7. Bilateral renal agenesis/hypoplasia/dysplasia (BRAHD: postmortem analysis of 45 cases with breakpoint mapping of two de novo translocations.

    Directory of Open Access Journals (Sweden)

    Louise Harewood

    2010-08-01

    Full Text Available Bilateral renal agenesis/hypoplasia/dysplasia (BRAHD is a relatively common, lethal malformation in humans. Established clinical risk factors include maternal insulin dependent diabetes mellitus and male sex of the fetus. In the majority of cases, no specific etiology can be established, although teratogenic, syndromal and single gene causes can be assigned to some cases.45 unrelated fetuses, stillbirths or infants with lethal BRAHD were ascertained through a single regional paediatric pathology service (male:female 34:11 or 3.1:1. The previously reported phenotypic overlaps with VACTERL, caudal dysgenesis, hemifacial microsomia and Müllerian defects were confirmed. A new finding is that 16/45 (35.6%; m:f 13:3 or 4.3:1 BRAHD cases had one or more extrarenal malformations indicative of a disoder of laterality determination including; incomplete lobulation of right lung (seven cases, malrotation of the gut (seven cases and persistence of the left superior vena cava (five cases. One such case with multiple laterality defects and sirelomelia was found to have a de novo apparently balanced reciprocal translocation 46,XY,t(2;6(p22.3;q12. Translocation breakpoint mapping was performed by interphase fluorescent in-situ hybridization (FISH using nuclei extracted from archival tissue sections in both this case and an isolated bilateral renal agenesis case associated with a de novo 46,XY,t(1;2(q41;p25.3. Both t(2;6 breakpoints mapped to gene-free regions with no strong evidence of cis-regulatory potential. Ten genes localized within 500 kb of the t(1;2 breakpoints. Wholemount in-situ expression analyses of the mouse orthologs of these genes in embryonic mouse kidneys showed strong expression of Esrrg, encoding a nuclear steroid hormone receptor. Immunohistochemical analysis showed that Esrrg was restricted to proximal ductal tissue within the embryonic kidney.The previously unreported association of BRAHD with laterality defects suggests that renal

  8. FISH approach to determine cat eye syndrome chromosome breakpoints of a patient with cat eye syndrome type II.

    Science.gov (United States)

    Gentile, M; De Sanctis, S; Cariola, F; Spezzi, T; Di Carlo, A; Tontoli, F; Lista, F; Buonadonna, A L

    2005-01-01

    We report a 19-year-old man with craniofacial dysmorphic features, anorectal malformations, eye colobomas, orthopaedic anomalies, and mild neurodevelopmental delay. Cat eye syndrome (CES) was suspected, and confirmed by cytogenetic analysis which showed the presence of a supernumerary bisatellited chromosome, identified by fluorescence in situ hybridization (FISH) as invdup(22). The marker was further analyzed with six BAC clones located at the 22q11.1 and 22q11.2 regions; this analysis allowed correct assignment at low copy repeat 4 on chromosome 22 (LCR22-4) of the two breakpoints, confirming the presence of a CES chromosome type II. The patient's phenotype is considered in the light of the cytogenetic, and FISH investigations results and other patients reported in literature. Molecular definition of the breakpoints at the LCR22-4 copy confirms the role of different chromosome 22-specific LCRs in CES chromosomes generation, as well as in other chromosome 22 germ line rearrangements. Our report confirms that, unlike other conditions, i.e. the invdup(15) bisatellited dicentric marker, the CES phenotype does not appear to correlate with the size of the marker chromosome. Additional cases are necessary to be able to draw more specific genotype-phenotype correlations and to determine the outcome of patients with CES, especially when this rare condition is diagnosed in prenatal age.

  9. Empirical third-generation cephalosporin therapy for adults with community-onset Enterobacteriaceae bacteraemia: Impact of revised CLSI breakpoints.

    Science.gov (United States)

    Hsieh, Chih-Chia; Lee, Chung-Hsun; Li, Ming-Chi; Hong, Ming-Yuan; Chi, Chih-Hsien; Lee, Ching-Chi

    2016-04-01

    Third-generation cephalosporins (3GCs) [ceftriaxone (CRO) and cefotaxime (CTX)] have remarkable potency against Enterobacteriaceae and are commonly prescribed for the treatment of community-onset bacteraemia. However, clinical evidence supporting the updated interpretive criteria of the Clinical and Laboratory Standards Institute (CLSI) is limited. Adults with community-onset monomicrobial Enterobacteriaceae bacteraemia treated empirically with CRO or CTX were recruited. Clinical information was collected from medical records and CTX MICs were determined using the broth microdilution method. Eligible patients (n=409) were categorised into de-escalation (260; 63.6%), no switch (115; 28.1%) and escalation (34; 8.3%) groups according to the type of definitive antibiotics. Multivariate regression revealed five independent predictors of 28-day mortality: fatal co-morbidities based on McCabe classification [odds ratio (OR)=19.96; PCLSI breakpoints) were not associated with mortality. Furthermore, clinical failure and 28-day mortality rates had a tendency to increase with increasing CTX MIC (γ=1.00; P=0.01). Conclusively, focusing on patients with community-onset Enterobacteriaceae bacteraemia receiving empirical 3GC therapy, the present study provides clinically critical evidence to validate the proposed reduction in the susceptibility breakpoint of CTX to MIC≤1mg/L. Copyright © 2016 Elsevier B.V. and the International Society of Chemotherapy. All rights reserved.

  10. Demarcation line depth after contact lens-assisted corneal crosslinking for progressive keratoconus: Comparison of dextran-based and hydroxypropyl methylcellulose-based riboflavin solutions.

    Science.gov (United States)

    Malhotra, Chintan; Jain, Arun K; Gupta, Amit; Ram, Jagat; Ramatchandirane, Balamurugan; Dhingra, Deepika; Sachdeva, Kulbhushan; Kumar, Amit

    2017-10-01

    To compare the demarcation line depth after contact lens-assisted corneal crosslinking (CXL) for progressive keratoconus using dextran-based and hydroxypropyl methylcellulose (HPMC)-based riboflavin solutions. Advanced Eye Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India. Retrospective case series. Patients with preoperative epithelium-on (epi-on) minimum corneal thickness between 350 μm and 450 μm having contact lens-assisted CXL for progressive keratoconus were crosslinked with isoosmolar 0.1% riboflavin in 20% dextran 500 or HPMC 1.1%. The primary outcome measure was the mean demarcation line depth measured 1 month postoperatively on anterior-segment optical coherence tomography. The secondary outcome measure was change in endothelial cell density (ECD) 6 months from baseline. The study comprised 21 patients (21 eyes, 9 in the HPMC group and 12 in the dextran group). The mean demarcation line depth was deeper in the HPMC group (308.22 μm ± 84.19 [SD]) than in the dextran group (235.33 ± 64.87 μm) (P < .04). This difference remained significant (P = .02) even after controlling for the preoperative lesser epi-on minimum corneal thickness in the HPMC group (385.56 ±13.81 μm) versus the dextran group (413.08 ± 29.58 μm) (P < .02). The ECD 6 months after contact lens-assisted CXL was comparable to the baseline levels in both groups (P = .19 and P = .09, respectively). During contact lens-assisted CXL, HPMC-based riboflavin seemed to be associated with a deeper demarcation line than dextran-based riboflavin, although both solutions were safe for the endothelium at 6 months. Copyright © 2017 ASCRS and ESCRS. Published by Elsevier Inc. All rights reserved.

  11. Nerve growth factor receptor gene is at human chromosome region 17q12-17q22, distal to the chromosome 17 breakpoint in acute leukemias

    Energy Technology Data Exchange (ETDEWEB)

    Huebner, K.; Isobe, M.; Chao, M.; Bothwell, M.; Ross, A.H.; Finan, J.; Hoxie, J.A.; Sehgal, A.; Buck, C.R.; Lanahan, A.

    1986-03-01

    Genomic and cDNA clones for the human nerve growth factor receptor have been used in conjunction with somatic cell hybrid analysis and in situ hybridization to localize the nerve growth factor receptor locus to human chromosome region 17q12-q22. Additionally, part, if not all, of the nerve growth factor receptor locus is present on the translocated portion of 17q (17q21-qter) from a poorly differential acute leukemia in which the chromosome 17 breakpoint was indistinguishable cytogenetically from the 17 breakpoint observed in the t(15;17)(q22;q21) translocation associated with acute promyelocytic leukemia. Thus the nerve growth factor receptor locus may be closely distal to the acute promyelocytic leukemia-associated chromosome 17 breakpoint at 17q21.

  12. Comparison of disk diffusion, Etest and VITEK2 for detection of carbapenemase-producing Klebsiella pneumoniae with the EUCAST and CLSI breakpoint systems.

    Science.gov (United States)

    Vading, M; Samuelsen, Ø; Haldorsen, B; Sundsfjord, A S; Giske, C G

    2011-05-01

    The aim of this study was to compare CLSI and EUCAST MIC and disk diffusion carbapenem breakpoints for the detection of carbapenemase-producing Klebsiella pneumoniae. K. pneumoniae strains with known KPC (n = 31) or VIM (n = 20) carbapenemases were characterized by disk diffusion (Oxoid) and Etest (bioMérieux) vs. imipenem, meropenem and ertapenem, and with VITEK2 (bioMérieux, five different cards). Extended-spectrum β-lactamase (ESBL) testing was performed with VITEK2 (bioMérieux), ESBL combination disks (Becton Dickinson) and the ESBL Etest (bioMérieux). With CLSI and EUCAST MIC breakpoints, respectively, 11 and seven of the strains were susceptible to imipenem, 12 and eight to meropenem, and seven and none to ertapenem. The EUCAST epidemiological cut-off (ECOFF) values for meropenem and ertapenem identified all carbapenemase producers, whereas the imipenem ECOFF failed in five strains. All carbapenemase producers were detected with EUCAST disk diffusion breakpoints for ertapenem and meropenem, and four strains were susceptible to imipenem. CLSI disk diffusion breakpoints characterized 18 (imipenem), 14 (meropenem) and three (ertapenem) isolates as susceptible. When cards with a single carbapenem were used, detection failures with VITEK2 were four for imipenem, none for meropenem and one for ertapenem. Cards containing all three carbapenems had one to two failures. With ESBL combination disks, 21/31 KPC producers and 2/20 VIM producers were positive. With VITEK2, no VIM producers and between none and seven KPC producers were ESBL-positive. All carbapenemase producers were detected with the meropenem MIC ECOFF, or the clinical EUCAST breakpoint for ertapenem. EUCAST disk diffusion breakpoints for meropenem and ertapenem detected all carbapenemase producers. VITEK2 had between none and four failures in detecting carbapenemase producers, depending on the antibiotic card. © 2010 The Authors. Clinical Microbiology and Infection © 2010 European Society

  13. Significant Role of Segmental Duplications and SIDD Sites in Chromosomal Translocations of Hematological Malignancies: A Multi-parametric Bioinformatic Analysis.

    Science.gov (United States)

    Daga, Aditi; Ansari, Afzal; Pandya, Medha; Shah, Krupa; Patel, Shanaya; Rawal, Rakesh; Umrania, Valentina

    2016-11-28

    Recurrent non-random chromosomal translocations are hallmark characteristics of leukemogenesis, and however, molecular mechanisms underlying these rearrangements are less explored. The fundamental question is, why and how chromosomes break and reunite so precisely in the genome. Meticulous understanding of mechanism leading to chromosomal rearrangement can be achieved by characterizing breakpoints. To address this hypothesis, a novel multi-parametric computational approach for characterization of major leukemic translocations within and around breakpoint region was performed. To best of our knowledge, this bioinformatic analysis is unique in finding the presence of segmental duplications (SDs) flanking breakpoints of all major leukemic translocation. Breakpoint islands (BpIs) were analyzed for stress-induced duplex destabilization (SIDD) sites along with other complex genomic architecture and physicochemical properties. Our study distinctly emphasizes on the probable correlative role of SDs, SIDD sites and various genomic features in the occurrence of breakpoints. Further, it also highlights potential features which may be playing a crucial role in causing double-strand breaks, leading to translocation.

  14. The clinical impact of chromosomal rearrangements with breakpoints upstream of the SOX9 gene: two novel de novo balanced translocations associated with acampomelic campomelic dysplasia.

    Science.gov (United States)

    Fonseca, Ana Carolina S; Bonaldi, Adriano; Bertola, Débora R; Kim, Chong A; Otto, Paulo A; Vianna-Morgante, Angela M

    2013-05-07

    The association of balanced rearrangements with breakpoints near SOX9 [SRY (sex determining region Y)-box 9] with skeletal abnormalities has been ascribed to the presumptive altering of SOX9 expression by the direct disruption of regulatory elements, their separation from SOX9 or the effect of juxtaposed sequences. We report on two sporadic apparently balanced translocations, t(7;17)(p13;q24) and t(17;20)(q24.3;q11.2), whose carriers have skeletal abnormalities that led to the diagnosis of acampomelic campomelic dysplasia (ACD; MIM 114290). No pathogenic chromosomal imbalances were detected by a-CGH. The chromosome 17 breakpoints were mapped, respectively, 917-855 kb and 601-585 kb upstream of the SOX9 gene. A distal cluster of balanced rearrangements breakpoints on chromosome 17 associated with SOX9-related skeletal disorders has been mapped to a segment 932-789 kb upstream of SOX9. In this cluster, the breakpoint of the herein described t(17;20) is the most telomeric to SOX9, thus allowing the redefining of the telomeric boundary of the distal breakpoint cluster region related to skeletal disorders to 601-585 kb upstream of SOX9. Although both patients have skeletal abnormalities, the t(7;17) carrier presents with relatively mild clinical features, whereas the t(17;20) was detected in a boy with severe broncheomalacia, depending on mechanical ventilation. Balanced and unbalanced rearrangements associated with disorders of sex determination led to the mapping of a regulatory region of SOX9 function on testicular differentiation to a 517-595 kb interval upstream of SOX9, in addition to TESCO (Testis-specific enhancer of SOX9 core). As the carrier of t(17;20) has an XY sex-chromosome constitution and normal male development for his age, the segment of chromosome 17 distal to the translocation breakpoint should contain the regulatory elements for normal testis development. These two novel translocations illustrate the clinical variability in carriers of balanced

  15. On the validity of setting breakpoint minimum inhibition concentrations at one quarter of the plasma concentration achieved following oral administration of oxytetracycline

    DEFF Research Database (Denmark)

    Coyne, R.; Samuelsen, O.; Bergh, Ø.

    2004-01-01

    .03125–0.0625 mg/l. These breakpoint values would, therefore, predict that the therapy should have had no beneficial effect and that any strain of A. salmonicida with MIC>0.0625 mg/l must be considered as resistant. A consideration of the pattern of the mortalities before and during the period of therapy suggests...... administration of OTC medicated feed were applied to investigate the validity of the application of the 4:1 ratio. Breakpoints generated by the application of this ratio to these data would suggest that OTC could never have had any value in combating A. salmonicida infections. As this conclusion is contrary...

  16. The clinical impact of chromosomal rearrangements with breakpoints upstream of the SOX9 gene: two novel de novo balanced translocations associated with acampomelic campomelic dysplasia

    Science.gov (United States)

    2013-01-01

    Background The association of balanced rearrangements with breakpoints near SOX9 [SRY (sex determining region Y)-box 9] with skeletal abnormalities has been ascribed to the presumptive altering of SOX9 expression by the direct disruption of regulatory elements, their separation from SOX9 or the effect of juxtaposed sequences. Case presentation We report on two sporadic apparently balanced translocations, t(7;17)(p13;q24) and t(17;20)(q24.3;q11.2), whose carriers have skeletal abnormalities that led to the diagnosis of acampomelic campomelic dysplasia (ACD; MIM 114290). No pathogenic chromosomal imbalances were detected by a-CGH. The chromosome 17 breakpoints were mapped, respectively, 917–855 kb and 601–585 kb upstream of the SOX9 gene. A distal cluster of balanced rearrangements breakpoints on chromosome 17 associated with SOX9-related skeletal disorders has been mapped to a segment 932–789 kb upstream of SOX9. In this cluster, the breakpoint of the herein described t(17;20) is the most telomeric to SOX9, thus allowing the redefining of the telomeric boundary of the distal breakpoint cluster region related to skeletal disorders to 601–585 kb upstream of SOX9. Although both patients have skeletal abnormalities, the t(7;17) carrier presents with relatively mild clinical features, whereas the t(17;20) was detected in a boy with severe broncheomalacia, depending on mechanical ventilation. Balanced and unbalanced rearrangements associated with disorders of sex determination led to the mapping of a regulatory region of SOX9 function on testicular differentiation to a 517–595 kb interval upstream of SOX9, in addition to TESCO (Testis-specific enhancer of SOX9 core). As the carrier of t(17;20) has an XY sex-chromosome constitution and normal male development for his age, the segment of chromosome 17 distal to the translocation breakpoint should contain the regulatory elements for normal testis development. Conclusions These two novel translocations illustrate

  17. The verification of wilderness area boundaries as part of a buffer zone demarcation process: A case study from the uKhahlamba Drakensberg Park World Heritage Site

    Science.gov (United States)

    Sonja C. Kruger; Ian A. Rusworth; Kirsten Oliver

    2011-01-01

    Wilderness areas are by definition free from the sights and sounds of modern man. The boundaries of wilderness areas have traditionally been defined based on the management authorities' perceptions of which areas have wilderness quality. Experience shows that many areas classified as wilderness do not actually have wilderness qualities and do not provide a true...

  18. Identification of a yeast artificial chromosome that spans the human papillary renal cell carcinoma-associated t(X;1) breakpoint in Xp11.2

    NARCIS (Netherlands)

    Suijkerbuijk, R F; Meloni, A M; Sinke, R J; de Leeuw, B; Wilbrink, M; Janssen, H A; Geraghty, M T; Monaco, A P; Sandberg, A A; Geurts van Kessel, A

    1993-01-01

    Recently, a specific chromosome abnormality, t(X;1)(p11;q21), was described for a subgroup of human papillary renal cell carcinomas. The translocation breakpoint in Xp11 is located in the same region as that in t(X;18)(p11;q11)-positive synovial sarcoma. We used fluorescence in situ hybridization

  19. A high-resolution comparative map between pig chromosome 17 and human chromosomes 4, 8, and 20: Identification of synteny breakpoints

    DEFF Research Database (Denmark)

    Lahbib-Mansais, Yvette; Karlskov-Mortensen, Peter; Mompart, Florence

    2005-01-01

    We report on the construction of a high-resolution comparative map of porcine chromosome 17 (SSC17) focusing on evolutionary breakpoints with human chromosomes. The comparative map shows high homology with human chromosome 20 but suggests more limited homologies with other human chromosomes. SSC1...

  20. Analysis of t(9;17)(q33.2;q25.3) chromosomal breakpoint regions and genetic association reveals novel candidate genes for bipolar disorder

    DEFF Research Database (Denmark)

    Rajkumar, Anto P; Christensen, Jane H; Mattheisen, Manuel

    2015-01-01

    ,856) data. Genetic associations between these disorders and single nucleotide polymorphisms within these breakpoint regions were analysed by BioQ, FORGE, and RegulomeDB programmes. RESULTS: Four protein-coding genes [coding for (endonuclease V (ENDOV), neuronal pentraxin I (NPTX1), ring finger protein 213...

  1. Susceptibility breakpoints and target values for therapeutic drug monitoring of voriconazole and Aspergillus fumigatus in an in vitro pharmacokinetic/pharmacodynamic model

    NARCIS (Netherlands)

    Siopi, M.; Mavridou, E.; Mouton, J.W.; Verweij, P.E.; Zerva, L.; Meletiadis, J.

    2014-01-01

    BACKGROUND: Although voriconazole reached the bedside 10 years ago and became the standard care in the treatment of invasive aspergillosis, reliable clinical breakpoints are still in high demand. Moreover, this has increased due to the recent emergence of azole resistance. METHODS: Four clinical

  2. GeneBreak: detection of recurrent DNA copy number aberration-associated chromosomal breakpoints within genes [version 2; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Evert van den Broek

    2017-07-01

    Full Text Available Development of cancer is driven by somatic alterations, including numerical and structural chromosomal aberrations. Currently, several computational methods are available and are widely applied to detect numerical copy number aberrations (CNAs of chromosomal segments in tumor genomes. However, there is lack of computational methods that systematically detect structural chromosomal aberrations by virtue of the genomic location of CNA-associated chromosomal breaks and identify genes that appear non-randomly affected by chromosomal breakpoints across (large series of tumor samples. ‘GeneBreak’ is developed to systematically identify genes recurrently affected by the genomic location of chromosomal CNA-associated breaks by a genome-wide approach, which can be applied to DNA copy number data obtained by array-Comparative Genomic Hybridization (CGH or by (low-pass whole genome sequencing (WGS. First, ‘GeneBreak’ collects the genomic locations of chromosomal CNA-associated breaks that were previously pinpointed by the segmentation algorithm that was applied to obtain CNA profiles. Next, a tailored annotation approach for breakpoint-to-gene mapping is implemented. Finally, dedicated cohort-based statistics is incorporated with correction for covariates that influence the probability to be a breakpoint gene. In addition, multiple testing correction is integrated to reveal recurrent breakpoint events. This easy-to-use algorithm, ‘GeneBreak’, is implemented in R (www.cran.r-project.org and is available from Bioconductor (www.bioconductor.org/packages/release/bioc/html/GeneBreak.html.

  3. Sequencing and characterisation of rearrangements in three S. pastorianus strains reveals the presence of chimeric genes and gives evidence of breakpoint reuse.

    Directory of Open Access Journals (Sweden)

    Sarah K Hewitt

    Full Text Available Gross chromosomal rearrangements have the potential to be evolutionarily advantageous to an adapting organism. The generation of a hybrid species increases opportunity for recombination by bringing together two homologous genomes. We sought to define the location of genomic rearrangements in three strains of Saccharomyces pastorianus, a natural lager-brewing yeast hybrid of Saccharomyces cerevisiae and Saccharomyces eubayanus, using whole genome shotgun sequencing. Each strain of S. pastorianus has lost species-specific portions of its genome and has undergone extensive recombination, producing chimeric chromosomes. We predicted 30 breakpoints that we confirmed at the single nucleotide level by designing species-specific primers that flank each breakpoint, and then sequencing the PCR product. These rearrangements are the result of recombination between areas of homology between the two subgenomes, rather than repetitive elements such as transposons or tRNAs. Interestingly, 28/30 S. cerevisiae-S. eubayanus recombination breakpoints are located within genic regions, generating chimeric genes. Furthermore we show evidence for the reuse of two breakpoints, located in HSP82 and KEM1, in strains of proposed independent origin.

  4. A Plasmodium Whole-Genome Synteny Map: Indels and Synteny Breakpoints as Foci for Species-Specific Genes.

    Directory of Open Access Journals (Sweden)

    2005-12-01

    Full Text Available Whole-genome comparisons are highly informative regarding genome evolution and can reveal the conservation of genome organization and gene content, gene regulatory elements, and presence of species-specific genes. Initial comparative genome analyses of the human malaria parasite Plasmodium falciparum and rodent malaria parasites (RMPs revealed a core set of 4,500 Plasmodium orthologs located in the highly syntenic central regions of the chromosomes that sharply defined the boundaries of the variable subtelomeric regions. We used composite RMP contigs, based on partial DNA sequences of three RMPs, to generate a whole-genome synteny map of P. falciparum and the RMPs. The core regions of the 14 chromosomes of P. falciparum and the RMPs are organized in 36 synteny blocks, representing groups of genes that have been stably inherited since these malaria species diverged, but whose relative organization has altered as a result of a predicted minimum of 15 recombination events. P. falciparum-specific genes and gene families are found in the variable subtelomeric regions (575 genes, at synteny breakpoints (42 genes, and as intrasyntenic indels (126 genes. Of the 168 non-subtelomeric P. falciparum genes, including two newly discovered gene families, 68% are predicted to be exported to the surface of the blood stage parasite or infected erythrocyte. Chromosomal rearrangements are implicated in the generation and dispersal of P. falciparum-specific gene families, including one encoding receptor-associated protein kinases. The data show that both synteny breakpoints and intrasyntenic indels can be foci for species-specific genes with a predicted role in host-parasite interactions and suggest that, besides rearrangements in the subtelomeric regions, chromosomal rearrangements may also be involved in the generation of species-specific gene families. A majority of these genes are expressed in blood stages, suggesting that the vertebrate host exerts a greater

  5. A Plasmodium whole-genome synteny map: indels and synteny breakpoints as foci for species-specific genes.

    Directory of Open Access Journals (Sweden)

    Taco W A Kooij

    2005-12-01

    Full Text Available Whole-genome comparisons are highly informative regarding genome evolution and can reveal the conservation of genome organization and gene content, gene regulatory elements, and presence of species-specific genes. Initial comparative genome analyses of the human malaria parasite Plasmodium falciparum and rodent malaria parasites (RMPs revealed a core set of 4,500 Plasmodium orthologs located in the highly syntenic central regions of the chromosomes that sharply defined the boundaries of the variable subtelomeric regions. We used composite RMP contigs, based on partial DNA sequences of three RMPs, to generate a whole-genome synteny map of P. falciparum and the RMPs. The core regions of the 14 chromosomes of P. falciparum and the RMPs are organized in 36 synteny blocks, representing groups of genes that have been stably inherited since these malaria species diverged, but whose relative organization has altered as a result of a predicted minimum of 15 recombination events. P. falciparum-specific genes and gene families are found in the variable subtelomeric regions (575 genes, at synteny breakpoints (42 genes, and as intrasyntenic indels (126 genes. Of the 168 non-subtelomeric P. falciparum genes, including two newly discovered gene families, 68% are predicted to be exported to the surface of the blood stage parasite or infected erythrocyte. Chromosomal rearrangements are implicated in the generation and dispersal of P. falciparum-specific gene families, including one encoding receptor-associated protein kinases. The data show that both synteny breakpoints and intrasyntenic indels can be foci for species-specific genes with a predicted role in host-parasite interactions and suggest that, besides rearrangements in the subtelomeric regions, chromosomal rearrangements may also be involved in the generation of species-specific gene families. A majority of these genes are expressed in blood stages, suggesting that the vertebrate host exerts a greater

  6. Pharmacokinetics and Pharmacodynamics of Fluconazole for Cryptococcal Meningoencephalitis: Implications for Antifungal Therapy and In Vitro Susceptibility Breakpoints

    Science.gov (United States)

    Sudan, Ajay; Livermore, Joanne; Howard, Susan J.; Al-Nakeeb, Zaid; Sharp, Andrew; Goodwin, Joanne; Gregson, Lea; Warn, Peter A.; Felton, Tim W.; Perfect, John R.; Harrison, Thomas S.

    2013-01-01

    Fluconazole is frequently the only antifungal agent that is available for induction therapy for cryptococcal meningitis. There is relatively little understanding of the pharmacokinetics and pharmacodynamics (PK-PD) of fluconazole in this setting. PK-PD relationships were estimated with 4 clinical isolates of Cryptococcus neoformans. MICs were determined using Clinical and Laboratory Standards Institute (CLSI) methodology. A nonimmunosuppressed murine model of cryptococcal meningitis was used. Mice received two different doses of fluconazole (125 mg/kg of body weight/day and 250 mg/kg of body weight/day) orally for 9 days; a control group of mice was not given fluconazole. Fluconazole concentrations in plasma and in the cerebrum were determined using high-performance liquid chromatography (HPLC). The cryptococcal density in the brain was estimated using quantitative cultures. A mathematical model was fitted to the PK-PD data. The experimental results were extrapolated to humans (bridging study). The PK were linear. A dose-dependent decline in fungal burden was observed, with near-maximal activity evident with dosages of 250 mg/kg/day. The MIC was important for understanding the exposure-response relationships. The mean AUC/MIC ratio associated with stasis was 389. The results of the bridging study suggested that only 66.7% of patients receiving 1,200 mg/kg would achieve or exceed an AUC/MIC ratio of 389. The potential breakpoints for fluconazole against Cryptococcus neoformans follow: susceptible, ≤2 mg/liter; resistant, >2 mg/liter. Fluconazole may be an inferior agent for induction therapy because many patients cannot achieve the pharmacodynamic target. Clinical breakpoints are likely to be significantly lower than epidemiological cutoff values. The MIC may guide the appropriate use of fluconazole. If fluconazole is the only option for induction therapy, then the highest possible dose should be used. PMID:23571544

  7. Beyond trend analysis: How a modified breakpoint analysis enhances knowledge of agricultural production after Zimbabwe's fast track land reform

    Science.gov (United States)

    Hentze, Konrad; Thonfeld, Frank; Menz, Gunter

    2017-10-01

    In the discourse on land reform assessments, a significant lack of spatial and time-series data has been identified, especially with respect to Zimbabwe's ;Fast-Track Land Reform Programme; (FTLRP). At the same time, interest persists among land use change scientists to evaluate causes of land use change and therefore to increase the explanatory power of remote sensing products. This study recognizes these demands and aims to provide input on both levels: Evaluating the potential of satellite remote sensing time-series to answer questions which evolved after intensive land redistribution efforts in Zimbabwe; and investigating how time-series analysis of Normalized Difference Vegetation Index (NDVI) can be enhanced to provide information on land reform induced land use change. To achieve this, two time-series methods are applied to MODIS NDVI data: Seasonal Trend Analysis (STA) and Breakpoint Analysis for Additive Season and Trend (BFAST). In our first analysis, a link of agricultural productivity trends to different land tenure regimes shows that regional clustering of trends is more dominant than a relationship between tenure and trend with a slightly negative slope for all regimes. We demonstrate that clusters of strong negative and positive productivity trends are results of changing irrigation patterns. To locate emerging and fallow irrigation schemes in semi-arid Zimbabwe, a new multi-method approach is developed which allows to map changes from bimodal seasonal phenological patterns to unimodal and vice versa. With an enhanced breakpoint analysis through the combination of STA and BFAST, we are able to provide a technique that can be applied on large scale to map status and development of highly productive cropping systems, which are key for food production, national export and local employment. We therefore conclude that the combination of existing and accessible time-series analysis methods: is able to achieve both: overcoming demonstrated limitations of

  8. Mapping Clearances in Tropical Dry Forests Using Breakpoints, Trend, and Seasonal Components from MODIS Time Series: Does Forest Type Matter?

    Directory of Open Access Journals (Sweden)

    Kenneth Grogan

    2016-08-01

    Full Text Available Tropical environments present a unique challenge for optical time series analysis, primarily owing to fragmented data availability, persistent cloud cover and atmospheric aerosols. Additionally, little is known of whether the performance of time series change detection is affected by diverse forest types found in tropical dry regions. In this paper, we develop a methodology for mapping forest clearing in Southeast Asia using a study region characterised by heterogeneous forest types. Moderate Resolution Imaging Spectroradiometer (MODIS time series are decomposed using Breaks For Additive Season and Trend (BFAST and breakpoints, trend, and seasonal components are combined in a binomial probability model to distinguish between cleared and stable forest. We found that the addition of seasonality and trend information improves the change model performance compared to using breakpoints alone. We also demonstrate the value of considering forest type in disturbance mapping in comparison to the more common approach that combines all forest types into a single generalised forest class. By taking a generalised forest approach, there is less control over the error distribution in each forest type. Dry-deciduous and evergreen forests are especially sensitive to error imbalances using a generalised forest model i.e., clearances were underestimated in evergreen forest, and overestimated in dry-deciduous forest. This suggests that forest type needs to be considered in time series change mapping, especially in heterogeneous forest regions. Our approach builds towards improving large-area monitoring of forest-diverse regions such as Southeast Asia. The findings of this study should also be transferable across optical sensors and are therefore relevant for the future availability of dense time series for the tropics at higher spatial resolutions.

  9. Modelling the association of dengue fever cases with temperature and relative humidity in Jeddah, Saudi Arabia-A generalised linear model with break-point analysis.

    Science.gov (United States)

    Alkhaldy, Ibrahim

    2017-04-01

    The aim of this study was to examine the role of environmental factors in the temporal distribution of dengue fever in Jeddah, Saudi Arabia. The relationship between dengue fever cases and climatic factors such as relative humidity and temperature was investigated during 2006-2009 to determine whether there is any relationship between dengue fever cases and climatic parameters in Jeddah City, Saudi Arabia. A generalised linear model (GLM) with a break-point was used to determine how different levels of temperature and relative humidity affected the distribution of the number of cases of dengue fever. Break-point analysis was performed to modelled the effect before and after a break-point (change point) in the explanatory parameters under various scenarios. Akaike information criterion (AIC) and cross validation (CV) were used to assess the performance of the models. The results showed that maximum temperature and mean relative humidity are most probably the better predictors of the number of dengue fever cases in Jeddah. In this study three scenarios were modelled: no time lag, 1-week lag and 2-weeks lag. Among these scenarios, the 1-week lag model using mean relative humidity as an explanatory variable showed better performance. This study showed a clear relationship between the meteorological variables and the number of dengue fever cases in Jeddah. The results also demonstrated that meteorological variables can be successfully used to estimate the number of dengue fever cases for a given period of time. Break-point analysis provides further insight into the association between meteorological parameters and dengue fever cases by dividing the meteorological parameters into certain break-points. Copyright © 2016 Elsevier B.V. All rights reserved.

  10. Fundamental challenges for autism research: the science-practice gap, demarcating autism and the unsuccessful search for the neurobiological basis of autism.

    Science.gov (United States)

    Verhoeff, Berend

    2015-08-01

    One of the central aims of autism research is to identify specific neurodevelopmental mechanisms that cause and explain the visible autistic signs and symptoms. In this short paper, I argue that the persistent search for autism-specific pathophysiologies has two fundamental difficulties. The first regards the growing gap between basic autism science and clinical practice. The second regards the difficulties with demarcating autism as a psychiatric condition. Instead of the unremitting search for the neurobiological basis of autism, I suggest that basic autism research should focus on experiences of impairment and distress, and on how these experiences relate to particular (autistic) behaviors in particular circumstances, regardless of whether we are dealing with an autism diagnosis or not.

  11. Performance of Vitek 2 for Antimicrobial Susceptibility Testing of Acinetobacter baumannii, Pseudomonas aeruginosa, and Stenotrophomonas maltophilia with Vitek 2 (2009 FDA) and CLSI M100S 26th Edition Breakpoints.

    Science.gov (United States)

    Bobenchik, April M; Deak, Eszter; Hindler, Janet A; Charlton, Carmen L; Humphries, Romney M

    2017-02-01

    The performances of Vitek 2 AST-GN69 and AST-XN06 cards were compared to Clinical and Laboratory Standards Institute (CLSI) reference broth microdilution (BMD) for 99 isolates of Pseudomonas aeruginosa, 26 Acinetobacter baumannii isolates, and 11 Stenotrophomonas maltophilia isolates. In total, 15 antimicrobials were evaluated, with 11 for P. aeruginosa, 14 for A. baumannii, and 2 for S. maltophilia Categorical agreement (CA) was assessed using both Vitek 2 breakpoints and 2016 CLSI M100S 26th edition breakpoints. The essential agreement values for P. aeruginosa, A. baumannii, and S. maltophilia were 99.5%, 99.2%, and 100%, respectively. The CA values for P. aeruginosa, A. baumannii, and S. maltophilia were 94.1%, 92.7%, and 95.5%, respectively, by the Vitek 2 breakpoints, and 93.4%, 92.3%, and 95.5%, respectively, by the CLSI breakpoints. Overall, the Vitek 2 performance was comparable to that of BMD using both Vitek 2 breakpoints and 2016 CLSI M100S 26th edition breakpoints. Improved performance was noted for the reformulated piperacillin-tazobactam and imipenem found on the AST-GN69 card, with no very major or major errors noted when using the CLSI breakpoints. Copyright © 2017 American Society for Microbiology.

  12. Chromosome breakage in Prader-Willi and Angelman syndrome deletions may involve recombination between a repeat at the proximal and distal breakpoints

    Energy Technology Data Exchange (ETDEWEB)

    Amos-Landgraf J.; Nicholls, R.D. [Case Western Reserve Univ., Cleveland, OH (United States); Gottlieb, W. [Univ. of Florida, Gainesville, FL (United States)] [and others

    1994-09-01

    Prader-Willi (PWS) and Angelman (AS) syndromes most commonly arise from large deletions of 15q11-q13. Deletions in PWS are paternal in origin, while those in AS are maternal in origin, clearly demonstrating genomic imprinting in these clinically distinct neurobehavioural disorders. In at least 90% of PWS and AS deletion patients, the same 4 Mb region within 15q11-q13 is deleted with breakpoints clustering in single YAC clones at the proximal and distal ends. To study the mechanism of chromosome breakage in PWS and AS, we have previously isolated 25 independent clones from these three YACs using Alu-vector PCR. Four clones were selected that appear to detect a low copy repeat that is located in the proximal and distal breakpoint regions of chromosome 15q11-q13. Three clones detect the same 4 HindIII bands in genomic DNA, all from 15q11-q13, with differing intensities for the probes located at the proximal or distal breakpoints region, respectively. This suggests that these probes detect related members of a low-copy repeat at either location. Moreover, the 254RL2 probe detects a novel HindIII band in two unrelated PWS deletion patients, suggesting that this may represent a breakpoint fragment, with recombination occurring within a similar interval in both patients. A fourth clone, 318RL3 detects 5 bands in HindIII-digested genomic DNA, all from 15q11-q13. This YAC endclone itself is not deleted in PWS and AS deletion patients, as seen by an invariant strong band. Two other strong bands are variably intact or deleted in different PWS or AS deletion patients, suggesting a relationship of this sequence to the breakpoints. Moreover, PCR using 318RL3 primers from the distal 93C9 YAC led to the isolation of a related clone with 96% identity, demonstrating the existence of a low-copy repeat with members close to the proximal and distal breakpoints. Taken together, our data suggest a complex, low-copy repeat with members at both the proximal and distal boundaries.

  13. Contemporary potencies of minocycline and tetracycline HCL tested against Gram-positive pathogens: SENTRY Program results using CLSI and EUCAST breakpoint criteria.

    Science.gov (United States)

    Jones, Ronald N; Wilson, Michael L; Weinstein, Melvin P; Stilwell, Matthew G; Mendes, Rodrigo E

    2013-04-01

    Tetracycline class agents vary widely in their activity against emerging important antimicrobial-resistant pathogens such as methicillin-resistant Staphylococcus aureus (MRSA) and Acinetobacter spp. Also, published susceptibility breakpoints are discordant between the Clinical and Laboratory Standards Institute (CLSI), the European Committee on Antimicrobial Susceptibility Testing (EUCAST), and regulatory-approved documents. We have assessed the impact of these differences for tetracycline HCL and minocycline when tested against contemporary Gram-positive pathogens. The SENTRY Antimicrobial Surveillance Program (2011) compared minocycline and tetracycline HCL activity via reference methods (M07-A9) using a worldwide collection of S. aureus (SA; 4917 strains with 1955 MRSA), Streptococcus pneumoniae (SPN; 1899), S. pyogenes (GRA; 246), and S. agalactiae (GRB; 217). Regardless of applied categorical breakpoints, minocycline exhibited wider coverage (% susceptible) than tetracycline HCL of 4.5-11.8/0.5-2.6/1.4-2.3/0.4-0.4% for MRSA/SPN/GRB/GRA, respectively. Lower EUCAST susceptible breakpoints produced reduced susceptibility rates for minocycline ranging from no difference (≤0.5 μg/mL) for GRA to -8.9% (≤1 μg/mL) for MRSA (97.2% susceptible by CLSI; 88.3% by EUCAST). Use of tetracycline HCL-susceptible results to predict minocycline susceptibility was very accurate (99.0-100.0%), with absolute categorical agreement rates ranging from 92.1% to 98.4% (CLSI) to 98.4% to 99.6% (EUCAST) for streptococci; greatest predictive error was noted using the CLSI breakpoints (14.7%) compared to EUCAST criteria (only 5.0%; acceptable), both for MRSA testing dominated by false-resistant results for minocycline. In conclusion, minocycline demonstrates continued superior in vitro activity compared to tetracycline HCL when testing SA (especially MRSA) and pathogenic streptococci. When testing tetracyclines, laboratories must recognize the expanded spectrum of minocycline against

  14. Impact of revised cefepime CLSI breakpoints on Escherichia coli and Klebsiella pneumoniae susceptibility and potential impact if applied to Pseudomonas aeruginosa.

    Science.gov (United States)

    Hamada, Yukihiro; Sutherland, Christina A; Nicolau, David P

    2015-05-01

    The CLSI reduced the cefepime Enterobacteriaceae susceptibility breakpoint and introduced the susceptible-dose-dependent (S-DD) category. In this study, MICs were determined for a Gram-negative collection to assess the impact of this change. For Enterobacteriaceae, this resulted in <2% reduction in susceptibility, with 1% being S-DD. If applied to Pseudomonas aeruginosa, the % susceptibility (%S) dropped from 77% to 43%, with 34% being S-DD. The new breakpoints did little to the Enterobacteriaceae %S, but for P. aeruginosa, a profound reduction was seen in %S. The recognition of a S-DD response to cefepime should alert clinicians to the possible need for higher doses. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  15. Three patients with structurally abnormal X chromosomes, each with Xq13 breakpoints and a history of idiopathic acquired sideroblastic anemia.

    Science.gov (United States)

    Dewald, G W; Pierre, R V; Phyliky, R L

    1982-01-01

    Structural abnormalities of the X chromosome are rarely found in neoplastic disorders. We describe three patients with a history of idiopathic acquired sideroblastic anemia (IASA); each one had an abnormal clone of cells in the bone marrow, characterized by a structurally abnormal X chromosome. In two of these patients, the predominant karyotype was 47,X,2idic(X)(q13); in the other patient, it was 46,X,t(X;11)(q13;p15). Inasmuch as all three of these cases involved chromosome band Xq13, as did two previously published cases, we suggest that band Xq13 may be more prone to structural rearrangement than other X chromosome bands in hematologic disorders. The common Xq13 chromosome breakpoint and clinical presentation (IASA) among these three patients and the occurrence of an X-linked type of sideroblastic anemia may suggest that an association exists between X chromosome abnormalities and IASA. Perhaps alteration of a gene or chromosome structure in or near band Xq13 predisposes to development of IASA. The fact that two of these patients had preleukemia and the third had overt acute leukemia may imply that patients with IASA and X chromosome abnormalities have a poor prognosis. Cases of IASA without associated X chromosome abnormalities are known; thus, if an association between IASA and an abnormal X chromosome does exist, most likely it involves only some patients with IASA.

  16. Correlation of Minimum Inhibitory Concentration Breakpoints and Methicillin Resistance Gene Carriage in Clinical Isolates of Staphylococcus epidermidis

    Directory of Open Access Journals (Sweden)

    Fereshteh Eftekhar,

    2011-09-01

    Full Text Available Staphylococcus epidermidis is the most important member of coagulase negative staphylococci responsible for community and hospital acquired infections. Most clinical isolates of S. epidermidis are resistant to methicillin making these infections difficult to treat. In this study, correlation of methicillin resistance phenotype was compared with methicillin resistance (mecA gene carriage in 55 clinical isolates of S. epidermidis. Susceptibility was measured by disc diffusion using methicillin discs, and minimum inhibitory concentrations (MIC were measured using broth microdilution. Methicillin resistance gene (MecA gene carriage was detected by specific primers and PCR. Disc susceptibility results showed 90.9% resistance to methicillin. Considering a MIC of 4 µg/ml, 78.1% of the isolates were methicillin resistant, 76.36% of which carried the mecA gene. On the other hand, when a breakpoint of 0.5 µg/ml was used, 89.09% were methicillin resistant, of which 93.75% were mecA positive. There was a better correlation between MIC of 0.5 µg/ml with disc diffusion results and mecA gene carriage. The findings suggest that despite the usefulness of molecular methods for rapid diagnosis of virulence genes, gene carriage does not necessarily account for virulence phenotype. Ultimately, gene expression, which is controlled by the environment, would determine the outcome

  17. Effects of clinical breakpoint changes in CLSI guidelines 2010/2011 and EUCAST guidelines 2011 on antibiotic susceptibility test reporting of Gram-negative bacilli

    OpenAIRE

    Hombach, Michael; Bloemberg, Guido V.; Böttger, Erik C.

    2017-01-01

    Objectives The aim of this study was to analyse the effects of clinical breakpoint changes in CLSI 2010 and 2011 guidelines and EUCAST 2011 guidelines on antibiotic susceptibility testing (AST) reports. Methods In total, 3713 non-duplicate clinical isolates of Enterobacteriaceae, Pseudomonas aeruginosa, Stenotrophomonas maltophilia and Acinetobacter baumannii were analysed. Inhibition zone diameters were determined for β-lactams, carbapenems, fluoroquinolones, aminoglycosides and trimethoprim...

  18. Reliable detection of paternal SNPs within deletion breakpoints for non-invasive prenatal exclusion of homozygous α-thalassemia in maternal plasma.

    Directory of Open Access Journals (Sweden)

    Ti-Zhen Yan

    Full Text Available Reliable detection of large deletions from cell-free fetal DNA (cffDNA in maternal plasma is challenging, especially when both parents have the same deletion owing to a lack of specific markers for fetal genotyping. In order to evaluate the efficacy of a non-invasive prenatal diagnosis (NIPD test to exclude α-thalassemia major that uses SNPs linked to the normal paternal α-globin allele, we established a novel protocol to reliably detect paternal SNPs within the (--(SEA breakpoints and performed evaluation of the diagnostic potential of the protocol in a total of 67 pregnancies, in whom plasma samples were collected prior to invasive obstetrics procedures in southern China. A group of nine SNPs identified within the deletion breakpoints were scanned to select the informative SNPs in each of the 67 couples DNA by multiplex PCR based mini-sequencing technique. The paternally inherited SNP allele from cffDNA was detected by allele specific real-time PCR. A protocol for reliable detection of paternal SNPs within the (--(SEA breakpoints was established and evaluation of the diagnostic potential of the protocol was performed in a total of 67 pregnancies. In 97% of the couples one or more different SNPs within the deletion breakpoint occurred between paternal and maternal alleles. Homozygosity for the (--(SEA deletion was accurately excluded in 33 out of 67 (49.3%, 95% CI, 25.4-78.6% pregnancies through the implementation of the protocol. Protocol was completely concordant with the traditional reference methods, except for two cases that exhibited uncertain results due to sample hemolysis. This method could be used as a routine NIPD test to exclude gross fetal deletions in α-thalassemia major, and could further be employed to test for other diseases due to gene deletion.

  19. First application of liquid-metal-jet sources for small-animal imaging: high-resolution CT and phase-contrast tumor demarcation.

    Science.gov (United States)

    Larsson, Daniel H; Lundström, Ulf; Westermark, Ulrica K; Arsenian Henriksson, Marie; Burvall, Anna; Hertz, Hans M

    2013-02-01

    Small-animal studies require images with high spatial resolution and high contrast due to the small scale of the structures. X-ray imaging systems for small animals are often limited by the microfocus source. Here, the authors investigate the applicability of liquid-metal-jet x-ray sources for such high-resolution small-animal imaging, both in tomography based on absorption and in soft-tissue tumor imaging based on in-line phase contrast. The experimental arrangement consists of a liquid-metal-jet x-ray source, the small-animal object on a rotating stage, and an imaging detector. The source-to-object and object-to-detector distances are adjusted for the preferred contrast mechanism. Two different liquid-metal-jet sources are used, one circulating a Ga∕In∕Sn alloy and the other an In∕Ga alloy for higher penetration through thick tissue. Both sources are operated at 40-50 W electron-beam power with ∼7 μm x-ray spots, providing high spatial resolution in absorption imaging and high spatial coherence for the phase-contrast imaging. High-resolution absorption imaging is demonstrated on mice with CT, showing 50 μm bone details in the reconstructed slices. High-resolution phase-contrast soft-tissue imaging shows clear demarcation of mm-sized tumors at much lower dose than is required in absorption. This is the first application of liquid-metal-jet x-ray sources for whole-body small-animal x-ray imaging. In absorption, the method allows high-resolution tomographic skeletal imaging with potential for significantly shorter exposure times due to the power scalability of liquid-metal-jet sources. In phase contrast, the authors use a simple in-line arrangement to show distinct tumor demarcation of few-mm-sized tumors. This is, to their knowledge, the first small-animal tumor visualization with a laboratory phase-contrast system.

  20. The Xq22 inversion breakpoint interrupted a novel Ras-like GTPase gene in a patient with Duchenne muscular dystrophy and profound mental retardation.

    Science.gov (United States)

    Saito-Ohara, Fumiko; Fukuda, Yoji; Ito, Masahiro; Agarwala, Kishan Lal; Hayashi, Masaharu; Matsuo, Masafumi; Imoto, Issei; Yamakawa, Kazuhiro; Nakamura, Yusuke; Inazawa, Johji

    2002-09-01

    A male patient with profound mental retardation, athetosis, nystagmus, and severe congenital hypotonia (Duchenne muscular dystrophy [DMD]) was previously shown to carry a pericentric inversion of the X chromosome, 46,Y,inv(X)(p21.2q22.2). His mother carried this inversion on one X allele. The patient's condition was originally misdiagnosed as cerebral palsy, and only later was it diagnosed as DMD. Because the DMD gene is located at Xp21.2, which is one breakpoint of the inv(X), and because its defects are rarely associated with severe mental retardation, the other clinical features of this patient were deemed likely to be associated with the opposite breakpoint at Xq22. Our precise molecular-cytogenetic characterization of both breakpoints revealed three catastrophic genetic events that had probably influenced neuromuscular and cognitive development: deletion of part of the DMD gene at Xp21.2, duplication of the human proteolipid protein gene (PLP) at Xq22.2, and disruption of a novel gene. The latter sequence, showing a high degree of homology to the Sec4 gene of yeast, encoded a putative small guanine-protein, Ras-like GTPase that we have termed "RLGP." Immunocytochemistry located RLGP at mitochondria. We speculate that disruption of RLGP was responsible for the patient's profound mental retardation.

  1. Non-random distribution of instability-associated chromosomal rearrangement breakpoints in human lymphoblastoid cells

    Energy Technology Data Exchange (ETDEWEB)

    Moore, Stephen R. [Environmental Toxicology Graduate Program, Department of Cell Biology and Neuroscience, University of California, Riverside, CA (United States); Radiation and Genome Stability Unit, Medical Research Council, Harwell, Oxfordshire (United Kingdom); Papworth, David [Radiation and Genome Stability Unit, Medical Research Council, Harwell, Oxfordshire (United Kingdom); Grosovsky, Andrew J. [Environmental Toxicology Graduate Program, Department of Cell Biology and Neuroscience, University of California, Riverside, CA (United States)]. E-mail: Grosovsky@ucr.edu

    2006-08-30

    Genomic instability is observed in tumors and in a large fraction of the progeny surviving irradiation. One of the best-characterized phenotypic manifestations of genomic instability is delayed chromosome aberrations. Our working hypothesis for the current study was that if genomic instability is in part attributable to cis mechanisms, we should observe a non-random distribution of chromosomes or sites involved in instability-associated rearrangements, regardless of radiation quality, dose, or trans factor expression. We report here the karyotypic examination of 296 instability-associated chromosomal rearrangement breaksites (IACRB) from 118 unstable TK6 human B lymphoblast, and isogenic derivative, clones. When we tested whether IACRB were distributed across the chromosomes based on target size, a significant non-random distribution was evident (p < 0.00001), and three IACRB hotspots (chromosomes 11, 12, and 22) and one IACRB coldspot (chromosome 2) were identified. Statistical analysis at the chromosomal band-level identified four IACRB hotspots accounting for 20% of all instability-associated breaks, two of which account for over 14% of all IACRB. Further, analysis of independent clones provided evidence within 14 individual clones of IACRB clustering at the chromosomal band level, suggesting a predisposition for further breaks after an initial break at some chromosomal bands. All of these events, independently, or when taken together, were highly unlikely to have occurred by chance (p < 0.000001). These IACRB band-level cluster hotspots were observed independent of radiation quality, dose, or cellular p53 status. The non-random distribution of instability-associated chromosomal rearrangements described here significantly differs from the distribution that was observed in a first-division post-irradiation metaphase analysis (p = 0.0004). Taken together, these results suggest that genomic instability may be in part driven by chromosomal cis mechanisms.

  2. Acquired, Idiopathic, Patterned Facial Pigmentation (AIPFP including periorbital pigmentation and pigmentary demarcation lines on face follows the Lines of Blaschko on face

    Directory of Open Access Journals (Sweden)

    Nilendu Sarma

    2014-01-01

    Full Text Available Background: Acquired, non-nevoid, apparently idiopathic facial pigmentation are distributed over some specific locations like periorbital area, zygomatic area, malar area, root of nose, perioral and mandibular area. Periorbital pigmentation is the most well known entity in this group. These are bilaterally distributed homogenously diffuse gray to dark gray or slate-gray colored patches showing progressive intensification of pigmentation. These are often considered as physiologic or constitutional pigmentation. Some portions of the margins of these patches were described previously as pigmentary demarcation line (PDL- F, G, H. Aim : To analyze the distributional patterns of acquired, apparently idiopathic facial pigmentations and to evaluate the etiologic aspects of these conditions. Materials and Methods: Spatial patterns, distribution, and orientation were analyzed among 187 individuals with idiopathic non-nevoid, facial pigmentation. Observed patterns were compared with various pigmentary nevi and Blaschko′s lines on face. Results: It was found that most of the idiopathic facial pigmentary alterations including periorbital pigmentation and PDL on face had specific patterned distribution that had high similarity to that of the pigmentary nevi and Blaschko′s lines on face. Conclusion: It is hypothesized here that phenotypic expression of acquired patterned pigmentation (AIFPFP is due to genetically determined increased pigmentary functional activity to various known and unknown yet natural factors like UV rays and aging. Mosaicism is a definite possibility. We also consider that these patterns actually reflect the normal patterns of embryological human pigmentation on face.

  3. Acquired, Idiopathic, Patterned Facial Pigmentation (AIPFP) Including Periorbital Pigmentation and Pigmentary Demarcation Lines on Face Follows the Lines of Blaschko on Face

    Science.gov (United States)

    Sarma, Nilendu; Chakraborty, Sayantani; Bhattacharya, Sneha Ranjan

    2014-01-01

    Background: Acquired, non-nevoid, apparently idiopathic facial pigmentation are distributed over some specific locations like periorbital area, zygomatic area, malar area, root of nose, perioral and mandibular area. Periorbital pigmentation is the most well known entity in this group. These are bilaterally distributed homogenously diffuse gray to dark gray or slate-gray colored patches showing progressive intensification of pigmentation. These are often considered as physiologic or constitutional pigmentation. Some portions of the margins of these patches were described previously as pigmentary demarcation line (PDL- F, G, H). Aim: To analyze the distributional patterns of acquired, apparently idiopathic facial pigmentations and to evaluate the etiologic aspects of these conditions. Materials and Methods: Spatial patterns, distribution, and orientation were analyzed among 187 individuals with idiopathic non-nevoid, facial pigmentation. Observed patterns were compared with various pigmentary nevi and Blaschko's lines on face. Results: It was found that most of the idiopathic facial pigmentary alterations including periorbital pigmentation and PDL on face had specific patterned distribution that had high similarity to that of the pigmentary nevi and Blaschko's lines on face. Conclusion: It is hypothesized here that phenotypic expression of acquired patterned pigmentation (AIFPFP) is due to genetically determined increased pigmentary functional activity to various known and unknown yet natural factors like UV rays and aging. Mosaicism was a definite possibility. We also consider that the patterns actually reflected the normal patterns of embryological human pigmentation on face. PMID:24470659

  4. Useful condition of chromoendoscopy with indigo carmine and acetic acid for identifying a demarcation line prior to endoscopic submucosal dissection for early gastric cancer.

    Science.gov (United States)

    Numata, Norifumi; Oka, Shiro; Tanaka, Shinji; Yoshifuku, Yoshikazu; Miwata, Tomohiro; Sanomura, Yoji; Arihiro, Koji; Shimamoto, Fumio; Chayama, Kazuaki

    2016-07-19

    Identifying a precise demarcation line (DL) is indispensable for pathological complete en bloc endoscopic submucosal dissection (ESD) for early gastric cancer (EGC). We evaluated the useful condition of chromoendoscopy with indigo carmine and acetic acid for marking dots around lesions before ESD for EGC. We examined 98 consecutive patients with 109 intramucosal EGCs (mean diameter, 17.8 ± 12.4 mm; main histologic type, 96 intestinal and 13 diffuse) resected by en bloc ESD after chromoendoscopy with indigo carmine and acetic acid between December 2012 and February 2014. The DL was identified by this technique just before ESD (mean chromoendoscopy observation time, 71.6 s); subsequently, marking dots were placed around the EGC. EGCs were classified into two groups: useful for identifying the DL or useless. Clinicopathological characteristics and clinical outcomes were evaluated in each group. Forty-two of the 109 cases (38.5 %) were determined useful for chromoendoscopy with indigo carmine and acetic acid. Multivariate analysis with logistic regression showed that macroscopic type (protruded or flat elevated-type) and atrophic border (the oral side of tumor) were independently associated with the usefulness of chromoendoscopy using indigo carmine and acetic acid for identifying the DL of EGCs (P indigo carmine and acetic acid can be used for creating precise markings in protruded or flat elevated-type EGC or at the atrophic border on the oral side of EGCs.

  5. Demarcation of mineral rich zones in areas adjoining to a copper prospect in Rajasthan, India using ASTER, DEM (ALOS) and spaceborne gravity data

    Science.gov (United States)

    Sengar, Vivek K.; Champati Ray, P. K.; Chattoraj, Shovan L.; Venkatesh, A. S.; Sajeev, R.; Konwar, Purnima; Thapa, Shailaja

    2017-10-01

    The objective of this work is to identify the potential zones for detailed mineral exploration studies in areas adjoining to a copper prospect using Remotely Sensed data sets. In this study visualization of ASTER data has been enhanced to highlight the mineral-rich areas using various remote sensing techniques such as colour composites and band ratios. VNIR region of ASTER is significant to detect iron oxides while, clay minerals, carbonates and chlorites have characteristic absorption in the SWIR wavelength region. Therefore, an attempt has been made to target the mineral abundant regions through ASTER data processing. Height based information was extracted using high-resolution ALOSDEM to analyse the topographical controls in the region considering the fact that mineral deposits often found associated with geological structures and geomorphological units. Gravity data was used to generate gravity anomaly map which gives clues about subsurface density differences. In this context, base metal ores may show anomalous (high) gravity values in comparison to the non-mineralised areas. Outputs from all the data sets were analysed and correlated with the geological map and available literature. Final validation of results has been done through proper ground checks and laboratory analysis of rock samples collected from the litho-units present in the study area. Based on this study some new areas have been successfully demarcated which may be potential for base metal exploration.

  6. Increased expression of aphidicolin-induced common fragile sites in Tourette syndrome: The key to understand the genetics of comorbid phenotypes?

    Energy Technology Data Exchange (ETDEWEB)

    Gericke, G.S.; Simonic, I.; Cloete, E.; Becker, P.J. [Univ. of Pretoria (South Africa)

    1996-02-16

    In a comparison of 80 common aphidicolin-induced fragile sites (FS) between 26 DSM-IV Tourette syndrome (TS) and 24 control individuals, the mean of the summed break frequencies following mild aphidicolin pretreatment was significantly higher in TS individuals than in controls (P < 0.001). Other breakpoints encountered during this study, i.e., random breaks, breaks corresponding to rare FS, and breakpoints recorded by others but not listed as common FS according to the Chromosome Coordinating Meeting were listed as category II breakpoints. By using the most significantly different mean FS breakage figures between TS and control individuals, further stepwise discriminant analysis allowed identification of TS individuals from only a few sites in both the common FS and category II breakpoint groups. Future research needs to focus on confirmation of altered common fragile site expression in association with behavioral variation, whether expression of certain discriminatory sites concurs with specific comorbid disorder expression; the nature of the molecular alterations at these FS and the implications of a genomic instability phenotype for the mapping of a primary TS gene or genes. 45 refs., 1 fig., 2 tabs.

  7. Non Random Distribution of DMD Deletion Breakpoints and Implication of Double Strand Breaks Repair and Replication Error Repair Mechanisms.

    Science.gov (United States)

    Marey, Isabelle; Ben Yaou, Rabah; Deburgrave, Nathalie; Vasson, Aurélie; Nectoux, Juliette; Leturcq, France; Eymard, Bruno; Laforet, Pascal; Behin, Anthony; Stojkovic, Tanya; Mayer, Michèle; Tiffreau, Vincent; Desguerre, Isabelle; Boyer, François Constant; Nadaj-Pakleza, Aleksandra; Ferrer, Xavier; Wahbi, Karim; Becane, Henri-Marc; Claustres, Mireille; Chelly, Jamel; Cossee, Mireille

    2016-05-27

    Dystrophinopathies are mostly caused by copy number variations, especially deletions, in the dystrophin gene (DMD). Despite the large size of the gene, deletions do not occur randomly but mainly in two hot spots, the main one involving exons 45 to 55. The underlying mechanisms are complex and implicate two main mechanisms: Non-homologous end joining (NHEJ) and micro-homology mediated replication-dependent recombination (MMRDR). Our goals were to assess the distribution of intronic breakpoints (BPs) in the genomic sequence of the main hot spot of deletions within DMD gene and to search for specific sequences at or near to BPs that might promote BP occurrence or be associated with DNA break repair. Using comparative genomic hybridization microarray, 57 deletions within the intron 44 to 55 region were mapped. Moreover, 21 junction fragments were sequenced to search for specific sequences. Non-randomly distributed BPs were found in introns 44, 47, 48, 49 and 53 and 50% of BPs clustered within genomic regions of less than 700bp. Repeated elements (REs), known to promote gene rearrangement via several mechanisms, were present in the vicinity of 90% of clustered BPs and less frequently (72%) close to scattered BPs, illustrating the important role of such elements in the occurrence of DMD deletions. Palindromic and TTTAAA sequences, which also promote DNA instability, were identified at fragment junctions in 20% and 5% of cases, respectively. Micro-homologies (76%) and insertions or deletions of small sequences were frequently found at BP junctions. Our results illustrate, in a large series of patients, the important role of RE and other genomic features in DNA breaks, and the involvement of different mechanisms in DMD gene deletions: Mainly replication error repair mechanisms, but also NHEJ and potentially aberrant firing of replication origins. A combination of these mechanisms may also be possible.

  8. Multicenter evaluation of the new Vitek 2 yeast susceptibility test using new CLSI clinical breakpoints for fluconazole.

    Science.gov (United States)

    Pfaller, M A; Diekema, D J; Procop, G W; Wiederhold, N P

    2014-06-01

    A fully automated antifungal susceptibility test system recently updated to reflect the new species-specific clinical breakpoints (CBPs) of fluconazole for Candida (Vitek 2 AF03 yeast susceptibility test; bioMérieux, Inc., Durham, NC) was compared in three different laboratories with the Clinical and Laboratory Standards Institute (CLSI) reference broth microdilution (BMD) method by testing 2 quality control strains, 10 reproducibility strains (4 Candida species and 6 Cryptococcus neoformans strains), and 746 isolates of Candida species (702 isolates, 13 species) and 44 isolates of C. neoformans against fluconazole. Excellent essential agreement (EA) (within 2 dilutions) between the reference and Vitek 2 MICs was observed for fluconazole and Candida species (94.0%). The EA was lower for fluconazole and C. neoformans at 86.4%. The mean times to a result with the Vitek 2 test were 9.1 h for Candida species and 12.1 h for C. neoformans. Categorical agreement (CA) between the two methods was assessed by using the new species-specific CBPs. For less common species without fluconazole CBPs, the epidemiological cutoff values (ECVs) were used to differentiate wild-type (WT; MIC, ≤ ECV) from non-WT (MIC, >ECV) strains. The CAs between the two methods were 92.0% for Candida species (0.3% very major errors [VME] and 2.6% major errors [ME]) and 84.1% for C. neoformans (4.5% VME and 11.4% ME). The updated Vitek 2 AF03 IUO yeast susceptibility system is comparable to the CLSI BMD reference method for testing the susceptibility of clinically important yeasts to fluconazole when using the new (lower) CBPs and ECVs. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  9. An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1.

    Directory of Open Access Journals (Sweden)

    Sergei L Kosakovsky Pond

    2009-11-01

    Full Text Available Genetically diverse pathogens (such as Human Immunodeficiency virus type 1, HIV-1 are frequently stratified into phylogenetically or immunologically defined subtypes for classification purposes. Computational identification of such subtypes is helpful in surveillance, epidemiological analysis and detection of novel variants, e.g., circulating recombinant forms in HIV-1. A number of conceptually and technically different techniques have been proposed for determining the subtype of a query sequence, but there is not a universally optimal approach. We present a model-based phylogenetic method for automatically subtyping an HIV-1 (or other viral or bacterial sequence, mapping the location of breakpoints and assigning parental sequences in recombinant strains as well as computing confidence levels for the inferred quantities. Our Subtype Classification Using Evolutionary ALgorithms (SCUEAL procedure is shown to perform very well in a variety of simulation scenarios, runs in parallel when multiple sequences are being screened, and matches or exceeds the performance of existing approaches on typical empirical cases. We applied SCUEAL to all available polymerase (pol sequences from two large databases, the Stanford Drug Resistance database and the UK HIV Drug Resistance Database. Comparing with subtypes which had previously been assigned revealed that a minor but substantial (approximately 5% fraction of pure subtype sequences may in fact be within- or inter-subtype recombinants. A free implementation of SCUEAL is provided as a module for the HyPhy package and the Datamonkey web server. Our method is especially useful when an accurate automatic classification of an unknown strain is desired, and is positioned to complement and extend faster but less accurate methods. Given the increasingly frequent use of HIV subtype information in studies focusing on the effect of subtype on treatment, clinical outcome, pathogenicity and vaccine design, the importance

  10. [Comparison of microdilution and disk diffusion methods for the detection of fluconazole and voriconazole susceptibility against clinical Candida glabrata isolates and determination of changing susceptibility with new CLSI breakpoints].

    Science.gov (United States)

    Hazırolan, Gülşen; Sarıbaş, Zeynep; Arıkan Akdağlı, Sevtap

    2016-07-01

    Candida albicans is the most frequently isolated species as the causative agent of Candida infections. However, in recent years, the isolation rate of non-albicans Candida species have increased. In many centers, Candida glabrata is one of the commonly isolated non-albicans species of C.glabrata infections which are difficult-to-treat due to decreased susceptibility to fluconazole and cross-resistance to other azoles. The aims of this study were to determine the in vitro susceptibility profiles of clinical C.glabrata isolates against fluconazole and voriconazole by microdilution and disk diffusion methods and to evaluate the results with both the previous (CLSI) and current species-specific CLSI (Clinical and Laboratory Standards Institute) clinical breakpoints. A total of 70 C.glabrata strains isolated from clinical samples were included in the study. The identification of the isolates was performed by morphologic examination on cornmeal Tween 80 agar and assimilation profiles obtained by using ID32C (BioMérieux, France). Broth microdilution and disk diffusion methods were performed according to CLSI M27-A3 and CLSI M44-A2 documents, respectively. The results were evaluated according to CLSI M27-A3 and M44-A2 documents and new vs. species-specific CLSI breakpoints. By using both previous and new CLSI breakpoints, broth microdilution test results showed that voriconazole has greater in vitro activity than fluconazole against C.glabrata isolates. For the two drugs tested, very major error was not observed with disk diffusion method when microdilution method was considered as the reference method. Since "susceptible" category no more exists for fluconazole vs. C.glabrata, the isolates that were interpreted as susceptible by previous breakpoints were evaluated as susceptible-dose dependent by current CLSI breakpoints. Since species-specific breakpoints remain yet undetermined for voriconazole, comparative analysis was not possible for this agent. The results obtained

  11. Mathematical modelling breakpoints

    OpenAIRE

    Sedlák Vladimír

    1996-01-01

    V príspevku je prezentovaná teória matematického modelovania polynomiálnych lomových bodov pri analýze deformaèných charakteristík poklesových kotlín. Teória urèovania lomových bodov bola vyvinutá ako súèas kinematických analýz horninového masívu dobývacieho loiskového po¾a magnezitu vo východoslovenskom regióne. Teoretické poznatky modelovania sú doplnené praktickými výsledkami deformaèných meraní in situ.

  12. Identification of a B lymphoid disorder defined by specific morphologic features, a del(11)(q13) and a same breakpoint far from CCND1

    Energy Technology Data Exchange (ETDEWEB)

    Morel, D.; Callet, E.; Reynaud, S. [Laboratoire d`Hematologie, Pierre-Benite (France)] [and others

    1994-09-01

    Chromosome rearrangements in 11q13 have been shown to occur in a variety of diffuse small B-cell lymphomas/leukemias, including, beside mantle cell lymphomas (MCL), some cases of CLL/SLL, PLL, and SLVL. If t(11;14)(q13;q32) may be considered as a hallmark of MCL, less is known about deletions involving 11q13. A series of 13 patients with a diffuse small B-lymphoma/leukemia was examined for morphology (cytology and histology), immunology, cytogenetics and FISH for some of them. According to karyotype findings, 2 groups were identified: Group 1: 9 patients (6M,3F), median age 60 yrs. without 11q anomalies. Apart from trisomy 12 (3 cases), diverse anomalies were identified including chromosomes 1, 2, 7, 8, 12, 17. Cases were classified as CLL (2), SLL/SLP (5), blast-rich immunocytomas (2). Group 2: 4 patients, all males, median age 52 yrs. with breakpoints in 11q13; there were 3 deletions, and a t(11;14) was present in another case. 2 patients presented with refractory disease followed for 23 and 9 months, respectively, without any consistent morphologic change, the chromosomal anomaly being present at diagnosis in 1.3 cases. Cytologically, a nucleolated cell component was the constant and striking feature and FISH study by cos 14, pHS 11, cos 17, cos 105 revealed the same breakpoint located far from CCND1. The fourth case, bearing the t(11;14), was diagnosed as CLL/PLL in cytology, but was histologically consistent with MCL; the breakpoint was located by FISH into the BCL1 locus. Even if this study needs further confirmation, it points at the 11q13 deletion as a genetic event leading to a more aggressive disease, associated with distinct cytologic features differing from MCL and a molecular event probably not involving BCL1/CCND1.

  13. Effects of clinical breakpoint changes in CLSI guidelines 2010/2011 and EUCAST guidelines 2011 on antibiotic susceptibility test reporting of Gram-negative bacilli.

    Science.gov (United States)

    Hombach, Michael; Bloemberg, Guido V; Böttger, Erik C

    2012-03-01

    The aim of this study was to analyse the effects of clinical breakpoint changes in CLSI 2010 and 2011 guidelines and EUCAST 2011 guidelines on antibiotic susceptibility testing (AST) reports. In total, 3713 non-duplicate clinical isolates of Enterobacteriaceae, Pseudomonas aeruginosa, Stenotrophomonas maltophilia and Acinetobacter baumannii were analysed. Inhibition zone diameters were determined for β-lactams, carbapenems, fluoroquinolones, aminoglycosides and trimethoprim/sulfamethoxazole. CLSI 2009-11 and EUCAST 2011 clinical breakpoints were applied. Changes in resistance as defined per the guidelines affected individual species and drug classes differently. The cefepime resistance rate in Escherichia coli and Enterobacter cloacae increased from 2.1% and 1.3% to 8.2% and 6.9%, respectively, applying CLSI 2009-11 versus EUCAST 2011 guidelines. Ertapenem resistance rates in E. cloacae increased from 2.6% with CLSI 2009 to 7.2% for CLSI 2010 and 2011, and to 10.1% when applying EUCAST 2011. Cefepime and meropenem resistance rates in P. aeruginosa increased from 12.2% and 20.6% to 19.8% and 27.7%, respectively, comparing CLSI 2009-11 with EUCAST 2011. Tobramycin and gentamicin resistance rates in A. baumannii increased from 15.9% and 25.4% to 34.9% and 44.4% applying CLSI 2009-11 versus EUCAST 2011. Higher resistance rates reported due to breakpoint changes in CLSI and EUCAST guidelines will result in increasing numbers of Gram-negative bacilli reported as multidrug resistant. AST reports classifying amoxicillin/clavulanic acid, cefepime or carbapenem resistance will lead clinicians to use alternative agents. Upon implementation of the EUCAST guidelines, laboratories should be aware of the implications of modified drug susceptibility testing reports on antibiotic prescription policies.

  14. Identification of a new DPY19L2 mutation and a better definition of DPY19L2 deletion breakpoints leading to globozoospermia.

    Science.gov (United States)

    Ghédir, Houda; Ibala-Romdhane, Samira; Okutman, Ozlem; Viot, Géraldine; Saad, Ali; Viville, Stéphane

    2016-01-01

    The purpose of this study was to analyze DPY19L2 sequence variants to investigate the mechanism leading to the entire DPY19L2 deletion in a large cohort of infertile globozoospermic patients. An improved analysis of the DPY19L2 deletion breakpoints (BPs) allowed us to identify two BPs located in a small 1 kb region and to more precisely localize the BPs reported previously. Three genes [spermatogenesis associated 16 (SPATA16), protein interacting with PRKCA (PICK1) and DPY19L2] were previously correlated with globozoospermia, but a homozygous deletion of the entire DPY19L2 was identified as the most frequent alteration causing this phenotype. In addition, several point mutations in this gene were reported. In previous work, we have identified nine BPs for the DPY19L2 deletion clustered in two hotspot regions, while others reported a total of five BPs. We screened for the DPY19L2 deletion and for mutations in the DPY19L2, SPATA16 and PICK1 genes in a cohort of 21 Tunisian globozoospermic patients. In order to characterize the DPY19L2 deletion BPs, we sequenced a 2 kb fragment on low copy repeat (LCR) 1 and LCR2 in Tunisian fertile controls to distinguish between single-nucleotide polymorphisms (SNPs) and LCR-specific markers. Molecular analyses performed on 18 genetically independent individuals showed that 11 (61.1%) were homozygous for the DPY19L2 deletion, 2 (11.1%) were homozygous for the non-synonymous mutation (p.R298C) in exon 8, 1 patient (5.6%) was homozygous for a new splice-site mutation at the junction exon-intron 16 [c.1579_1580+4delAGGTAAinsTCAT] and no DPY19L2, SPATA16 or PICK1 mutations were identified for 4 patients (22.2%). By defining 15 specific LCR markers, we characterized 2 BPs for the DPY19L2 deletion in 11 patients showing the homozygous deletion. Using 20 non-LCR-specific SNPs, we identified 8 distinct haplotypes. A limitation of this study is the small number of patients owing to the rarity of this form of male infertility. Our data showed

  15. N-nitrosodimethylamine (NDMA) formation potential of amine-based water treatment polymers: Effects of in situ chloramination, breakpoint chlorination, and pre-oxidation.

    Science.gov (United States)

    Park, Sang Hyuck; Padhye, Lokesh P; Wang, Pei; Cho, Min; Kim, Jae-Hong; Huang, Ching-Hua

    2015-01-23

    Recent studies show that cationic amine-based water treatment polymers may be important precursors that contribute to formation of the probable human carcinogen N-nitrosodimethylamine (NDMA) during water treatment and disinfection. To better understand how water treatment parameters affect NDMA formation from the polymers, the effects of in situ chloramination, breakpoint chlorination, and pre-oxidation on the NDMA formation from the polymers were investigated. NDMA formation potential (NDMA-FP) as well as dimethylamine (DMA) residual concentration were measured from poly(epichlorohydrin dimethylamine) (polyamine) and poly(diallyldimethylammonium chloride) (polyDADMAC) solutions upon reactions with oxidants including free chlorine, chlorine dioxide, ozone, and monochloramine under different treatment conditions. The results supported that dichloramine (NHCl2) formation was the critical factor affecting NDMA formation from the polymers during in situ chloramination. The highest NDMA formation from the polymers occurred near the breakpoint of chlorination. Polymer chain breakdown and transformation of the released DMA and other intermediates were important factors affecting NDMA formation from the polymers in pre-oxidation followed by post-chloramination. Pre-oxidation generally reduced NDMA-FP of the polymers; however, the treatments involving pre-ozonation increased polyDADMAC's NDMA-FP and DMA release. The strategies for reducing NDMA formation from the polymers may include the avoidance of the conditions favorable to NHCl2 formation and the avoidance of polymer exposure to strong oxidants such as ozone. Copyright © 2014 Elsevier B.V. All rights reserved.

  16. Two patients with balanced translocations and autistic disorder: CSMD3 as a candidate gene for autism found in their common 8q23 breakpoint area.

    Science.gov (United States)

    Floris, Chiara; Rassu, Stefania; Boccone, Loredana; Gasperini, Daniela; Cao, Antonio; Crisponi, Laura

    2008-06-01

    Recent studies estimated a rate of 3-5% of cytogenetic abnormalities involving many different chromosomes in autistic spectrum disorders (ASDs). Here, we report on two unrelated male patients with de novo translocations, autistic behaviour and psychomotor delay. These two patients carry a balanced chromosome translocation t(5;8)(q14.3;q23.3) and t(6;8)(q13;q23.2), respectively. A detailed physical map covering the regions involved in the translocations was constructed using BAC clones mapping on chromosomes 5q14.3, 6q13 and 8q23. Fluorescence in situ hybridisation (FISH) analyses were carried out using these genomic clones. We fine mapped the two translocation breakpoints on chromosomes 8 identifying their position within a short 5 Mb genomic region. Breakpoints on chromosomes 8 in both patients do not interrupt any known gene but both map in a region containing the CSMD3 gene, which thereby can be considered as a candidate for ASDs.

  17. Population biology of Schistosoma mating, aggregation, and transmission breakpoints: more reliable model analysis for the end-game in communities at risk.

    Directory of Open Access Journals (Sweden)

    David Gurarie

    Full Text Available Mathematical modeling is widely used for predictive analysis of control options for infectious agents. Challenging problems arise for modeling host-parasite systems having complex life-cycles and transmission environments. Macroparasites, like Schistosoma, inhabit highly fragmented habitats that shape their reproductive success and distribution. Overdispersion and mating success are important factors to consider in modeling control options for such systems. Simpler models based on mean worm burden (MWB formulations do not take these into account and overestimate transmission. Proposed MWB revisions have employed prescribed distributions and mating factor corrections to derive modified MWB models that have qualitatively different equilibria, including 'breakpoints' below which the parasite goes to extinction, suggesting the possibility of elimination via long-term mass-treatment control. Despite common use, no one has attempted to validate the scope and hypotheses underlying such MWB approaches. We conducted a systematic analysis of both the classical MWB and more recent "stratified worm burden" (SWB modeling that accounts for mating and reproductive hurdles (Allee effect. Our analysis reveals some similarities, including breakpoints, between MWB and SWB, but also significant differences between the two types of model. We show the classic MWB has inherent inconsistencies, and propose SWB as a reliable alternative for projection of long-term control outcomes.

  18. Impact of changes in CLSI and EUCAST breakpoints for susceptibility in bloodstream infections due to extended-spectrum β-lactamase-producing Escherichia coli.

    Science.gov (United States)

    Rodríguez-Baño, J; Picón, E; Navarro, M D; López-Cerero, L; Pascual, A

    2012-09-01

    The impact of recent changes in and discrepancies between the breakpoints for cephalosporins and other antimicrobials, as determined by CLSI and European Committee on Antimicrobial Susceptibility Testing (EUCAST), was analysed in patients with bloodstream infections caused by extended-spectrum β-lactamase (ESBL) producing Escherichia coli in Spain, was analysed. We studied a cohort of 191 episodes of bloodstream infection caused by ESBL-producing E. coli in 13 Spanish hospitals; the susceptibility of isolates to different antimicrobials was investigated by microdilution and interpreted according to recommendations established in 2009 and 2010 by CLSI, and in 2011 by EUCAST. Overall, 58.6% and 14.7% of isolates were susceptible to ceftazidime, and 35.1% and 14.7% to cefepime using the CLSI-2010 and EUCAST-2009/2011 recommendations, respectively (all isolates would have been considered resistant using the previous guidelines). Discrepancies between the CLSI-2010 and the EUCAST-2011 recommendations were statistically significant for other antimicrobials only in the case of amikacin (98.4% versus 75.9% of susceptible isolates; p CLSI-2010 guidelines died (all had severe sepsis or shock); these cases would have been considered resistant according to EUCAST-2011. In conclusion, by using current breakpoints, extended-spectrum cephalosporins would be regarded as active agents for treating a significant proportion of patients with bloodstream infections caused by ESBL-producing E. coli. © 2011 The Authors. Clinical Microbiology and Infection © 2011 European Society of Clinical Microbiology and Infectious Diseases.

  19. Clinical and Laboratory Standards Institute (CLSI) Evaluation of Oxacillin and Cefoxitin Disk Diffusion and Minimum Inhibitory Concentration Breakpoints for Detection of mecA-mediated Oxacillin Resistance in Staphylococcus schleiferi.

    Science.gov (United States)

    Huse, H K; Miller, S A; Chandrasekaran, S; Hindler, J A; Lawhon, S D; Bemis, D A; Westblade, L F; Humphries, R M

    2017-11-29

    Staphylococcus schleiferi is a beta-hemolytic, coagulase-variable colonizer of small animals that can cause opportunistic infections in humans. In veterinary isolates, mecA-mediated oxacillin resistance is significant, with reported resistance rates of >39%. The goal of this study was to evaluate oxacillin and cefoxitin disk diffusion (DD) and minimum inhibitory concentration (MIC) breakpoints for detection of mecA-mediated oxacillin resistance in 52 human and 38 veterinary isolates of S. schleiferi Isolates were tested on multiple brands of commercial media following Clinical and Laboratory Standards Institute (CLSI) methods. Zone diameters and MIC values were interpreted using breakpoints in the CLSI M100S 27th edition for Staphylococcus aureus/Staphylococcus lugdunensis, coagulase-negative staphylococci (CoNS), and Staphylococcus pseudintermedius Results were compared to mecA PCR. Twenty-nine of 90 (32%) isolates were mecA positive. Oxacillin zone sizes and MICs interpreted by S. pseudintermedius breakpoints reliably differentiated mecA positive and mecA negative isolates, with a categorical agreement (CA) of 100% and no very major errors (VMEs) or major errors (MEs) on all media. For cefoxitin DD interpreted using S. aureus/S. lugdunensis and CoNS breakpoints, CA was 85% and 75%, and there were 72% and 64% VMEs and 0 MEs, respectively. For cefoxitin MICs interpreted using S. aureus/S. lugdunensis breakpoints, CA was 81% and there were 60% VMEs and no MEs. Our data demonstrate that oxacillin DD or MIC testing methods using the current S. pseudintermedius breakpoints reliably identify mecA-mediated oxacillin resistance in S. schleiferi, while cefoxitin DD and MIC testing perform poorly. Copyright © 2017 American Society for Microbiology.

  20. Isolation of chromosome-specific DNA sequences from an Alu polymerase chain reaction library to define the breakpoint in a patient with a constitutional translocation t(1;13) (q22;q12) and ganglioneuroblastoma.

    Science.gov (United States)

    Michalski, A J; Cotter, F E; Cowell, J K

    1992-08-01

    We describe the cytogenetic and molecular characterization of a t(1;13)(q22;q12) constitutional rearrangement occurring in a patient with a relatively benign form of neuroblastoma, called ganglioneuroblastoma. Somatic cell hybrids were generated between mouse 3T3 cells and a lymphoblastoid cell line from this patient, D.G. One isolated subclone, DGF27C11, contained the derivative chromosome, 1pter-q22::13q12-qter, but no other material from either chromosome 1 or 13. Using available DNA probes the 13 breakpoint was assigned proximal to all reported markers. In order to generate flanking markers to define this translocation further, an Alu polymerase chain reaction library was constructed from a somatic cell hybrid containing only the proximal, 13pter-13q14, region of chromosome 13. Seven unique sequences have been isolated from the library, three of which lie below and four of which lie above the 13q12 breakpoint. More precise mapping of the distal markers was achieved using a panel of somatic cell hybrids with overlapping deletions of chromosome 13. The paucity of probes in the 1q22 region has made a precise assignment of this breakpoint difficult, however it has been shown to lie distal to c-SKI and proximal to APOA2. This refined characterization of the breakpoint is a prerequisite for its cloning, which may yield genes important in the pathogenesis of ganglioneuroblastoma.

  1. Detection of a case of chronic myeloid leukaemia with deletions at the t(9;22) translocation breakpoints by a genome-wide non-invasive prenatal test.

    Science.gov (United States)

    Janssens, Katrien; Deiteren, Kathleen; Verlinden, Anke; Rooms, Liesbeth; Beckers, Sigri; Holmgren, Philip; Vermeulen, Katrien; Maes, Marie-Berthe; Mortier, Geert; Blaumeiser, Bettina

    2016-08-01

    Non-invasive prenatal tests (NIPTs) interrogating the complete genome are able to detect not only fetal trisomy 13, 18 or 21 but additionally provide information on other (sub)chromosomal aberrations that can be fetal or maternal in origin. We demonstrate that in a subset of cases, this information is clinically relevant and should be reported to ensure adequate follow-up. Genome-wide NIPT was carried out and followed by a software analysis pipeline optimized to detect subchromosomal aberrations. The NIPT profile showed deletions on chromosomes 9 and 22: NIPT 9q33.3q34.12(129150001-133750000)x1,22q11.23(23550001-25450000)x1,22q13.1(37850001-39600000)x1. This result was confirmed by single nucleotide polymorphism array on maternal genomic DNA, which also demonstrated that the deletions were somatic in nature. Fluorescence in situ hybridization and quantitative real-time polymerase chain reaction revealed that the deletions were flanking the translocation breakpoint on the derivative chromosome 9 as the result of a t(9;22)(q34;q11.2) translocation with BCR-ABL1 fusion typical for chronic myeloid leukaemia (CML). Multidisciplinary counselling, together with complete blood count, taught that the woman was in an early chronic phase CML. The woman was followed up closely, and treatment could be postponed until after delivery. Genome-wide NIPT identified a CML in chronic phase caused by the typical t(9;22)(q34;q11.2) translocation and accompanied by deletions flanking the translocation breakpoints. © 2016 John Wiley & Sons, Ltd. © 2016 John Wiley & Sons, Ltd.

  2. Evaluation by data mining techniques of fluconazole breakpoints established by the Clinical and Laboratory Standards Institute (CLSI) and comparison with those of the European Committee on Antimicrobial Susceptibility Testing (EUCAST).

    Science.gov (United States)

    Cuesta, Isabel; Bielza, Concha; Cuenca-Estrella, Manuel; Larrañaga, Pedro; Rodríguez-Tudela, Juan L

    2010-04-01

    The EUCAST and the CLSI have established different breakpoints for fluconazole and Candida spp. However, the reference methodologies employed to obtain the MICs provide similar results. The aim of this work was to apply supervised classification algorithms to analyze the clinical data used by the CLSI to establish fluconazole breakpoints for Candida infections and to compare these data with the results obtained with the data set used to set up EUCAST fluconazole breakpoints, where the MIC for detecting failures was >4 mg/liter, with a sensitivity of 87%, a false-positive rate of 8%, and an area under the receiver operating characteristic (ROC) curve of 0.89. Five supervised classifiers (J48 and CART decision trees, the OneR decision rule, the naïve Bayes classifier, and simple logistic regression) were used to analyze the original cohort of patients (Rex's data set), which was used to establish CLSI breakpoints, and a later cohort of candidemia (Clancy's data set), with which CLSI breakpoints were validated. The target variable was the outcome of the infections, and the predictor variable was the MIC or dose/MIC ratio. For Rex's data set, the MIC detecting failures was >8 mg/liter, and for Clancy's data set, the MIC detecting failures was >4 mg/liter, in close agreement with the EUCAST breakpoint (MIC > 4 mg/liter). The sensitivities, false-positive rates, and areas under the ROC curve obtained by means of CART, the algorithm with the best statistical results, were 52%, 18%, and 0.7, respectively, for Rex's data set and 65%, 6%, and 0.72, respectively, for Clancy's data set. In addition, the correlation between outcome and dose/MIC ratio was analyzed for Clancy's data set, where a dose/MIC ratio of >75 was associated with successes, with a sensitivity of 93%, a false-positive rate of 29%, and an area under the ROC curve of 0.83. This dose/MIC ratio of >75 was identical to that found for the cohorts used by EUCAST to establish their breakpoints (a dose/MIC ratio of

  3. ⁴⁰ Ar/³⁹Ar and (U-Th)/He dating attempts on the fossil-bearing cave deposits of the Malapa and Sterkfontein hominin sites of the Cradle of Humankind, South Africa

    OpenAIRE

    2015-01-01

    M.Sc. (Geology) The Cradle of Humankind is a 47 000 hectare demarcated area with over three dozen fossil-bearing cave sites well known for the preservation of fossil evidence of early hominin taxa such as Australopithecus Africanus, Australopithecus Sediba, Paranthropus Robustus and Early Homo. As a result, a database of precise and accurate chronological data for fossil-bearing cave deposits of the Cradle of Humankind (similar to that for East African fossil sites) is very important, but ...

  4. Usefulness of Microscan System panels with EUCAST clinical breakpoints to evaluate the antimicrobial susceptibility of ß-lactamase producing- Gram negative isolates

    Directory of Open Access Journals (Sweden)

    Elisabetta Nucleo

    2011-12-01

    Full Text Available The study aimed to evaluate the ability of NBC45, NBC46 and NB40 Microscan (MS panels, updated to 2010 EUCAST breakpoints, to identify at species level and to correctly define the susceptibility to ß-lactams of 61 ß-lactamases (BLs producing Gram-negative isolates. A collection of 73 fully identified strains was analyzed: 21 Klebsiella spp., 17 E. coli, 15 P. mirabilis, 9 A. baumannii (Ab, 7 P. aeruginosa and 4 Enterobacter spp.. 61/73 were BLs and/or carbapenemases producers: 15 were CTX-M-1/-2/-14/-15 positive, and among them two were also VIM-1 positive. Four were TEM-52/-92, 3 PER-1, 2 SHV-12/-18 and 6 CMY-16 producers, while 11 were KPC-2/-3, 9 OXA-51/-58/-23, 8 VIM-1 and 2 IMP-13 positive. One K. oxytoca K-1 iper-producer, 11 non-BL producers/ATCC control strains and a OprD2 porin lacking P. aeruginosa were also included. All isolates were identified by Api-20E and VITEK-2 System and antibiotic susceptibilities were obtained by broth microdilution method. Resistance genes were identified by PCR and sequencing. All 73 isolates were correctly identified and a complete agreement for susceptibility patterns was observed for both ATCC control strains and non-BL clinical isolates. MS failed to detect a BL/Extended-Spectrum-ß-Lactamase (ESâL production in 5/61 cases: any ESßL alert was detected using NBC46 panel for 3/15 CTX-M positive strains and 2 VIM-1/CTX-M-15 producing K. pneumoniae isolates. Intermediate resistance to cefoxitin (MIC 16 mg/L, susceptibility to cefepime (MIC 8 mg/L for ertapenem (ETP, according to previously results. All VIM-1 producers resulted intermediate/resistant to imipenem (IP and meropenem (MP; decreased MIC values were observed in 2/8 cases. Carbapenem MICs >8 mg/L were detected for IP-13 P. aeruginosa producers; 6/9 OXA carbapenemases- producing Ab showed IP MIC >8 mg/L and 3/6 MP MIC >8 mg/L. 3/9 Ab OXA-58/-51 producers, tested using NB40 panel, were intermediate or resistant to doripenem and meropenem

  5. Mapping of wheat mitochondrial mRNA termini and comparison with breakpoints in DNA homology among plants.

    Science.gov (United States)

    Choi, Boyoung; Acero, Maria M; Bonen, Linda

    2012-11-01

    Mitochondrial DNA rearrangements occur very frequently in flowering plants and when close to genes there must be concomitant acquisition of new regulatory cis-elements. To explore whether there might be limits to such DNA shuffling, we have mapped the termini of mitochondrial mRNAs in wheat, a monocot, and compared them to the known positions for counterpart genes in the eudicot Arabidopsis. Nine genes share homologous 3' UTRs over their full-length and for six of them, the termini map very close to the site of wheat/Arabidopsis DNA rearrangements. Only one such case was seen for comparisons of 5' UTRs, and the 5' ends of mRNAs are typically more heterogeneous than 3' termini. Approximately half of the thirty-one wheat mitochondrial transcriptional units are preceded by CRTA promoter-like motifs, and of the potential stem-loop or tRNA-like structures identified as candidate RNA processing/stability signals near the 5' or 3' ends, several are shared with Arabidopsis. Comparison of the mitochondrial gene flanking sequences from normal fertile wheat (Triticum aestivum) with those of Aegilops kotschyi which is the source of mitochondria present in K-type cytoplasmic male sterile wheat, revealed six cases where mRNAs are precluded from sharing full-length homologous UTRs because of genomic reorganization events, and the presence of short repeats located at the sites of discontinuity points to a reciprocal recombination-mediated mode of rearrangement.

  6. An Interaction with Ewing’s Sarcoma Breakpoint Protein EWS Defines a Specific Oncogenic Mechanism of ETS Factors Rearranged in Prostate Cancer

    Directory of Open Access Journals (Sweden)

    Vivekananda Kedage

    2016-10-01

    Full Text Available More than 50% of prostate tumors have a chromosomal rearrangement resulting in aberrant expression of an oncogenic ETS family transcription factor. However, mechanisms that differentiate the function of oncogenic ETS factors expressed in prostate tumors from non-oncogenic ETS factors expressed in normal prostate are unknown. Here, we find that four oncogenic ETS (ERG, ETV1, ETV4, and ETV5, and no other ETS, interact with the Ewing’s sarcoma breakpoint protein, EWS. This EWS interaction was necessary and sufficient for oncogenic ETS functions including gene activation, cell migration, clonogenic survival, and transformation. Significantly, the EWS interacting region of ERG has no homology with that of ETV1, ETV4, and ETV5. Therefore, this finding may explain how divergent ETS factors have a common oncogenic function. Strikingly, EWS is fused to various ETS factors by the chromosome translocations that cause Ewing’s sarcoma. Therefore, these findings link oncogenic ETS function in both prostate cancer and Ewing’s sarcoma.

  7. Antifungal susceptibility of Candida species isolated from patients with candidemia in southern Taiwan, 2007-2012: impact of new antifungal breakpoints.

    Science.gov (United States)

    Chen, Yi-Chun; Kuo, Shu-Fang; Chen, Fang-Ju; Lee, Chen-Hsiang

    2017-02-01

    The Clinical and Laboratory Standard Institute (CLSI) revised the clinical breakpoints (CBPs) for the azoles and echinocandins against Candida species in 2012. We aimed to report the epidemiology of candidemia and antifungal susceptibility of Candida species and evaluate the impact of new CBPs on antifungal susceptibility in our region. All blood isolates of Candida species were obtained from 2007 to 2012. The minimum inhibitory concentrations of fluconazole, voriconazole, echinocandins and flucytosine against Candida isolates were determined by Sensititre YeastOne system. Differences in susceptibility rates between the CBPs of previous and revised versions of CLSI were examined. Of 709 Candida isolates, the fluconazole-susceptible rate was 96.5% in Candida albicans, 85.8% in Candida tropicalis and 92.1% in Candida parapsilosis by the revised CBPs. Compared with the susceptibility results by previous CBPs, the marked reductions in susceptibility of C. albicans, C. tropicalis and C. parapsilosis to fluconazole, that of C. tropicalis and C. parapsilosis to voriconazole, that of C. tropicalis and Candida glabrata to anidulafungin and that of C. tropicalis, C. glabrata and Candida krusei to caspofungin by revised CBPs were found. In conclusion, Candida albicans and C. parapsilosis remain highly susceptible to fluconazole. The non-susceptible rates of Candida species to azoles and echinocandins increase with interpretation by the revised CBPs. © 2016 Blackwell Verlag GmbH.

  8. Molecular analysis of new subtypes of ELE/RET rearrangements, their reciprocal transcripts and breakpoints in papillary thyroid carcinomas of children after Chernobyl.

    Science.gov (United States)

    Klugbauer, S; Demidchik, E P; Lengfelder, E; Rabes, H M

    1998-02-05

    A high prevalence of RET rearrangements is found in papillary thyroid carcinomas (PTC) of children from Belarus after the Chernobyl reactor accident. The ELE/RET rearrangement (PTC3) is prevailing. Aberrant types of ELE/RET rearrangement have been found with a truncated ELE1 gene: As compared with the common form (PTC3r1) one aberrant type is shorter by one 144 bp exon (PTC3r2) (three cases); in the second atypic form (PTC3r3) the ELE1 part is 18 bp shorter than in PTC3r1. In agreement with the observation that the oncogenic RET is generated by a paracentric inversion at chromosome 10, we found not only ELE/RET, but also RET/ELE transcripts in these tumors. Sequencing of the breakpoint regions at the genomic DNA level revealed DNA modifications that might be relevant for illegitimate recombination after DNA doublestrand breaks. The high prevalence of ELE/RET rearrangements and various subtypes appears to be typical for radiation-induced thyroid carcinomas of children after the Chernobyl reactor accident.

  9. MLPA analysis of an Argentine cohort of patients with dystrophinopathy: Association of intron breakpoints hot spots with STR abundance in DMD gene.

    Science.gov (United States)

    Luce, Leonela N; Dalamon, Viviana; Ferrer, Marcela; Parma, Diana; Szijan, Irene; Giliberto, Florencia

    2016-06-15

    Dystrophinopathies are X-linked recessive diseases caused by mutations in the DMD gene. Our objective was to identify mutations in this gene by Multiplex Ligation Probe Amplification (MLPA), to confirm the clinical diagnosis and determine the carrier status of at-risk relatives. Also, we aimed to characterize the Dystrophinopathies argentine population and the DMD gene. We analyzed a cohort of 121 individuals (70 affected boys, 11 symptomatic women, 37 at-risk women and 3 male villus samples). The MLPA technique identified 56 mutations (45 deletions, 9 duplications and 2 point mutations). These results allowed confirming the clinical diagnosis in 63% (51/81) of patients and symptomatic females. We established the carrier status of 54% (20/37) of females at-risk and 3 male villus samples. We could establish an association between the most frequent deletion intron breakpoints and the abundance of dinucleotide microsatellites loci, despite the underlying mutational molecular mechanism remains to be elucidated. The MLPA demonstrate, again, to be the appropriate first mutation screening methodology for molecular diagnosis of Dystrophinopathies. The reported results permitted to characterize the Dystrophinopathies argentine population and lead to better understanding of the genetic and molecular basis of rearrangements in the DMD gene, useful information for the gene therapies being developed. Copyright © 2016 Elsevier B.V. All rights reserved.

  10. Deletion of UBE3A in brothers with Angelman syndrome at the breakpoint with an inversion at 15q11.2.

    Science.gov (United States)

    Kuroda, Yukiko; Ohashi, Ikuko; Saito, Toshiyuki; Nagai, Jun-Ichi; Ida, Kazumi; Naruto, Takuya; Wada, Takahito; Kurosawa, Kenji

    2014-11-01

    Angelman syndrome (AS) is characterized by severe intellectual disability with ataxia, epilepsy, and behavioral uniqueness. The underlining molecular deficit is the absence of the maternal copy of the imprinted UBE3A gene due to maternal deletions, which is observed in 70-75% of cases, and can be detected using fluorescent in situ hybridization (FISH) of the UBE3A region. Only a few familial AS cases have been reported with a complete deletion of UBE3A. Here, we report on siblings with AS caused by a microdeletion of 15q11.2-q12 encompassing UBE3A at the breakpoint of an inversion at 15q11.2 and 15q26.1. Karyotyping revealed an inversion of 15q, and FISH revealed the deletion of the UBE3A region. Array comparative genomic hybridization (CGH) demonstrated a 467 kb deletion at 15q11.2-q12, encompassing only UBE3A, SNORD115, and PAR1, and a 53 kb deletion at 15q26.1, encompassing a part of SLCO3A1. Their mother had a normal karyotype and array CGH detected no deletion of 15q11.2-q12, so we assumed gonadal mosaicism. This report describes a rare type of familial AS detected using the D15S10 FISH test. © 2014 Wiley Periodicals, Inc.

  11. Breakpoint cluster region-c-abl oncogene 1, non-receptor tyrosine kinase signaling: Current patterns of the versatile regulator revisited

    Directory of Open Access Journals (Sweden)

    Aamir Rana

    2013-01-01

    Full Text Available Increasing sophisticated information suggests that cancer cells express constitutively active oncogenic kinases such as breakpoint cluster region- c-abl oncogene 1, non-receptor tyrosine kinase (BCR-ABL1 that promote carcinogenesis independent of extrinsic growth factors. It is a well-established fact that through the aberrant activation of BCR-ABL1 signal transduction cascade, the perception of cellular growth signals becomes disconnected from the processes promoting cell growth, and this underlies the pathophysiology of leukemia. In this particular review we discuss the oncogenes and tumor suppressors comprising the regulatory network upstream and downstream of BCR-ABL1 and dismantle how derailed BCR-ABL1 signaling provides cell a selective growth advantage. Besides, we discuss why activation of BCR-ABL1, as an outcome of distinct oncogenic events, results in miscellaneous clinical outcomes, and how the intricacy of the BCR-ABL1 signaling network might dictate therapeutic approaches. In this review, our current comprehension of BCR-ABL1 signaling will be summarized.

  12. Clinical usefulness of the 2010 clinical and laboratory standards institute revised breakpoints for cephalosporin use in the treatment of bacteremia caused by Escherichia coli or Klebsiella spp.

    Science.gov (United States)

    Ku, Nam Su; Chung, Hae-Sun; Choi, Jun Yong; Yong, Dongeun; Lee, Kyungwon; Kim, June Myung; Chong, Yunsop

    2015-01-01

    We investigated the clinical usefulness of the revised 2010 Clinical and Laboratory Standards Institute (CLSI) breakpoints for Escherichia coli and Klebsiella spp. Of 2,623 patients with bacteremia caused by E. coli or Klebsiella spp., 573 who had been treated appropriately with cephalosporin based on the CLSI 2009 guidelines were enrolled. There were no differences in the rates of treatment failure or mortality between the appropriately and inappropriately treated groups according to the CLSI 2010 guidelines. Additionally, in the matched case-control analysis, the treatment failure rate was higher in bacteremic patients with extended-spectrum β-lactamase- (ESBL-) producing but cephalosporin-susceptible organisms than in those with ESBL-nonproducing isolates when patients with urinary tract infections were excluded (44% and 0%, resp., P = 0.026). In patients with bacteremia caused by E. coli or Klebsiella spp., the revised CLSI 2010 guidelines did not lead to poorer outcomes. However, ESBL production appeared to be associated with poor clinical outcomes in patients with bacteremia from sources other than the urinary tract.

  13. Refinement of the Seathre-Chotzen syndrome locus between D7S664 and D7S507 which flank a translocation breakpoint in an affected individual

    Energy Technology Data Exchange (ETDEWEB)

    Lewanda, A.F. [Johns Hopkins Univ., Baltimore, MD (United States)]|[Children`s National Medical Center, Washington, DC (United States); Taylor, E.W.; Jabs, E.W. [Johns Hopkins Univ., Baltimore, MD (United States)] [and others

    1994-09-01

    Saethre-Chotzen syndrome (SCS) is a common autosomal dominant craniosynostosis disorder that has been mapped to distal chromosome 7p. In addition to craniosynostosis, patients with SCS have facial asymmetry, low frontal hairline, ptosis, deviated nasal septum, brachydactyly, and partial cutaneous syndactyly. We evaluated 66 individuals in 10 SCS families. Linkage analysis was performed with 11 dinucleotide repeat markers between D7S513 and D7S516, spanning a genetic distance of 27 cM. The tightest linkage was to marker D7S664 (Z = 7.16, {theta} = 0.00), with a confidence interval of 8 cM. Haplotype analysis of those families with informative recombination events showed the disease locus to lie within the 12 cM region between markers D7S513 and D7S507. We used FISH to physically map the gene using chromosome spreads from the SCS patient with t(2;7)(p23;p22) reported by Reid et al. and YAC clones from a contig spanning the critical interval. These studies confirmed that the breakpoint lies within this region, and in fact identified a microdeletion. Further studies will be targeted towards identification of candidate genes for Saethre-Chotzen syndrome.

  14. The Selective Serotonin Reuptake Inhibitor Paroxetine Decreases Breakpoint of Rats Engaging in a Progressive Ratio Licking Task for Sucrose and Quinine Solutions

    Science.gov (United States)

    2013-01-01

    Increased serotonergic activity has been shown to reduce motivation to ingest, which may involve, in part, gustatory processes. Here, we examined the effect of paroxetine, a selective serotonin reuptake inhibitor, on appetitive responding for a preferred and an avoided taste solution using a progressive ratio (PR) task in which licking was employed as the operant. Male Sprague-Dawley rats (n = 8/taste stimulus) were trained to respond for a concentration series of sucrose or quinine on fixed and PR schedules of reinforcement. Performance for sucrose was assessed while the rats were partially food- and water-restricted and nondeprived, and performance for water and quinine was assessed while the rats were water-deprived. Then, the rats were injected with vehicle (10% dimethyl sulfoxide, 1mL/kg intraperitoneal [ip], −1h) or paroxetine (5mg/kg), and their responding on a PR schedule for sucrose measured when the rats were nondeprived or for water and quinine when the rats were water-deprived. Paroxetine decreased breakpoint, which was defined as the number of operant (e.g., dry) licks in the final reinforced ratio, for water, quinine, and sucrose. This demonstrates that a general systemic increase in serotonergic activity decreases the appetitive-based responses to both preferred and nonpreferred fluids under different deprivation states. PMID:23254343

  15. Evaluation of CLSI M44-A2 disk diffusion and associated breakpoint testing of caspofungin and micafungin using a well-characterized panel of wild-type and fks hot spot mutant Candida isolates.

    Science.gov (United States)

    Arendrup, Maiken Cavling; Park, Steven; Brown, Steven; Pfaller, Michael; Perlin, David S

    2011-05-01

    Disk diffusion testing has recently been standardized by the CLSI, and susceptibility breakpoints have been established for several antifungal compounds. For caspofungin, 5-μg disks are approved, and for micafungin, 10-μg disks are under evaluation. We evaluated the performances of caspofungin and micafungin disk testing using a panel of Candida isolates with and without known FKS echinocandin resistance mechanisms. Disk diffusion and microdilution assays were performed strictly according to CLSI documents M44-A2 and M27-A3. Eighty-nine clinical Candida isolates were included: Candida albicans (20 isolates/10 mutants), C. glabrata (19 isolates/10 mutants), C. dubliniensis (2 isolates/1 mutant), C. krusei (16 isolates/3 mutants), C. parapsilosis (14 isolates/0 mutants), and C. tropicalis (18 isolates/4 mutants). Quality control strains were C. parapsilosis ATCC 22019 and C. krusei ATCC 6258. The correlations between zone diameters and MIC results were good for both compounds, with identical susceptibility classifications for 93.3% of the isolates by applying the current CLSI breakpoints. However, the numbers of fks hot spot mutant isolates misclassified as being susceptible (S) (very major errors [VMEs]) were high (61% for caspofungin [S, ≥11 mm] and 93% for micafungin [S, ≥14 mm]). Changing the disk diffusion breakpoint to S at ≥22 mm significantly improved the discrimination. For caspofungin, 1 VME was detected (a C. tropicalis isolate with an F76S substitution) (3.5%), and for micafungin, 10 VMEs were detected, the majority of which were for C. glabrata (8/10). The broadest separation between zone diameter ranges for wild-type (WT) and mutant isolates was seen for caspofungin (6 to 12 mm versus -4 to 7 mm). In conclusion, caspofungin disk diffusion testing with a modified breakpoint led to excellent separation between WT and mutant isolates for all Candida species.

  16. Evaluation of CLSI M44-A2 Disk Diffusion and Associated Breakpoint Testing of Caspofungin and Micafungin Using a Well-Characterized Panel of Wild-Type and fks Hot Spot Mutant Candida Isolates▿

    Science.gov (United States)

    Arendrup, Maiken Cavling; Park, Steven; Brown, Steven; Pfaller, Michael; Perlin, David S.

    2011-01-01

    Disk diffusion testing has recently been standardized by the CLSI, and susceptibility breakpoints have been established for several antifungal compounds. For caspofungin, 5-μg disks are approved, and for micafungin, 10-μg disks are under evaluation. We evaluated the performances of caspofungin and micafungin disk testing using a panel of Candida isolates with and without known FKS echinocandin resistance mechanisms. Disk diffusion and microdilution assays were performed strictly according to CLSI documents M44-A2 and M27-A3. Eighty-nine clinical Candida isolates were included: Candida albicans (20 isolates/10 mutants), C. glabrata (19 isolates/10 mutants), C. dubliniensis (2 isolates/1 mutant), C. krusei (16 isolates/3 mutants), C. parapsilosis (14 isolates/0 mutants), and C. tropicalis (18 isolates/4 mutants). Quality control strains were C. parapsilosis ATCC 22019 and C. krusei ATCC 6258. The correlations between zone diameters and MIC results were good for both compounds, with identical susceptibility classifications for 93.3% of the isolates by applying the current CLSI breakpoints. However, the numbers of fks hot spot mutant isolates misclassified as being susceptible (S) (very major errors [VMEs]) were high (61% for caspofungin [S, ≥11 mm] and 93% for micafungin [S, ≥14 mm]). Changing the disk diffusion breakpoint to S at ≥22 mm significantly improved the discrimination. For caspofungin, 1 VME was detected (a C. tropicalis isolate with an F76S substitution) (3.5%), and for micafungin, 10 VMEs were detected, the majority of which were for C. glabrata (8/10). The broadest separation between zone diameter ranges for wild-type (WT) and mutant isolates was seen for caspofungin (6 to 12 mm versus −4 to 7 mm). In conclusion, caspofungin disk diffusion testing with a modified breakpoint led to excellent separation between WT and mutant isolates for all Candida species. PMID:21357293

  17. Characterization of 26 deletion CNVs reveals the frequent occurrence of micro-mutations within the breakpoint-flanking regions and frequent repair of double-strand breaks by templated insertions derived from remote genomic regions.

    Science.gov (United States)

    Wang, Ye; Su, Peiqiang; Hu, Bin; Zhu, Wenjuan; Li, Qibin; Yuan, Ping; Li, Jiangchao; Guan, Xinyuan; Li, Fucheng; Jing, Xiangyi; Li, Ru; Zhang, Yongling; Férec, Claude; Cooper, David N; Wang, Jun; Huang, Dongsheng; Chen, Jian-Min; Wang, Yiming

    2015-06-01

    Copy number variations (CNVs) have increasingly been reported to cause, or predispose to, human disease. However, a large fraction of these CNVs have not been accurately characterized at the single-base-pair level, thereby hampering a better understanding of the mutational mechanisms underlying CNV formation. Here, employing a composite pipeline method derived from various inference-based programs, we have characterized 26 deletion CNVs [including three novel pathogenic CNVs involving an autosomal gene (EXT2) causing hereditary osteochondromas and an X-linked gene (CLCN5) causing Dent disease, as well as 23 CNVs previously identified by inference from a cohort of Canadian autism spectrum disorder families] to the single-base-pair level of accuracy from whole-genome sequencing data. We found that breakpoint-flanking micro-mutations (within 22 bp of the breakpoint) are present in a significant fraction (5/26; 19%) of the deletion CNVs. This analysis also provided evidence that a recently described error-prone form of DNA repair (i.e., repair of DNA double-strand breaks by templated nucleotide sequence insertions derived from distant regions of the genome) not only causes human genetic disease but also impacts on human genome evolution. Our findings illustrate the importance of precise CNV breakpoint delineation for understanding the underlying mutational mechanisms and have implications for primer design in relation to the detection of deletion CNVs in clinical diagnosis.

  18. First report on an X-linked hypohidrotic ectodermal dysplasia family with X chromosome inversion: Breakpoint mapping reveals the pathogenic mechanism and preimplantation genetics diagnosis achieves an unaffected birth.

    Science.gov (United States)

    Wu, Tonghua; Yin, Biao; Zhu, Yuanchang; Li, Guangui; Ye, Lijun; Liang, Desheng; Zeng, Yong

    2017-10-14

    To investigate the etiology of X-linked hypohidrotic ectodermal dysplasia (XLHED) in a family with an inversion of the X chromosome [inv(X)(p21q13)] and to achieve a healthy birth following preimplantation genetic diagnosis (PGD). Next generation sequencing (NGS) and Sanger sequencing analysis were carried out to define the inversion breakpoint. Multiple displacement amplification, amplification of breakpoint junction fragments, Sanger sequencing of exon 1 of ED1, haplotyping of informative short tandem repeat markers and gender determination were performed for PGD. NGS data of the proband sample revealed that the size of the possible inverted fragment was over 42Mb, spanning from position 26, 814, 206 to position 69, 231, 915 on the X chromosome. The breakpoints were confirmed by Sanger sequencing. A total of 5 blastocyst embryos underwent trophectoderm biopsy. Two embryos were diagnosed as carriers and three were unaffected. Two unaffected blastocysts were transferred and a singleton pregnancy was achieved. Following confirmation by prenatal diagnosis, a healthy baby was delivered. This is the first report of an XLHED family with inv(X). ED1 is disrupted by the X chromosome inversion in this XLHED family and embryos with the X chromosomal abnormality can be accurately identified by means of PGD. Copyright © 2017. Published by Elsevier B.V.

  19. Identification of subtelomeric genomic imbalances and breakpoint mapping with quantitative PCR in 296 individuals with congenital defects and/or mental retardation

    Directory of Open Access Journals (Sweden)

    Brockmann Knut

    2009-03-01

    Full Text Available Abstract Background Submicroscopic imbalances in the subtelomeric regions of the chromosomes are considered to play an important role in the aetiology of mental retardation (MR. The aim of the study was to evaluate a quantitative PCR (qPCR protocol established by Boehm et al. (2004 in the clinical routine of subtelomeric testing. Results 296 patients with MR and a normal karyotype (500–550 bands were screened for subtelomeric imbalances by using qPCR combined with SYBR green detection. In total, 17 patients (5.8% with 20 subtelomeric imbalances were identified. Six of the aberrations (2% were classified as causative for the symptoms, because they occurred either de novo in the patients (5 cases or the aberration were be detected in the patient and an equally affected parent (1 case. The extent of the deletions ranged from 1.8 to approximately 10 Mb, duplications were 1.8 to approximately 5 Mb in size. In 6 patients, the copy number variations (CNVs were rated as benign polymorphisms, and the clinical relevance of these CNVs remains unclear in 5 patients (1.7%. Therefore, the overall frequency of clinically relevant imbalances ranges between 2% and 3.7% in our cohort. Conclusion This study illustrates that the qPCR/SYBR green technique represents a rapid and versatile method for the detection of subtelomeric imbalances and the option to map the breakpoint. Thus, this technique is highly suitable for genotype/phenotype studies in patients with MR/developmental delay and/or congenital defects.

  20. Wild-type MIC distributions, epidemiological cutoff values and species-specific clinical breakpoints for fluconazole and Candida: time for harmonization of CLSI and EUCAST broth microdilution methods.

    Science.gov (United States)

    Pfaller, M A; Andes, D; Diekema, D J; Espinel-Ingroff, A; Sheehan, D

    2010-12-01

    Both the Clinical and Laboratory Standards Institute (CLSI) and the European Committee on Antimicrobial Susceptibility Testing (EUCAST) have MIC clinical breakpoints (CBPs) for fluconazole (FLU) and Candida. EUCAST CBPs are species-specific, and apply only to C. albicans, C. tropicalis and C. parapsilosis, while CLSI CBPs apply to all species. We reassessed the CLSI CBPs for FLU and Candida in light of recent data. We examined (1) molecular mechanisms of resistance and cross-resistance profiles, (2) wild-type (WT) MICs and epidemiological cutoff values (ECVs) for FLU and major Candida species by both CLSI and EUCAST methods, (3) determination of essential (EA) and categorical agreement (CA) between CLSI and EUCAST methods, (4) correlation of MICs with outcomes from previously published data using CLSI and EUCAST methods, and (5) pharmacokinetic and pharmacodynamic considerations. We applied these findings to propose new species-specific CLSI CBPs for FLU and Candida. WT distributions from large collections of Candida revealed similar ECVs by both CLSI and EUCAST methods (0.5-1 mcg/ml for C. albicans, 2 mcg/ml for C. parapsilosis and C. tropicalis, 32 mcg/ml for C. glabrata, and 64-128 for C. krusei). Comparison of CLSI and EUCAST MICs reveal EA and CA of 95% and 96%, respectively. Datasets correlating CLSI and EUCAST FLU MICs with outcomes revealed decreased response rates when MICs were > 4 mcg/ml for C. albicans, C. tropicalis and C. parapsilosis, and > 16 mcg/ml for C. glabrata. Adjusted CLSI CBPs for FLU and C. albicans, C. parapsilosis, C. tropicalis (S, ≤ 2 mcg/ml; SDD, 4 mcg/ml; R, ≥ 8 mcg/ml), and C. glabrata (SDD, ≤ 32 mcg/ml; R, ≥ 64 mcg/ml) should be more sensitive for detecting emerging resistance among common Candida species and provide consistency with EUCAST CBPs. Copyright © 2010 Elsevier Ltd. All rights reserved.

  1. Influence of Minimum Inhibitory Concentration in Clinical Outcomes of Enterococcus faecium Bacteremia Treated With Daptomycin: Is it Time to Change the Breakpoint?

    Science.gov (United States)

    Shukla, Bhavarth S; Shelburne, Samuel; Reyes, Katherine; Kamboj, Mini; Lewis, Jessica D; Rincon, Sandra L; Reyes, Jinnethe; Carvajal, Lina P; Panesso, Diana; Sifri, Costi D; Zervos, Marcus J; Pamer, Eric G; Tran, Truc T; Adachi, Javier; Munita, Jose M; Hasbun, Rodrigo; Arias, Cesar A

    2016-06-15

    Daptomycin has become a front-line antibiotic for multidrug-resistant Enterococcus faecium bloodstream infections (BSIs). We previously showed that E. faecium strains with daptomycin minimum inhibitory concentrations (MICs) in the higher end of susceptibility frequently harbor mutations associated with daptomycin resistance. We postulate that patients with E. faecium BSIs exhibiting daptomycin MICs of 3-4 µg/mL treated with daptomycin are more likely to have worse clinical outcomes than those exhibiting daptomycin MICs ≤2 µg/mL. We conducted a multicenter retrospective cohort study that included adult patients with E. faecium BSI for whom initial isolates, follow-up blood culture data, and daptomycin administration data were available. A central laboratory performed standardized daptomycin MIC testing for all isolates. The primary outcome was microbiologic failure, defined as clearance of bacteremia ≥4 days after the index blood culture. The secondary outcome was all-cause in-hospital mortality. A total of 62 patients were included. Thirty-one patients were infected with isolates that exhibited daptomycin MICs of 3-4 µg/mL. Overall, 34 patients had microbiologic failure and 25 died during hospitalization. In a multivariate logistic regression model, daptomycin MICs of 3-4 µg/mL (odds ratio [OR], 4.7 [1.37-16.12]; P = .014) and immunosuppression (OR, 5.32 [1.20-23.54]; P = .028) were significantly associated with microbiologic failure. Initial daptomycin dose of ≥8 mg/kg was not significantly associated with evaluated outcomes. Daptomycin MICs of 3-4 µg/mL in the initial E. faecium blood isolate predicted microbiological failure of daptomycin therapy, suggesting that modification in the daptomycin breakpoint for enterococci should be considered. © The Author 2016. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

  2. Site Features

    Data.gov (United States)

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

  3. 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...

  4. Oncogenes create a unique landscape of fragile sites.

    Science.gov (United States)

    Miron, Karin; Golan-Lev, Tamar; Dvir, Raz; Ben-David, Eyal; Kerem, Batsheva

    2015-05-11

    Recurrent genomic instability in cancer is attributed to positive selection and/or the sensitivity of specific genomic regions to breakage. Among these regions are fragile sites (FSs), genomic regions sensitive to replication stress conditions induced by the DNA polymerase inhibitor aphidicolin. However, the basis for the majority of cancer genomic instability hotspots remains unclear. Aberrant oncogene expression induces replication stress, leading to DNA breaks and genomic instability. Here we map the cytogenetic locations of oncogene-induced FSs and show that in the same cells, each oncogene creates a unique fragility landscape that only partially overlaps with aphidicolin-induced FSs. Oncogene-induced FSs colocalize with cancer breakpoints and large genes, similar to aphidicolin-induced FSs. The observed plasticity in the fragility landscape of the same cell type following oncogene expression highlights an additional level of complexity in the molecular basis for recurrent fragility in cancer.

  5. 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....

  6. 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...

  7. Site calibration

    DEFF Research Database (Denmark)

    Gómez Arranz, Paula; Georgieva Yankova, Ginka

    The report describes site calibration measurements carried out on a site in Denmark. The measurements are carried out in accordance to Ref. [1]. 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 [2]. The possible measurement sector for power performance...... according to [1] is also described in [2] and no results from the site calibration have shown any necessary exclusion from this sector. All parts of the sensors and the measurement system have been installed by DTU....

  8. Demarcation of Security in Authentication Protocols

    DEFF Research Database (Denmark)

    Ahmed, Naveed; Jensen, Christian D.

    2011-01-01

    Security analysis of communication protocols is a slippery business; many “secure” protocols later turn out to be insecure. Among many, two complains are more frequent: inadequate definition of security and unstated assumptions in the security model. In our experience, one principal cause...... for such state of affairs is an apparent overlap of security and correctness, which may lead to many sloppy security definitions and security models. Although there is no inherent need to separate security and correctness requirements, practically, such separation is significant. It makes security analysis...... easier, and enables us to define security goals with a fine granularity. We present one such separation, by introducing the notion of binding sequence as a security primitive. A binding sequence, roughly speaking, is the only required security property of an authentication protocol. All other...

  9. Cognitive frames in psychology: demarcations and ruptures.

    Science.gov (United States)

    Yurevich, Andrey V

    2009-06-01

    As there seems to be a recurrent feeling of crisis in psychology, its present state is analyzed in this article. The author believes that in addition to the traditional manifestations that have dogged psychology since it emerged as an independent science some new features of the crisis have emerged. Three fundamental "ruptures" are identified: the "horizontal" rupture between various schools and trends, the "vertical" rupture between natural science and humanitarian psychology, and the "diagonal" rupture between academic research and applied practice of psychology. These manifestations of the crisis of psychology have recently been compounded by the crisis of its rationalistic foundations. This situation is described in terms of the cognitive systems in psychology which include meta-theories, paradigms, sociodigms and metadigms.

  10. Demarcating misconduct from misinterpretations and mistakes

    DEFF Research Database (Denmark)

    Andersen, Hanne

    2008-01-01

    Within recent years, scientific misconduct has become an increasingly important topic, not only in the scientific community, but in the general public as well. Spectacular cases have been extensively covered in the news media, such as the cases of the Korean stem cell researcher Hwang, the German...

  11. Planning model for the expansion of the electrical generation system with risk demarcation criteria; Modelo para la planificacion de la expansion del sistema electrico de generacion con criterios de acotamiento de riesgo

    Energy Technology Data Exchange (ETDEWEB)

    Hernandez Galicia, Julio Alberto; Nieva Gomez, Rolando [Instituto de Investigaciones Electricas, Cuernavaca, Morelos (Mexico)

    2009-07-01

    The general characteristics of a planning model for the electrical generation system expansion with risk demarcation criteria, as well as the main results of a representative study case of the Mexican Electrical System is presented. The model is based on a methodology of multiannual optimization for the generation expansion plans determination. In this context, every expansion plan defines the technology type to be installed, as well as the installation year, unit size and its location within a regional electric network. For this purpose, the model considers an interregional representation of the system identifying the necessary reinforcements to the capacity of the interregional connections. It also incorporates a Demarcation of Risk module that considers the uncertainty of the future scenarios of fuels prices to generate a set of expansion plans, among which includes the following: a) For every future of the fuel prices: the plan that diminishes the present value of the total cost (investment plus production). b) The plan that diminishes the economic risk derived from the uncertainty in the future of the fuel prices. c) A subgroup of expansion plans that are located in the efficient borders of decision, under the context of three criteria of interest: the economic risk, the investment cost of and the total cost in the future considered of greater relevance. [Spanish] Se presentan las caracteristicas generales de un modelo de planificacion de la expansion del sistema electrico de generacion con criterios de acotamiento de riesgo, asi como los principales resultados de un caso de estudio representativo del Sistema Electrico Mexicano. El modelo se basa en una metodologia de optimacion multi-anual para la determinacion de planes de expansion de la generacion. En este contexto, cada plan de expansion define el tipo de tecnologia que debera instalarse, asi como el ano de instalacion, el tamano de la unidad y su localizacion dentro de una red electrica regional. Para

  12. 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...

  13. [Antifungal susceptibility profiles of Candida species to triazole: application of new CLSI species-specific clinical breakpoints and epidemiological cutoff values for characterization of antifungal resistance].

    Science.gov (United States)

    Karabıçak, Nilgün; Alem, Nihal

    2016-01-01

    The Clinical and Laboratory Standards Institute (CLSI) Subcommittee on Antifungal Susceptibility Testing has newly introduced species-specific clinical breakpoints (CBPs) for fluconazole and voriconazole. When CBPs can not be determined, wild-type minimal inhibitory concentration (MIC) distributions are detected and epidemiological cutoff values (ECVs) provide valuable means for the detection of emerging resistance. The aim of this study is to determine triazole resistance patterns in Candida species by the recently revised CLSI CBPs. A total of 140 Candida strains isolated from blood cultures of patients with invasive candidiasis hospitalized in various intensive care units in Turkey and sent to our reference laboratory between 2011-2012, were included in the study. The isolates were identified by conventional methods, and susceptibility testing was performed against fluconazole, itraconazole and voriconazole, by the 24-h CLSI broth microdilution (BMD) method. Azole resistance rates for all Candida species were determined using the new species-specific CLSI CBPs and ECVs criteria, when appropriate. The species distribution of the isolates were as follows; C.parapsilosis (n= 31 ), C.tropicalis (n= 26 ), C.glabrata (n= 21), C.albicans (n= 18), C.lusitaniae (n= 16), C.krusei (n= 16), C.kefyr (n= 9), C.guilliermondii (n= 2), and C.dubliniensis (n= 1). According to the newly determined CLSI CBPs for fluconazole and C.albicans, C.parapsilosis, C.tropicalis [susceptible (S), ≤ 2 µg/ml; dose-dependent susceptible (SDD), 4 µg/ml; resistant (R), ≥ 8 µg/ml], and C.glabrata (SDD, ≤ 32 µg/ml; R≥ 64 µg/ml) and for voriconazole and C.albicans, C.parapsilosis, C.tropicalis (S, ≤ 0.12 µg/ml; SDD, 0.25-0.5 µg/ml; R, ≥ 1 µg/ml), and C.krusei (S, ≤ 0.5 µg/ml; SDD, 1 µg/ml; R, ≥ 2 µg/ml), it was found that three of C.albicans, one of C.parapsilosis and one of C.glabrata isolates were resistant to fluconazole, while two of C.albicans and two of C

  14. Sites internet

    Science.gov (United States)

    Couderc

    2000-07-01

    http://biotribune.com/ Biotribune.com ou la biologie medicale sur internet. Ce site est concu comme un portail sur la biologie clinique. Accueil d'internautes sur une page comportant, entre autres, les rubriques : actualite, evenements, revue des connaissances, rubrique juridique et petites annonces. Biotribune propose regulierement des dossiers rediges par des specialistes comportant une mise a jour des connaissances orientee sur l'interet diagnostique des tests de biologie clinique. Le site propose egalement une revue de presse scientifique avec des resumes courts d'articles parus dans les grands journaux internationaux tels que The Lancet, New England Journal of Medicine, Science, etc. Vous pouvez aussi y tester vos connaissances grace a des cas cliniques et des QCM. Ce site propose egalement des petites annonces pratiques pour les laboratoires de ville (remplacement, materiel d'occasion, etc.). Les problemes touchant l'assurance qualite, les RMO et la nomenclature font egalement l'objet d'information et de commentaires. Enfin, vous pourrez vous inscrire a l'un des forums proposes : discussion biomedicale ou opinion et reaction sur les sujets touchant au professionnel de la biologie medicale. En conclusion, un site complet et agreable que l'on souhaite voir s'enrichir et se renouveler regulierement. http://www.arcol.asso.fr Site du Comite francais de coordination de recherche sur l'atherosclerose et le cholesterol (Arcol). Ce site s'adresse a la fois aux cliniciens, aux biologistes et aux non-specialistes interesses par la pathologie cardio-vasculaire et ses traitements. On y trouve des rubriques tres didactiques sur la physiopathologie et les facteurs de risque de l'atherosclerose, la prise en charge nutritionnelle et medicamenteuse des patients. On peut tester ses connaissances a l'aide des nombreux cas cliniques richement commentes. Ce site regulierement mis a jour contient egalement les recommandations nationales et internationales sur la prise en charge du

  15. Ultraviolet-fluorescent tattoo location of cutaneous biopsy site.

    Science.gov (United States)

    Chuang, Gary S; Gilchrest, Barbara A

    2012-03-01

    Cutaneous biopsies often heal with little or no scarring. Prior studies have shown an alarming percentage of patients who incorrectly identify biopsy sites at the time of surgery. To investigate the safety and utility of an ultraviolet (UV)-fluorescent tattoo for biopsy site identification. A preclinical proof of concept was established with skin culture. An UV-fluorescent tattoo was applied to discarded neonatal foreskin in culture medium. The stability of the tattooed skin was examined clinically and histologically. One patient with a recurrent basal cell carcinoma in a difficult-to-identify location underwent tattoo application at the time of biopsy to demarcate the site. The patient was monitored for tattoo reaction and referred for surgical excision. The cultured tissue exhibited stable UV fluorescence with daily washing. Tissue histology demonstrated tattoo particles lining the skin edge under fluorescent microscopy. The patient was reluctant to undergo another surgical procedure and instead returned to our clinic at 3 months and 17 months after the biopsy for management of other tumors. The patient had no symptoms of allergic reaction to the tattoo dye. The fluorescent tattoo remains invisible under visible light and visible only under Wood's light. The present study documents the utility of an UV-fluorescent tattoo to locate a biopsy site. © 2011 by the American Society for Dermatologic Surgery, Inc. Published by Wiley Periodicals, Inc.

  16. Site Practice

    DEFF Research Database (Denmark)

    Wahedi, Haseebullah

    2016-01-01

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

  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. Impact of revised CLSI breakpoints for susceptibility to third-generation cephalosporins and carbapenems among Enterobacteriaceae isolates in the Asia-Pacific region: results from the Study for Monitoring Antimicrobial Resistance Trends (SMART), 2002-2010.

    Science.gov (United States)

    Huang, Chi-Chang; Chen, Yao-Shen; Toh, Han-Siong; Lee, Yu-Lin; Liu, Yuag-Meng; Ho, Cheng-Mao; Lu, Po-Liang; Liu, Chun-Eng; Chen, Yen-Hsu; Wang, Jen-Hsien; Tang, Hung-Jen; Yu, Kwok-Woon; Liu, Yung-Ching; Chuang, Yin-Ching; Xu, Yingchun; Ni, Yuxing; Ko, Wen-Chien; Hsueh, Po-Ren

    2012-06-01

    This study examined the rates of susceptibility to third-generation cephalosporins and carbapenems among Enterobacteriaceae isolates that had been obtained from patients with intraabdominal infections in the Asia-Pacific region as part of the Study for Monitoring Antimicrobial Resistance Trends (SMART). Susceptibility profiles obtained using 2009 Clinical and Laboratory Standards Institute (CLSI) breakpoints were compared with those obtained using the 2011 CLSI breakpoints. From 2002 to 2010, Escherichia coli and Klebsiella pneumoniae together accounted for more than 60% of the 13714 Enterobacteriaceae isolates analyzed during the study period. Extended-spectrum β-lactamase (ESBL) producers comprised 28.2% of E. coli isolates and 22.1% of K. pneumoniae isolates in the Asia-Pacific region, with China (55.6% and 33.7%, respectively) and Thailand (43.1% and 40.7%, respectively) having the highest proportions of ESBL producers. Based on the 2011 CLSI criteria, 77.2% of the Enterobacteriaceae isolates, 40.4% of ESBL-producing E. coli, and 25.2% of ESBL-producing K. pneumoniae isolates were susceptible to ceftazidime. Carbapenems showed in vitro activity against >90% of Enterobacteriaceae isolates in all participating countries, except for ertapenem in South Korea (susceptibility rate 82.2%). Marked differences (>5%) in susceptibility of ESBL-producing E. coli and K. pneumoniae isolates to carbapenems were noted between the profiles obtained using the 2009 CLSI criteria and those using the 2011 CLSI criteria. Continuous monitoring of antimicrobial resistance is necessary in the Asia-Pacific region. Copyright © 2012 Elsevier B.V. All rights reserved.

  19. Site Restoration

    Energy Technology Data Exchange (ETDEWEB)

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

    2002-04-01

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

  20. Use of a CEPH meiotic breakpoint panel to refine the locus of limb-girdle muscular dystrophy type 1A (LGMD1A) to a 2-Mb interval on 5q31.

    Science.gov (United States)

    Bartoloni, L; Horrigan, S K; Viles, K D; Gilchrist, J M; Stajich, J M; Vance, J M; Yamaoka, L H; Pericak-Vance, M A; Westbrook, C A; Speer, M C

    1998-12-01

    Limb-girdle muscular dystrophy type 1A (LGMD1A) is an autosomal dominant disease characterized by progressive weakness of the hip and shoulder girdle. The gene for LGMD1A had been localized to a 7-cM interval at 5q31 in a single large family (Family 39). To refine the localization of LGMD1A further and to aid in its identification, a high-resolution physical map of the locus was used to identify and provisionally localize 25 polymorphic markers. A subset of these markers was then ordered genetically, using a CEPH meiotic breakpoint panel, resulting in an integrated physical-genetic map of the locus. Relevant markers were genotyped on the members of Family 39 who contained informative recombination events, resulting in a further narrowing of LGMD1A to an interval bounded by D5S479 and D5S594, estimated to be 2 Mb in size. Integration of the genetic and physical map permits the identification of several transcription units from within the narrowed LGMD1A interval, including one that is muscle specific, representing candidate genes for this familial dystrophy. Copyright 1998 Academic Press.

  1. High-resolution mapping of the [gamma]-aminobutyric acid receptor subunit [beta]3 and [alpha]5 gene cluster on chromosome 15q11-q13, and localization of breakpoints in two Angelman syndrome patients

    Energy Technology Data Exchange (ETDEWEB)

    Sinnett, D.; Wagstaff, J.; Woolf, E. (Children' s Hospital, Boston, MA (United States) Harvard Medical School, Boston, MA (United States)); Glatt, K. (Children' s Hospital, Boston, MA (United States)); Kirkness, E.J. (National Inst. of Alcohol Abuse and Alcoholism, Rockville, MD (United States))Lalande, M. (Children' s Hospital, Boston, MA (United States) Harvard Medical School, Boston, MA (United States) Howard Hughes Medical Inst., Boston, MA (United States))

    1993-06-01

    The [gamma]-aminobutyric acid (GABA[sub A]) receptors are a family of ligand-gated chloride channels constituting the major inhibitory neurotransmitter receptors in the nervous system. In order to determine the genomic organization of the GABA[sub A] receptor [beta]3 subunit gene (GABRB3) and [alpha]5 subunit gene (GABRA5) in chromosome 15q11-q13, the authors have constructed a high-resolution physical map using the combined techniques of field-inversion gel electrophoresis and phage genomic library screening. This map, which covers nearly 1.0 Mb, shows that GABRB3 and GABRA5 are separated by less than 100 kb and are arranged in a head-to-head configuration. GABRB3 encompasses approximately 250 kb, while GABRA5 is contained within 70 kb. This difference in size is due in large part to an intron of 150 kb within GABRB3. The authors have also identified seven putative CpG islands within a 600-kb interval. Chromosomal rearrangement breakpoints -- in one Angelman syndrome (AS) patient with an unbalanced translocation and in another patient with a submicroscopic deletion -- are located within the large GABRB3 intron. These findings will facilitate chromosomal walking strategies for cloning the regions disrupted by the DNA rearrangements in these AS patients and will be valuable for mapping new genes to the AS chromosomal region. 64 refs., 6 figs., 2 tabs.

  2. Six-year susceptibility trends and effect of revised Clinical Laboratory Standards Institute breakpoints on ciprofloxacin susceptibility reporting in typhoidal Salmonellae in a tertiary care paediatric hospital in Northern India

    Directory of Open Access Journals (Sweden)

    R Saksena

    2016-01-01

    Full Text Available The antimicrobial trends over 6 years were studied, and the effect of revised Clinical Laboratory Standards Institute (CLSI breakpoints (2012 for ciprofloxacin susceptibility reporting in typhoidal Salmonellae was determined. A total of 874 (95.4% isolates were nalidixic acid-resistant (NAR. Using the CLSI 2011 guidelines (M100-S21, 585 (66.9% isolates were ciprofloxacin susceptible. The susceptibility reduced to 11 (1.25% isolates when interpreted using 2012 guidelines (M100-S22. Among the forty nalidixic acid susceptible (NAS Salmonellae, susceptibility to ciprofloxacin decreased from 37 isolates (M100-S21 to 12 isolates (M100-S22. The 25 cases which appeared resistant with newer guidelines had a minimum inhibitory concentration (MIC range between 0.125 and 0.5 μg/ml. MIC50 for the third generation cephalosporins varied between 0.125 and 0.5 μg/ml over 6 years whereas MIC90 varied with a broader range of 0.19–1 μg/ml. The gap between NAR and ciprofloxacin-resistant strains identified using 2011 guidelines has been reduced; however, it remains to be seen whether additional NAS, ciprofloxacin-resistant isolates are truly resistant to ciprofloxacin by other mechanisms of resistance.

  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. Sensibilidad a colistín: evaluación de los puntos de corte disponibles en el antibiograma por difusión Susceptibility to colistin: evaluation of breakpoints available in disk diffusion test

    Directory of Open Access Journals (Sweden)

    C.H. Rodríguez

    2004-09-01

    agar dilution test and disk diffusion test were evaluated against 186 gram-negative strains isolated at the Hospital de Clínicas “José de San Martín” of Buenos Aires city. All susceptibility tests were performed according to the NCCLS recommendations. Were evaluated two breakpoints, NCCLS 1981 (£ 8mm and >11mm, and R. Jones 2001 (£ 11 mm and > 14 mm. Discrepancies on interpretative category were found (0.5% minor; 2.2% major and 4.4% very major with NCCLS 1981, and (18.9% minor; 3.8% majorand 0.5% very major with R. Jones 2001 criteria. Conclusions. In spite of the fact that the breakpoint used by R. Jones 2001decreases the very major error but increases the minor error, according to our results we recommend the use of MIC methods to assist the therapeutic application of colistin; however resistance to colistin was not detected with zone diameters > 16mm.

  5. 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.

  6. 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.

  7. 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...

  8. 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...

  9. Identification of novel HMGA2 fusion sequences in lipoma: evidence that deletion of let-7 miRNA consensus binding site 1 in the HMGA2 3' UTR is not critical for HMGA2 transcriptional upregulation.

    Science.gov (United States)

    Wang, Xiaoke; Hulshizer, Rachael L; Erickson-Johnson, Michele R; Flynn, Heather C; Jenkins, Robert B; Lloyd, Ricardo V; Oliveira, Andre M

    2009-08-01

    Lipoma is a benign tumor composed of mature adipocytes and one of the most common mesenchymal tumors seen in adults. Rearrangement of HMGA2 in chromosome band 12q15 has been found in approximately 60-70% of ordinary lipomas with cytogenetic abnormalities. Herein, we report two novel HMGA2 fusion sequences in lipomas with chromosome 12 rearrangements. Cytogenetic studies showed 12q abnormalities in both cases, and fluorescence in situ hybridization (FISH) confirmed the involvement of HMGA2 in each instance. Rapid amplification of cDNA ends (RACE) PCR experiments revealed that one lipoma contained a fusion of the HMGA2 3' untranslated region (UTR) to a genomic area downstream of the DYRK2 locus on 12q15; the second lipoma showed a fusion of the HMGA2 3' UTR to a genomic sequence upstream of the DCN locus on 12q21. In both instances the breakpoint on HMGA2 occurred downstream to let-7 miRNA (microRNA) consensus binding site (CBS) 1. These two and several other previously reported tumors containing HMGA2 3' UTR rearrangements show breakpoints after let-7 miRNA CBS 1, which suggests that the elimination of this miRNA binding site is not critical for driving HMGA2 transcriptional upregulation.

  10. Hanford Site Development Plan

    Energy Technology Data Exchange (ETDEWEB)

    Hathaway, H.B.; Daly, K.S.; Rinne, C.A.; Seiler, S.W.

    1993-05-01

    The Hanford Site Development Plan (HSDP) provides an overview of land use, infrastructure, and facility requirements to support US Department of Energy (DOE) programs at the Hanford Site. The HSDP`s primary purpose is to inform senior managers and interested parties of development activities and issues that require a commitment of resources to support the Hanford Site. The HSDP provides an existing and future land use plan for the Hanford Site. The HSDP is updated annually in accordance with DOE Order 4320.1B, Site Development Planning, to reflect the mission and overall site development process. Further details about Hanford Site development are defined in individual area development plans.

  11. Region 9 NPL Sites (Superfund Sites) Polygons

    Science.gov (United States)

    NPL site POLYGON locations for the US EPA Region 9. NPL (National Priorities List) sites are hazardous waste sites that are eligible for extensive long-term cleanup under the Superfund program. Eligibility is determined by a scoring method called Hazard Ranking System. Sites with high scores are listed on the NPL. Area covered by this data set include Arizona, California, Nevada, Hawaii, Guam, American Samoa, Northern Marianas and Trust Territories. Attributes include NPL status codes, NPL industry type codes and environmental indicators. Related table, NPL_Contaminants contains information about contaminated media types and chemicals. This is a one-to-many relate and can be related to the feature class using the relationship classes under the Feature Data Set ENVIRO_CONTAMINANT. Generally, each NPL polygon has a separate source. Information about sources for each polygon can be found in the related table, NPL_POLY_METADATA. This table contains a record for each site that has information about the source. Polygons for non-Federal Facility sites were updated in January, 2007 for the Superfund Work Load Models project. Each polygon was approved by the site RPM. Where available, the majority of these polygons represent the surface expression of the extent of the contamination. All Federal Facilities are represented by the facility boundary. The following sites currently have no polygon data available at this time: Alameda Naval Air Station, Jet Pr

  12. Analysis of Unit Breakpoints in Land Combat

    Science.gov (United States)

    1975-03-01

    Lanchester’s equations for "modern warfare." At this point it is convenient to introduce the following notation: x( kjk ) is an estimate of x(k) given that...error. R Ck) = E Iv(k) v(k) T1 For the model developed previously the appropriate Kalman filter equations are: 1. Gain equation G(k) - P( kjk -l) T[c (klk

  13. Site amplifications for generic rock sites

    Science.gov (United States)

    Boore, D.M.; Joyner, W.B.

    1997-01-01

    Seismic shear-wave velocity as a function of depth for generic rock sites has been estimated from borehole data and studies of crustal velocities, and these velocities have been used to compute frequency-dependent amplifications for zero attenuation for use in simulations of strong ground motion. We define a generic rock site as one whose velocity at shallow depths equals the average of those from the rock sites sampled by the borehole data. Most of the boreholes are in populated areas; for that reason, the rock sites sampled are of particular engineering significance. We consider two generic rock sites: rock, corresponding to the bulk of the borehole data, and very hard rock, such as is found in glaciated regions in large areas of eastern North America or in portions of western North America. The amplifications on rock sites can be in excess of 3.5 at high frequencies, in contrast to the amplifications of less than 1.2 on very hard rock sites. The consideration of unattenuated amplification alone is computationally convenient, but what matters for ground-motion estimation is the combined effect of amplification and attenuation. For reasonable values of the attenuation parameter K0, the combined effect of attenuation and amplification for rock sites peaks between about 2 and 5 Hz with a maximum level of less than 1.8. The combined effect is about a factor of 1.5 at 1 Hz and is less than unity for frequencies in the range of 10 to 20 Hz (depending on K0). Using these amplifications, we find provisional values of about ???? = 70 bars and K0 = 0.035 sec for rock sites in western North America by fitting our empirically determined response spectra for an M 6.5 event to simulated values. The borehole data yield shear velocities (V??30) of 618 and 306 m/sec for "rock" and "soil" sites, respectively, when averaged over the upper 30 m. From this, we recommend that V??30 equals 620 and 310 m/sec for applications requiring the average velocity for rock and soil sites in

  14. Echinocandin and Triazole Antifungal Susceptibility Profiles for Clinical Opportunistic Yeast and Mold Isolates Collected from 2010 to 2011: Application of New CLSI Clinical Breakpoints and Epidemiological Cutoff Values for Characterization of Geographic and Temporal Trends of Antifungal Resistance

    Science.gov (United States)

    Messer, Shawn A.; Woosley, Leah N.; Jones, Ronald N.; Castanheira, Mariana

    2013-01-01

    The SENTRY Antimicrobial Surveillance Program monitors global susceptibility and resistance rates of newer and established antifungal agents. We report the echinocandin and triazole antifungal susceptibility patterns for 3,418 contemporary clinical isolates of yeasts and molds. The isolates were obtained from 98 laboratories in 34 countries during 2010 and 2011. Yeasts not presumptively identified by CHROMagar, the trehalose test, or growth at 42°C and all molds were sequence identified using internal transcribed spacer (ITS) and 28S (yeasts) or ITS, translation elongation factor (TEF), and 28S (molds) genes. Susceptibility testing was performed against 7 antifungals (anidulafungin, caspofungin, micafungin, fluconazole, itraconazole, posaconazole, and voriconazole) using CLSI methods. Rates of resistance to all agents were determined using the new CLSI clinical breakpoints and epidemiological cutoff value criteria, as appropriate. Sequencing of fks hot spots was performed for echinocandin non-wild-type (WT) strains. Isolates included 3,107 from 21 Candida spp., 146 from 9 Aspergillus spp., 84 from Cryptococcus neoformans, 40 from 23 other mold species, and 41 from 9 other yeast species. Among Candida spp., resistance to the echinocandins was low (0.0 to 1.7%). Candida albicans and Candida glabrata that were resistant to anidulafungin, caspofungin, or micafungin were shown to have fks mutations. Resistance to fluconazole was low among the isolates of C. albicans (0.4%), Candida tropicalis (1.3%), and Candida parapsilosis (2.1%); however, 8.8% of C. glabrata isolates were resistant to fluconazole. Among echinocandin-resistant C. glabrata isolates from 2011, 38% were fluconazole resistant. Voriconazole was active against all Candida spp. except C. glabrata (10.5% non-WT), whereas posaconazole showed decreased activity against C. albicans (4.4%) and Candida krusei (15.2% non-WT). All agents except for the echinocandins were active against C. neoformans, and the

  15. Echinocandin and triazole antifungal susceptibility profiles for clinical opportunistic yeast and mold isolates collected from 2010 to 2011: application of new CLSI clinical breakpoints and epidemiological cutoff values for characterization of geographic and temporal trends of antifungal resistance.

    Science.gov (United States)

    Pfaller, Michael A; Messer, Shawn A; Woosley, Leah N; Jones, Ronald N; Castanheira, Mariana

    2013-08-01

    The SENTRY Antimicrobial Surveillance Program monitors global susceptibility and resistance rates of newer and established antifungal agents. We report the echinocandin and triazole antifungal susceptibility patterns for 3,418 contemporary clinical isolates of yeasts and molds. The isolates were obtained from 98 laboratories in 34 countries during 2010 and 2011. Yeasts not presumptively identified by CHROMagar, the trehalose test, or growth at 42°C and all molds were sequence identified using internal transcribed spacer (ITS) and 28S (yeasts) or ITS, translation elongation factor (TEF), and 28S (molds) genes. Susceptibility testing was performed against 7 antifungals (anidulafungin, caspofungin, micafungin, fluconazole, itraconazole, posaconazole, and voriconazole) using CLSI methods. Rates of resistance to all agents were determined using the new CLSI clinical breakpoints and epidemiological cutoff value criteria, as appropriate. Sequencing of fks hot spots was performed for echinocandin non-wild-type (WT) strains. Isolates included 3,107 from 21 Candida spp., 146 from 9 Aspergillus spp., 84 from Cryptococcus neoformans, 40 from 23 other mold species, and 41 from 9 other yeast species. Among Candida spp., resistance to the echinocandins was low (0.0 to 1.7%). Candida albicans and Candida glabrata that were resistant to anidulafungin, caspofungin, or micafungin were shown to have fks mutations. Resistance to fluconazole was low among the isolates of C. albicans (0.4%), Candida tropicalis (1.3%), and Candida parapsilosis (2.1%); however, 8.8% of C. glabrata isolates were resistant to fluconazole. Among echinocandin-resistant C. glabrata isolates from 2011, 38% were fluconazole resistant. Voriconazole was active against all Candida spp. except C. glabrata (10.5% non-WT), whereas posaconazole showed decreased activity against C. albicans (4.4%) and Candida krusei (15.2% non-WT). All agents except for the echinocandins were active against C. neoformans, and the

  16. Comparison of the Sensititre YeastOne colorimetric antifungal panel with CLSI microdilution for antifungal susceptibility testing of the echinocandins against Candida spp., using new clinical breakpoints and epidemiological cutoff values.

    Science.gov (United States)

    Pfaller, M A; Chaturvedi, V; Diekema, D J; Ghannoum, M A; Holliday, N M; Killian, S B; Knapp, C C; Messer, S A; Miskou, A; Ramani, R

    2012-08-01

    A commercially prepared dried colorimetric microdilution panel (Sensititre Yeast One, TREK Diagnostic Systems, Cleveland, OH, USA) was compared in 3 different laboratories with the Clinical and Laboratory Standards Institute (CLSI) reference microdilution method by testing 2 quality control strains, 25 reproducibility strains, and 404 isolates of Candida spp. against anidulafungin, caspofungin, and micafungin. Reference CLSI BMD MIC end points and YeastOne colorimetric end points were read after 24 h of incubation. Excellent (100%) essential agreement (within 2 dilutions) between the reference and colorimetric MICs was observed. Categorical agreement (CA) between the 2 methods was assessed using the new species-specific clinical breakpoints (CBPs): susceptible (S), ≤0.25 μg/mL; intermediate (I), 0.5 μg/mL; and resistant (R), ≥1 μg/mL, for C. albicans, C. tropicalis, and C. krusei, and ≤2 μg/mL (S), 4 μg/mL (I), and ≥8 μg/mL (R) for C. parapsilosis and all 3 echinocandins. The new CBPs for anidulafungin and caspofungin and C. glabrata are ≤0.12 μg/mL (S), 0.25 μg/mL (I), and ≥0.5 μg/mL (R), whereas those for micafungin are ≤0.06 μg/mL (S), 0.12 μg/mL (I), and ≥0.25 μg/mL (R). Due to the lack of CBPs for any of the echinocandins and C. lusitaniae, the epidemiological cutoff values (ECVs) were used for this species to categorize the isolates as wild-type (WT; MIC ≤ECV) and non-WT (MIC >ECV), respectively, for anidulafungin (≤2 μg/mL/>2 μg/mL), caspofungin (≤1 μg/mL/>1 μg/mL), and micafungin (≤0.5 μg/mL/>0.5 μg/mL). CA ranged from 93.6% (caspofungin) to 99.6% (micafungin) with less than 1% very major or major errors. The YeastOne colorimetric method remains comparable to the CLSI BMD reference method for testing the susceptibility of Candida spp. to the echinocandins when using the new (lower) CBPs and ECVs. Further study using defined fks mutant strains of Candida is warranted. Copyright © 2012 Elsevier Inc. All rights

  17. NPL Site Boundaries

    Data.gov (United States)

    U.S. Environmental Protection Agency — The National Priorities List (NPL) is a list published by EPA of Superfund sites. A site must be added to this list before remediation can begin under Superfund. The...

  18. NPL Site Locations

    Data.gov (United States)

    U.S. Environmental Protection Agency — The National Priorities List (NPL) is a list published by EPA of Superfund sites. A site must be added to this list before remediation can begin under Superfund. The...

  19. Site Area Boundaries

    Data.gov (United States)

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

  20. 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.

  1. Site Calibration report

    DEFF Research Database (Denmark)

    Gómez Arranz, Paula; Vesth, Allan

    This report describes the site calibration carried out at Østerild, during a given period. The site calibration was performed with two Windcube WLS7 (v1) lidars at ten measurements heights. The lidar is not a sensor approved by the current version of the IEC 61400-12-1 [1] and therefore the site...

  2. Olkiluoto site description 2011

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2012-12-15

    This fourth version of the Olkiluoto Site Report, produced by the OMTF (Olkiluoto Modelling Task Force), updates the Olkiluoto Site Report 2008 with the data and knowledge obtained up to December 2010. A descriptive model of the site (the Site Descriptive Model, SDM), i.e. a model describing the geological and hydrogeological structure of the site, properties of the bedrock and the groundwater and its flow, and the associated interacting processes and mechanisms. The SDM is divided into six parts: surface system, geology, rock mechanics, hydrogeology, hydrogeochemistry and transport properties.

  3. Site Calibration, FGW

    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...

  4. Site Environmental Report, 1993

    Energy Technology Data Exchange (ETDEWEB)

    1994-06-01

    The Site Environmental Report (SER) is prepared annually in accordance with DOE Order 5400.1, ``General Environmental Protection Program.`` This 1993 SER provides the general public as well as scientists and engineers with the results from the site`s ongoing Environmental Monitoring Program. Also included in this report is information concerning the site`s progress toward achieving full compliance with requirements set forth by DOE, US Environmental Protection Agency (USEPA), and Ohio EPA (OEPA). For some readers, the highlights provided in the Executive Summary may provide sufficient information. Many readers, however, may wish to read more detailed descriptions of the information than those which are presented here.

  5. Selecting a repository site

    Energy Technology Data Exchange (ETDEWEB)

    Ghovanlou, A.H. (MITRE Corp., McLean, VA); Ettlinger, L.; Cotton, T.; Barnard, W.; Siever, R.

    1982-01-01

    Present knowledge about the regional and local geologic predictions as it relates to waste repository sites and some related knowledge gained from oil and mining explorations are summarized. The types of geologic testing involved in selecting a repository site are described, and a simple analytic scheme for estimating the costs of such a program is discussed. This scheme is based on the sequential accumulation of knowledge throughout the process of siting. It is concluded that several sites should be investigated simultaneously since there is a trade-off to be made between the economic costs of carrying forward all the sites that pass the screening process and the political costs of selecting from a limited number of qualified sites. This would help to insure that a qualified site would be publicly acceptable at some point in the future. (BLM)

  6. Hanford Site Comprehensive site Compliance Evaluation Report

    Energy Technology Data Exchange (ETDEWEB)

    Tollefson, K.S.

    1997-08-05

    This document is the second annual submittal by WHC, ICF/KH, PNL and BHI and contains the results of inspections of the stormwater outfalls listed in the Hanford Site Storm Water Pollution Prevention Plan (SWPPP) (WHC 1993a) as required by General Permit No. WA-R-00-000F (WA-R-00-A17F): This report also describes the methods used to conduct the Storm Water Comprehensive Site Compliance Evaluation, as required in Part IV, Section D, {ampersand} C of the General Permit, summarizes the results of the compliance evaluation, and documents significant leaks and spills.

  7. Comparison of the Vitek 2 yeast susceptibility system with CLSI microdilution for antifungal susceptibility testing of fluconazole and voriconazole against Candida spp., using new clinical breakpoints and epidemiological cutoff values.

    Science.gov (United States)

    Pfaller, Michael A; Diekema, Daniel J; Procop, Gary W; Rinaldi, Michael G

    2013-09-01

    A commercially available, fully automated yeast susceptibility test system (Vitek 2; bioMérieux, Marcy d'Etoile, France) was compared in 3 different laboratories with the Clinical and Laboratory Standards Institute (CLSI) reference microdilution (BMD) method by testing 2 quality control strains, 10 reproducibility strains, and 425 isolates of Candida spp. against fluconazole and voriconazole. Reference CLSI BMD MIC endpoints and Vitek 2 MIC endpoints were read after 24 hours and 9.1-27.1 hours incubation, respectively. Excellent essential agreement (within 2 dilutions) between the reference and Vitek 2 MICs was observed for fluconazole (97.9%) and voriconazole (96.7%). Categorical agreement (CA) between the 2 methods was assessed using the new species-specific clinical breakpoints (CBPs): susceptible (S) ≤2 μg/mL, susceptible dose-dependent (SDD) 4 μg/mL, and resistant (R) ≥8 μg/mL for fluconazole and Candida albicans, Candida tropicalis, and Candida parapsilosis and ≤32 μg/mL (SDD), ≥64 μg/mL (R) for Candida glabrata; S ≤0.12 μg/mL, SDD 0.25-0.5 μg/mL, R ≥1 μg/mL for voriconazole and C. albicans, C. tropicalis, and C. parapsilosis, and ≤0.5 μg/mL (S), 1 μg/mL (SDD), ≥2 μg/mL (R) for Candida krusei. The epidemiological cutoff value (ECV) of 0.5 μg/mL for voriconazole and C. glabrata was used to differentiate wild-type (WT; MIC ≤ ECV) from non-WT (MIC > ECV) strains of this species. Due to the lack of CBPs for the less common species, the ECVs for fluconazole and voriconazole, respectively, were used for Candida lusitaniae (2 μg/mL and 0.03 μg/mL), Candida dubliniensis (0.5 μg/mL and 0.03 μg/mL), Candida guilliermondii (8 μg/mL and 0.25 μg/mL), and Candida pelliculosa (4 μg/mL and 0.25 μg/mL) to categorize isolates of these species as WT and non-WT. CA between the 2 methods was 96.8% for fluconazole and 96.5% for voriconazole with less than 1% very major errors and 1.3-3.0% major errors. The Vitek 2 yeast susceptibility system

  8. Genomic analysis of the chromosome 15q11-q13 Prader-Willi syndrome region and characterization of transcripts for GOLGA8E and WHCD1L1 from the proximal breakpoint region

    Directory of Open Access Journals (Sweden)

    Kashork Catherine D

    2008-01-01

    Full Text Available Abstract Background Prader-Willi syndrome (PWS is a neurobehavioral disorder characterized by neonatal hypotonia, childhood obesity, dysmorphic features, hypogonadism, mental retardation, and behavioral problems. Although PWS is most often caused by a paternal interstitial deletion of a 6-Mb region of chromosome 15q11-q13, the identity of the exact protein coding or noncoding RNAs whose deficiency produces the PWS phenotype is uncertain. There are also reports describing a PWS-like phenotype in a subset of patients with full mutations in the FMR1 (fragile X mental retardation 1 gene. Taking advantage of the human genome sequence, we have performed extensive sequence analysis and molecular studies for the PWS candidate region. Results We have characterized transcripts for the first time for two UCSC Genome Browser predicted protein-coding genes, GOLGA8E (golgin subfamily a, 8E and WHDC1L1 (WAS protein homology region containing 1-like 1 and have further characterized two previously reported genes, CYF1P1 and NIPA2; all four genes are in the region close to the proximal/centromeric deletion breakpoint (BP1. GOLGA8E belongs to the golgin subfamily of coiled-coil proteins associated with the Golgi apparatus. Six out of 16 golgin subfamily proteins in the human genome have been mapped in the chromosome 15q11-q13 and 15q24-q26 regions. We have also identified more than 38 copies of GOLGA8E-like sequence in the 15q11-q14 and 15q23-q26 regions which supports the presence of a GOLGA8E-associated low copy repeat (LCR. Analysis of the 15q11-q13 region by PFGE also revealed a polymorphic region between BP1 and BP2. WHDC1L1 is a novel gene with similarity to mouse Whdc1 (WAS protein homology region 2 domain containing 1 and human JMY protein (junction-mediating and regulatory protein. Expression analysis of cultured human cells and brain tissues from PWS patients indicates that CYFIP1 and NIPA2 are biallelically expressed. However, we were not able to

  9. Site environmental programs

    Energy Technology Data Exchange (ETDEWEB)

    Schmidt, J.W.; Hanf, R.W.

    1995-06-01

    This section of the 1994 Hanford Site Environmental Report summarizes the site environmental programs. Effluent monitoring and environmental surveillance programs monitor for impacts from operations in several areas. The first area consists of the point of possible release into the environment. The second area consists of possible contamination adjacent to DOE facilities, and the third area is the general environment both on and off the site.

  10. 1994 Site environmental report

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-07-01

    The Fernald site is a Department of Energy (DOE)-owned facility that produced high-quality uranium metals for military defense for nearly 40 years. DOE suspended production at the site in 1989 and formally ended production in 1991. Although production activities have ceased, the site continues to examine the air and liquid pathways as possible routes through which pollutants from past operations and current remedial activities may leave the site. The Site Environmental Report (SER) is prepared annually in accordance with DOE Order 5400.1, General Environmental Protection Program. This 1994 SER provides the general public as well as scientists and engineers with the results from the site`s ongoing Environmental Monitoring Program. Also included in this report is information concerning the site`s progress toward achieving full compliance with requirements set forth by DOE, U.S. Environmental Protection Agency (USEPA), and Ohio EPA (OEPA). For some readers, the highlights provided in this Executive Summary may provide sufficient information. Many readers, however, may wish to read more detailed descriptions of the information than those which are presented here. All information presented in this summary is discussed more fully in the main body of this report.

  11. Land allocation, boundary demarcation and tenure security in tribal ...

    African Journals Online (AJOL)

    Four themes related to customary land allocation processes in South Africa have emerged from the data: Applicant, Authority, Acceptance and Allocation. These themes are used as the basis for comparison across the cases. The case studies are also used to test a published conceptual model of land tenure security.

  12. Symbolic Boundary Work in Schools: Demarcating and Denying Ethnic Boundaries

    Science.gov (United States)

    Tabib-Calif, Yosepha; Lomsky-Feder, Edna

    2014-01-01

    This article examines the symbolic boundary work that is carried out at a school whose student population is heterogeneous in terms of ethnicity and class. Based on ethnography, the article demonstrates how the school's staff seeks to neutralize ethnic boundaries and their accompanying discourse, while the pupils try to bring ethnic…

  13. Emergence of Xin demarcates a key innovation in heart evolution.

    Directory of Open Access Journals (Sweden)

    Shaun E Grosskurth

    2008-08-01

    Full Text Available The mouse Xin repeat-containing proteins (mXinalpha and mXinbeta localize to the intercalated disc in the heart. mXinalpha is able to bundle actin filaments and to interact with beta-catenin, suggesting a role in linking the actin cytoskeleton to N-cadherin/beta-catenin adhesion. mXinalpha-null mouse hearts display progressively ultrastructural alterations at the intercalated discs, and develop cardiac hypertrophy and cardiomyopathy with conduction defects. The up-regulation of mXinbeta in mXinalpha-deficient mice suggests a partial compensation for the loss of mXinalpha. To elucidate the evolutionary relationship between these proteins and to identify the origin of Xin, a phylogenetic analysis was done with 40 vertebrate Xins. Our results show that the ancestral Xin originated prior to the emergence of lamprey and subsequently underwent gene duplication early in the vertebrate lineage. A subsequent teleost-specific genome duplication resulted in most teleosts encoding at least three genes. All Xins contain a highly conserved beta-catenin-binding domain within the Xin repeat region. Similar to mouse Xins, chicken, frog and zebrafish Xins also co-localized with beta-catenin to structures that appear to be the intercalated disc. A putative DNA-binding domain in the N-terminus of all Xins is strongly conserved, whereas the previously characterized Mena/VASP-binding domain is a derived trait found only in Xinalphas from placental mammals. In the C-terminus, Xinalphas and Xinbetas are more divergent relative to each other but each isoform from mammals shows a high degree of within-isoform sequence identity. This suggests different but conserved functions for mammalian Xinalpha and Xinbeta. Interestingly, the origin of Xin ca. 550 million years ago coincides with the genesis of heart chambers with complete endothelial and myocardial layers. We postulate that the emergence of the Xin paralogs and their functional differentiation may have played a key role in the evolutionary development of the heart.

  14. Demarcation of coastal vulnerability line along the Indian coast

    Digital Repository Service at National Institute of Oceanography (India)

    Ajai; Baba, M.; Unnikrishnan, A.S.; Rajawat, A.S.; Bhattacharya, S.; Ratheesh, R.; Kurian, N.P.; Hameed, S.; Sundar, D.

    been considered. Changes along the shoreline are considered as net impact of dynamic coastal processes and are mapped using multidate satellite data. Vulnerability due to coastal erosion has been assessed based on rate of coastal erosion. Coastal...

  15. Land allocation, boundary demarcation and tenure security in tribal ...

    African Journals Online (AJOL)

    Hull

    -case study is then presented followed by the research findings. The conceptual model is then used to evaluate the state of tenure security in the .... In keeping with the spirit of the grounded theory approach to qualitative data analysis as.

  16. Power in competition. Territorial demarcation of supply regions indispensable

    Energy Technology Data Exchange (ETDEWEB)

    Buderath, J.

    1989-03-01

    From time to time at almost regular intervals one comes across articles in newspapers and journals which demand that the electricity industry make structural changes. Abolish licensing contracts and demarkation contracts and - so these preachers say - give way to competition so that power becomes less costly. Is this really so.

  17. 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.

  18. Site-Specific Innovation

    DEFF Research Database (Denmark)

    Reeh, Henrik; Hemmersam, Peter

    2015-01-01

    Currently, cities across the Northern European region are actively redeveloping their former industrial harbours. Indeed, harbours areas are essential in the long-term transition from industrial to information and experience societies; harbours are becoming sites for new businesses and residences...... question is how innovation may contribute to urban life and site-specific qualities....

  19. The Greenland Ramsar Sites

    DEFF Research Database (Denmark)

    Egevang, C.; Boertmann, D.

    The eleven Ramsar sites in Greenland are reviewed in terms of their status as habitats for waterbirds and other fauna. Management and monitoring is proposed, as well as revisions of their boundaries. A number of potential new Ramsar sites are described...

  20. Site characterization handbook

    Energy Technology Data Exchange (ETDEWEB)

    1988-06-01

    This Handbook discusses both management and technical elements that should be considered in developing a comprehensive site characterization program. Management elements typical of any project of a comparable magnitude and complexity are combined with a discussion of strategies specific to site characterization. Information specific to the technical elements involved in site characterization is based on guidance published by the Nuclear Regulatory Commission (NRC) with respect to licensing requirements for LLW disposal facilities. The objective of this Handbook is to provide a reference for both NRC Agreement States and non-Agreement States for use in developing a comprehensive site characterization program that meets the specific objectives of the State and/or site developer/licensee. Each site characterization program will vary depending on the objectives, licensing requirements, schedules/budgets, physical characteristics of the site, proposed facility design, and the specific concerns raised by government agencies and the public. Therefore, the Handbook is not a prescriptive guide to site characterization. 18 refs., 6 figs.

  1. Horus Web Site Evaluation

    OpenAIRE

    Atef Qattan Ben Mohamed Qattan

    2005-01-01

    An Evaluative study for the children web site Horus, it begins with general description for the web site and its components, then it evaluates it according to 6 criteria ; Authority, Coverage, Contents, Accuracy, Design, and pictures and Multimedia. Finally it summarizes its results.

  2. 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.

  3. Site Calibration report

    DEFF Research Database (Denmark)

    Yordanova, Ginka; Vesth, Allan

    The report describes site calibration measurements carried out on a site in Denmark. The measurements are carried out in accordance to Ref. [1]. 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 [2]. The possible measurement sector for power performance...... according to [1] is also described in [2] and no results from the site calibration have shown any necessary exclusion from this sector. All parts of the sensors and the measurement system have been installed by DTU....

  4. Site directed recombination

    Science.gov (United States)

    Jurka, Jerzy W.

    1997-01-01

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

  5. Resistencia a cefalosporinas de espectro extendido en enterobacterias sin AmpC inducible: Evaluación de los nuevos puntos de corte Resistance to extended-spectrum cephalosporins in non-inducible AmpC enterobacteria: Evaluation of the new MIC breakpoints

    Directory of Open Access Journals (Sweden)

    Marcela Nastro

    2012-03-01

    the mechanisms of resistance (ESBL, plasmid-mediated AmpC and KPC and to evaluate the interpretation criteria proposed by the existing recommendations and the new breakpoints established by the CLSI and the EUCAST. Susceptibility tests and PCR multiplex for b/aSHV and b/aCTX-M and amplification using specific primers was performed. One hundred sixty nine resistant isolates: K/ebsie//a pneumoniae (95, Escherichia co/i (55, and Proteus mirabi/is (19 were recovered. ESC resistance was 56.2 %, 32.6%, and 11.2 %, respectively. ESBL was detected in 152 (90 % isolates, plasmid-mediated AmpC in 12 (7 % and KPC in 5 (3 %. The CLSI 2009 recommendations and the breakpoints sµggested by the CLSI 2010 and the EUCAST for ceftriaxone were efficacious to detect ESBL, whereas the different breakpoints for ceftazidime presented discrepancies. The CLSI 2010 breakpoints only detected 55 % of the ESBL-producing isolates due to the endemic presence of CTX-M ESBLs in our country. Regarding the plasmid-mediated AmpC producers, the recommendations of the CLSI 2010 and the EUCAST 2010 proved to be more efficient than the old ones.

  6. Superfund Site Information

    Data.gov (United States)

    U.S. Environmental Protection Agency — This asset includes a number of individual data sets related to site-specific information for Superfund, which is governed under the Comprehensive Environmental...

  7. Outdoor Recreation Sites Inventory

    Data.gov (United States)

    Vermont Center for Geographic Information — The RECSITES data layer contains a wide range of recreational sites in Vermont. This point data layer includes parks, ski areas, boat access points, and many other...

  8. Retroviral integration: Site matters

    Science.gov (United States)

    Demeulemeester, Jonas; De Rijck, Jan

    2015-01-01

    Here, we review genomic target site selection during retroviral integration as a multistep process in which specific biases are introduced at each level. The first asymmetries are introduced when the virus takes a specific route into the nucleus. Next, by co‐opting distinct host cofactors, the integration machinery is guided to particular chromatin contexts. As the viral integrase captures a local target nucleosome, specific contacts introduce fine‐grained biases in the integration site distribution. In vivo, the established population of proviruses is subject to both positive and negative selection, thereby continuously reshaping the integration site distribution. By affecting stochastic proviral expression as well as the mutagenic potential of the virus, integration site choice may be an inherent part of the evolutionary strategies used by different retroviruses to maximise reproductive success. PMID:26293289

  9. 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...

  10. Summer Meal Sites

    Data.gov (United States)

    Allegheny County / City of Pittsburgh / Western PA Regional Data Center — Information pertaining to Summer Meal Sites, as collected by Citiparks in the City of Pittsburgh Department of Parks and Recreation. This dataset includes the...

  11. Coal mine site reclamation

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2013-02-15

    Coal mine sites can have significant effects on local environments. In addition to the physical disruption of land forms and ecosystems, mining can also leave behind a legacy of secondary detrimental effects due to leaching of acid and trace elements from discarded materials. This report looks at the remediation of both deep mine and opencast mine sites, covering reclamation methods, back-filling issues, drainage and restoration. Examples of national variations in the applicable legislation and in the definition of rehabilitation are compared. Ultimately, mine site rehabilitation should return sites to conditions where land forms, soils, hydrology, and flora and fauna are self-sustaining and compatible with surrounding land uses. Case studies are given to show what can be achieved and how some landscapes can actually be improved as a result of mining activity.

  12. Sites and Enactments

    DEFF Research Database (Denmark)

    Korsgaard, Steffen; Neergaard, Helle

    2010-01-01

    This paper develops a framework for researching entrepreneurial opportunities. We argue that these can best be understood as dynamic and fluid effects of entrepreneurial processes that are enacted differently across different sites. On this basis we develop a framework for studying entrepreneurial...... opportunities that is suited to track those opportunities across enactments and sites. The framework is demonstrated through an analysis of the genesis of the company The Republic ofTea, as portrayed in the book of the same name...

  13. The Federation of Indian Organizations of the Negro River’s journey for traditional land demarcation in Brazil La jornada de la Federación de Organizaciones Indígenas del Río Negro para la demarcación de las tierras tradicionales en Brasil

    Directory of Open Access Journals (Sweden)

    Fernanda Martinez de Oliveira

    2011-07-01

    Full Text Available The article aims to present the fight for government recognition of indigenous collective rights to land ownership in the Upper Rio Negro region in Brazil. It contextualizes the historical aspects of the colonization process in the region and the efforts to create the  Federation of Indian Organizations of the Negro River (FOIRN. Focus of particular interest is how the organizational strategy adopted by the FOIRN has allowed the Indian population of the Upper Rio Negro to active participate in the land demarcation process, with their opinions heard and respected. The article was written with basis on information obtained from a variety of sources, such as documents, conversations and interviews with the main social actors involved in the area, carried out during a field visit to São Gabriel da Cachoeira in January 2010.

     

    El artículo tiene como objetivo presentar la lucha por el reconocimiento gubernamental de los derechos colectivos indígenas de la propiedad de la tierra en la región del Alto Río Negro en Brasil. Se contextualizan los aspectos históricos del proceso de colonización de la región y los esfuerzos para crear la Federación de Organizaciones Indígenas del Río Negro (FOIRN. El foco de interés particular es cómo la estrategia de organización adoptada por la FOIRN ha permitido a la población indígena del Alto Río Negro participar activamente en el proceso de demarcación de tierras, escuchando y respetando sus opiniones. El artículo fue escrito con base en informaciones obtenidas de diversas fuentes, tales como documentos, conversaciones y entrevistas con los principales actores sociales involucrados en el área, llevadas a cabo durante una visita a São Gabriel da Cachoeira, en enero de 2010.

     

     

  14. Studies on the use of SIR-C and X-SAR data for identification, demarcation, and assessment of forest ecosystems. Final report; Untersuchungen zum Einsatz von SIR-C und X-SAR Daten fuer die Identifizierung, Abgrenzung und Beurteilung von Waldoekosystemen. Abschlussbericht

    Energy Technology Data Exchange (ETDEWEB)

    Johlige, A.; Foerster, B.; Ammer, U.

    1997-12-31

    The purpose of the present evaluation was to use SIR-C and X-SAR data for forest surveying and assess their suitability for this task. Amongst other work this included the discrimination of forest and non-forest, demarcation of cleared areas within forests, discrimination of different forest types, and assessment of the influence of foliation. The chief steps of the study were the preparation of radar data, accompanying aerial photo evaluation for the extraction of training and verification areas, and detailed signature analysis. Evaluation trials in ``Oberpfaffenhofen`` supertest area yielded unsatisfactory results when it came to discriminating different forest ecosystems. This can be attributed to the very heterogeneous and small-scale structure of the area and the absence of topographically coded X, C, and L band data. In the second study area, located in the ``Bavarian Forest National Park``, geocoded data of all three bands were available in the form of combined products. This permitted using the mask of the local angles of incidence to reduce the influence of relief. In this case distinguishability within wooded regions was also enhanced. A general finding was that ground resolution as it presents to the user is clearly poorer than the nominal resolution. What impressed us most was the high degree of weather-independence of the radar data. All data handled in this study were recorded under conditions that would have made photography impossible. (orig.) [Deutsch] Ziel der Auswertung ist es SIR-C/X-SAR Daten fuer die Waldbeobachtung einzusetzen und ihre Eignung dafuer zu bewerten. Zu loesende Teilaufgaben waren u.a. die Wald-Nichtwaldtrennung, die Abtrennung unbestockter Flaechen im Wald, Unterscheidung verschiedener Waldtypen selbst und die Beurteilung des Einflusses des Belaubungszustndes. Die zentralen Arbeitsschritte waren die Aufbereitung der Radardaten, die begleitende Luftbildauswertung zur Extraktion von Trainings- und Verifizierungsgebieten und die

  15. Site clearance working group

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-03-01

    The Gulf of Mexico and Louisiana continue to be areas with a high level of facility removal, and the pace of removal is projected to increase. Regulations were promulgated for the Gulf of Mexico and Louisiana requiring that abandoned sites be cleared of debris that could interfere with fishing and shrimping activities. The site clearance regulations also required verification that the sites were clear. Additionally, government programs were established to compensate fishermen for losses associated with snagging their equipment on oil and gas related objects that remained on the water bottoms in areas other than active producing sites and sites that had been verified as clear of obstructions and snags. The oil and gas industry funds the compensation programs. This paper reviews the regulations and evolving operating practices in the Gulf of Mexico and Louisiana where site clearance and fisherman`s gear compensation regulations have been in place for a number of years. Although regulations and guidelines may be in place elsewhere in the world, this paper focuses on the Gulf of Mexico and Louisiana. Workshop participants are encouraged to bring up international issues during the course of the workshop. Additionally, this paper raises questions and focuses on issues that are of concern to the various Gulf of Mexico and Louisiana water surface and water bottom stakeholders. This paper does not have answers to the questions or issues. During the workshop participants will debate the questions and issues in an attempt to develop consensus opinions and/or make suggestions that can be provided to the appropriate organizations, both private and government, for possible future research or policy adjustments. Site clearance and facility removal are different activities. Facility removal deals with removal of the structures used to produce oil and gas including platforms, wells, casing, piles, pipelines, well protection structures, etc.

  16. 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).

  17. 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...

  18. YUCCA MOUNTAIN SITE DESCRIPTION

    Energy Technology Data Exchange (ETDEWEB)

    A.M. Simmons

    2004-04-16

    The ''Yucca Mountain Site Description'' summarizes, in a single document, the current state of knowledge and understanding of the natural system at Yucca Mountain. It describes the geology; geochemistry; past, present, and projected future climate; regional hydrologic system; and flow and transport within the unsaturated and saturated zones at the site. In addition, it discusses factors affecting radionuclide transport, the effect of thermal loading on the natural system, and tectonic hazards. The ''Yucca Mountain Site Description'' is broad in nature. It summarizes investigations carried out as part of the Yucca Mountain Project since 1988, but it also includes work done at the site in earlier years, as well as studies performed by others. The document has been prepared under the Office of Civilian Radioactive Waste Management quality assurance program for the Yucca Mountain Project. Yucca Mountain is located in Nye County in southern Nevada. The site lies in the north-central part of the Basin and Range physiographic province, within the northernmost subprovince commonly referred to as the Great Basin. The basin and range physiography reflects the extensional tectonic regime that has affected the region during the middle and late Cenozoic Era. Yucca Mountain was initially selected for characterization, in part, because of its thick unsaturated zone, its arid to semiarid climate, and the existence of a rock type that would support excavation of stable openings. In 1987, the United States Congress directed that Yucca Mountain be the only site characterized to evaluate its suitability for development of a geologic repository for high-level radioactive waste and spent nuclear fuel.

  19. Allegheny County Illegal Dump Sites

    Data.gov (United States)

    Allegheny County / City of Pittsburgh / Western PA Regional Data Center — The Illegal Dump Site dataset includes information on illegal dump sites, their type of trash, and the estimate tons of trash at each site. The information was...

  20. 2014 Site Environmental Report

    Energy Technology Data Exchange (ETDEWEB)

    Paquette, Douglas [Brookhaven National Lab. (BNL), Upton, NY (United States); Remien, Jason [Brookhaven National Lab. (BNL), Upton, NY (United States); Foley, Brian [Brookhaven National Lab. (BNL), Upton, NY (United States); Burke, John [Brookhaven National Lab. (BNL), Upton, NY (United States); Dorsch, William [Brookhaven National Lab. (BNL), Upton, NY (United States); Ratel, Karen [Brookhaven National Lab. (BNL), Upton, NY (United States); Howe, Robert [Brookhaven National Lab. (BNL), Upton, NY (United States); Welty, Tim [Brookhaven National Lab. (BNL), Upton, NY (United States); Williams, Jeffrey [Brookhaven National Lab. (BNL), Upton, NY (United States); Pohlpt, Peter [Brookhaven National Lab. (BNL), Upton, NY (United States); Lagattolla, Richard [Brookhaven National Lab. (BNL), Upton, NY (United States); Metz, Robert [Brookhaven National Lab. (BNL), Upton, NY (United States); Milligan, James [Brookhaven National Lab. (BNL), Upton, NY (United States); Lettieri, Lawrence [Brookhaven National Lab. (BNL), Upton, NY (United States)

    2015-10-01

    BNL prepares an annual Site Environmental Report (SER) in accordance with DOE Order 231.1B, Environment, Safety and Health Reporting. The report is written to inform the public, regulators, employees, and other stakeholders of the Laboratory’s environmental performance during the calendar year in review.

  1. Surgical site infections

    African Journals Online (AJOL)

    Organ space SSI. • Infection occurs within 30 days if no implant, or within a year if implant and the infection seems to be related to the operation and infection occurs in any anatomical site ... Diagnosis of an organ/space SSI made by the surgeon or ..... selected projects ”enlist the best academic researchers and industry to.

  2. Sites and Enactments

    DEFF Research Database (Denmark)

    Korsgaard, Steffen T.; Neergaard, Helle

    2008-01-01

    is formulated where opportunities are seen as dynamic in the sense that they are enacted in different social practices at different sites. The method is illustrated through an analysis of the birth of The Republic of Tea, a very successful tea company, as presented in the book "The Republic of Tea"....

  3. Surveying Lab II site

    CERN Document Server

    1974-01-01

    The network of survey reference points on the Lab II site was extended to meet the geodetic needs of the SPS and its North Experimental Area. The work was greatly eased by a geodolite, a measuring instrument on loan from the Fermi Laboratory, which uses a modulated laser beam. (See CERN Courier 14 (1974) p. 247.)

  4. Surgical site infections

    African Journals Online (AJOL)

    Surgical site infections (SSIs) are a worldwide problem that has far reaching implications on patient morbidity and ... was complicated by a SSI had a 2-11% higher risk of death. In those patients who died, 75% was directly .... genital and uninfected urinary tract is not entered. In addition, clean wounds are primarily closed ...

  5. Power plant siting

    Energy Technology Data Exchange (ETDEWEB)

    Winter, J.V.; Conner, D.A.

    1978-01-01

    Just to keep up with expected demand, the US will need over 500 new power generation units by 1985. Where these power plants will be located is the subject of heated debate among utility officials, government leaders, conservationists, concerned citizens and a multitude of special interest groups. This book offers a balanced review of all of the salient factors that must be taken into consideration in selecting power plant locations. To deal with this enormously complex subject, the authors (1) offer a general overview of the history and reasoning behind present legislation on the state and national levels; (2) describe the many different agencies that have jurisdiction in power plant location, from local water authorities and city councils to state conservation boards and the Nuclear Regulatory Commission; and (3) include a state-by-state breakdown of siting laws, regulations and present licensing procedures. Architects, engineers, contractors, and others involved in plant construction and site evaluation will learn of the trade-offs that must be made in balancing the engineering, economic, and environmental impacts of plant location. The book covers such areas as availability of water supplies for generation or cooling; geology, typography, and demography of the proposed site; and even the selection of the fuel best suited for the area. Finally, the authors examine the numerous environmental aspects of power plant siting.

  6. Visit our Site

    NARCIS (Netherlands)

    Jos de Haan; Renée Mast; Marleen Varekamp; Susanne Janssen

    2006-01-01

    Original title: Bezoek onze site. More and more cultural organisations are digitising content and making this cultural treasure chest available to a wider public via the Internet. International comparison shows that the Netherlands is one of the leaders in this regard. This report summarises

  7. Small Wind Site Assessment Guidelines

    Energy Technology Data Exchange (ETDEWEB)

    Olsen, Tim [Advanced Energy Systems LLC, Eugene, OR (United States); Preus, Robert [National Renewable Energy Lab. (NREL), Golden, CO (United States)

    2015-09-01

    Site assessment for small wind energy systems is one of the key factors in the successful installation, operation, and performance of a small wind turbine. A proper site assessment is a difficult process that includes wind resource assessment and the evaluation of site characteristics. These guidelines address many of the relevant parts of a site assessment with an emphasis on wind resource assessment, using methods other than on-site data collection and creating a small wind site assessment report.

  8. Standardized UXO Technology Demonstration Site

    National Research Council Canada - National Science Library

    Overbay, Larry

    2004-01-01

    ...) utilizing the APG Standardized UXO Technology Demonstration Site Blind Grid. The scoring record was coordinated by Larry Overbay and by the Standardized UXO Technology Demonstration Site Scoring Committee...

  9. PhosphoSiteAnalyzer

    DEFF Research Database (Denmark)

    Bennetzen, Martin V; Cox, Jürgen; Mann, Matthias

    2012-01-01

    Phosphoproteomic experiments are routinely conducted in laboratories worldwide, and because of the fast development of mass spectrometric techniques and efficient phosphopeptide enrichment methods, researchers frequently end up having lists with tens of thousands of phosphorylation sites...... for further interrogation. To answer biologically relevant questions from these complex data sets, it becomes essential to apply computational, statistical, and predictive analytical methods. Here we provide an advanced bioinformatic platform termed "PhosphoSiteAnalyzer" to explore large phosphoproteomic data...... an algorithm to retrieve kinase predictions from the public NetworKIN webpage in a semiautomated way and applies hereafter advanced statistics to facilitate a user-tailored in-depth analysis of the phosphoproteomic data sets. The interface of the software provides a high degree of analytical flexibility...

  10. Placental site trophoblastic tumor

    Directory of Open Access Journals (Sweden)

    Jean eBouquet De Jolinière

    2014-08-01

    Full Text Available Trophoblastic tumors of placental site (PSTT are rare. They represent a rare form of gestational trophoblastic disease. (GTD. They occur mainly in women who have a history of miscarriage, termination of pregnancy, or even a normal or pathological ongoing pregnancy. The clinical course is unpredictable. This malignancy has different characteristics from other gestational trophoblastic tumors.Following a clinical case that we encountered and treated, we conducted a literary research and review, focusing primarily on prognostic factors and treatment.

  11. Site characterization techniques

    Science.gov (United States)

    ,

    1995-01-01

    Geoelectrical methods have been used since the 1920's to search for metallic ore deposits. During the last decade, traditional mining geophysical techniques have been adapted for environmental site characterization. Geoelectrical geophysics is now a well developed engineering specialty, with different methods to focus both on a range of targets and on depths below the surface. Most methods have also been adapted to borehole measurements.

  12. Web site for GAIN

    OpenAIRE

    Brænden, Stig; Gjerde, Stian; Hansen, Terje, TAR

    2001-01-01

    The project started with an inquiry from GAIN, Graphic Arts Intelligence Network, on the September 26. 2000. GAIN currently has a website that is static, and is not functioning in a satisfying way. The desire is therefore to establish a new dynamic web site with the possibility for the GAIN members to update the page via a browser interface, and maintain their own profiles. In addition to this they would like a brand new and more functional design. GAIN also wants to e...

  13. 1999 SITE ENVIRONMENTAL REPORT

    Energy Technology Data Exchange (ETDEWEB)

    ENGEL-COX,J.; ZIMMERMAN,E.; LEE,R.; WILLIAMS,J.; GREEN,T.; PAQUETTE,D.; HOODA,B.; SCARPITTA,S.; GENZER,P.; ET AL

    2000-09-01

    Throughout the scientific community, Brookhaven National Laboratory (BNL) is renowned for its leading-edge research in physics, medicine, chemistry, biology, materials, and the environment. BNL is committed to supporting its world-class scientific research with an internationally recognized environmental protection program. The 1999 Site Environmental Report (SER) summarizes the status of the Laboratory's environmental programs and performance, including the steady progress towards cleaning up the site and fully integrating environmental stewardship into all facets of the Laboratory's mission. BNL is located on 5,265 acres of pine barrens in Suffolk County in the center of Long Island, New York. The Laboratory is situated above a sole source aquifer at the headwaters of the Peconic River; therefore, protecting ground and surface water quality is a special concern. Approximately 3,600 acres of the site are undeveloped and serve as habitat for a wide variety of animals and plants, including one New York State endangered species, the tiger salamander, and two New York State threatened species, the banded sunfish and the stiff goldenrod. Monitoring, preserving, and restoring these ecological resources is a high priority for the Laboratory.

  14. 1994 Site Environmental Report

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-05-01

    The 1994 Site Environmental Report summarizes environmental activities at Lawrence Berkeley Laboratory (LBL) for the calendar year (CY) 1994. The report strives to present environmental data in a manner that characterizes the performance and compliance status of the Laboratory`s environmental management programs when measured against regulatory standards and DOE requirements. The report also discusses significant highlight and planning efforts of these programs. The format and content of the report are consistent with the requirements of the US Department of Energy (DOE) Order 5400.1, General Environmental Protection Program.

  15. Windows Azure web sites

    CERN Document Server

    Chambers, James

    2013-01-01

    A no-nonsense guide to maintaining websites in Windows Azure If you're looking for a straightforward, practical guide to get Azure websites up and running, then this is the book for you. This to-the-point guide provides you with the tools you need to move and maintain a website in the cloud. You'll discover the features that most affect developers and learn how they can be leveraged to work to your advantage. Accompanying projects enhance your learning experience and help you to walk away with a thorough understanding of Azure's supported technologies, site deployment, and manageme

  16. Present on Site

    DEFF Research Database (Denmark)

    Ingemann, Bruno

    Why are exhibitions and museums so important? What can they be used for? Who determines relevance in a transformative process? Transforming exhibitions is not just something you do, it is something that gets better the more you do it. This book looks at the intersection of the visitor or user, who...... gets personal and cultural meaning from their visit and the museum as it appears in the design of the exhibition. It examines on-site communication for intentional and hidden content and messages, and reveals possible relations to the visitor, his or her world and society in general. This investigation...

  17. 2003 SITE ENVIRONMENTAL REPORT

    Energy Technology Data Exchange (ETDEWEB)

    ENVIRONMENT AND WASTE MANAGMENT SERVICES DIVISION; ET AL.

    2004-10-01

    Each year, Brookhaven National Laboratory (BNL), a multi-program national laboratory, prepares an annual Site Environmental Report (SER) in accordance with Order 231.1A, Environment, Safety and Health Reporting, of the U.S. Department of Energy (DOE). The SER is written to inform outside regulators, the public, and Laboratory employees of BNL's environmental performance during the calendar year in review, and to summarize BNL's on-site environmental data; environmental management performance; compliance with applicable DOE, Environmental Protection Agency (EPA), state, and local regulations; and environmental, restoration, and surveillance monitoring programs. BNL has prepared annual SERs since 1971 and has documented nearly all of its environmental history since the Laboratory's inception in 1947. This report is intended to be a technical document. It is available in print and as a downloadable file on the BNL web page at http://www.bnl.ser.htm. A summary of the SER is also prepared each year to provide a general overview, and is distributed with a CD version of the full-length SER. The summary supports BNL's educational and community outreach program.

  18. AMF 1 Site Science

    Energy Technology Data Exchange (ETDEWEB)

    Miller, Mark Alan [Rutgers Univ., New Brunswick, NJ (United States)

    2016-08-18

    This report documents progress on DOE Grant# DE-FG02-08ER64531 funded by the Department of Energy’s Atmospheric Systems Research (ASR) program covering the period between its inception in 2008 and its conclusion in 2014. The Atmospheric Radiation Measurement (ARM) Program’s Mobile Facility #1 (AMF#1) is a collection of state-of-the art atmospheric sensing systems including remote and in situ instrumentation designed to characterize the atmospheric column above and in the immediate vicinity of the deployment location. The grant discussed in this report funded the activities of the AMF#1 Site Scientist Team. Broad responsibilities of this team included examining new deployment sites and recommending instrument deployment configurations; data quality control during the early stages of deployments and for certain instruments through the course of the deployment; scientific outreach in the host country or location (particularly international deployments); scientific research oriented toward basic questions about cloud physics and radiation transfer in the deployment region; and training of Ph.D. students to conduct future research relevant to the Atmospheric Systems Research (ASR) program.

  19. 1996 Site environmental report

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-06-01

    The FEMP is a Department of Energy (DOE)-owned facility that produced high-quality uranium metals for military defense for nearly 40 years. DOE suspended production at the FEMP in 1989 and formally ended production in 1991. Although production activities have ceased, the site continues to examine the air and liquid pathways as possible routes through which pollutants from past operations and current remedial activities may leave the FEMP. The Site Environmental Report (SER) is prepared annually in accordance with DOE Order 5400.1, General Environmental Protection Program. This 1996 SER provides the general public as well as scientists and engineers with the results from the ongoing Environmental Monitoring Program. Also included in this report is information concerning the FEMP progress toward achieving full compliance with requirements set forth by DOE, U.S. Environmental Protection Agency (EPA), and Ohio EPA (OEPA). For some readers, the highlights provided in this Executive Summary may provide sufficient information. Many readers, however, may wish are presented here. All information presented in this summary is discussed more fully in the main body of this report.

  20. Site-specific

    Directory of Open Access Journals (Sweden)

    Adel M.E. Mohamed

    2013-06-01

    Full Text Available In order to quantify the near-surface seismic properties (P- and S-wave velocities, and the dynamic elastic properties with respect to the depth at a specific area (6th of October club, we conducted a non-invasive and low cost active seismic survey. The primary wave velocity is determined by conducting a P-wave shallow seismic refraction survey. The dispersive characteristics of Rayleigh type surface waves were utilized for imaging the shallow subsurface layers by estimating the 1D (depth and 2D (depth and surface location shear wave velocities. The reliability of the Multi-channel Analysis of Surface Waves (MASW depends on the accurate determination of phase velocities for horizontally traveling fundamental mode Rayleigh waves. Consequently, the elastic properties are evaluated empirically. The Vs30 (average shear wave velocity down to 30 m depth, which is obtained from the MASW technique, plays a critical role in evaluating the site response of the upper 30 m depth. The distribution of the obtained values of Vs30 through the studied area demonstrates site classes of C and D, according to the NEHRP (National Earthquake Hazard Reduction Program and IBC (International Building Code standards.

  1. Multi-Sited Resilience

    DEFF Research Database (Denmark)

    Olwig, Mette Fog

    2012-01-01

    Participatory methods to build local resilience often involve the organization of local community groups. When global organizations use such methods, it reflects a desire to incorporate local agency. They thereby acknowledge the ability of a society to be innovative and adapt when faced with natu......Participatory methods to build local resilience often involve the organization of local community groups. When global organizations use such methods, it reflects a desire to incorporate local agency. They thereby acknowledge the ability of a society to be innovative and adapt when faced...... with natural disasters and climate change. In a globalized world, however, it is hard to discern what is “local” as global organizations play an increasingly visible and powerful role. This paper will argue that local understandings and practices of resilience cannot be disentangled from global understandings...... flooding in northern Ghana, this paper examines the mutual construction of “local” and “global” notions and practices of resilience through multi-sited processes. It is based on interviews and participant observation in multiple sites at the “local,” “regional” and “global” levels....

  2. Preliminary siting characterization Salt Disposition Facility - Site B

    Energy Technology Data Exchange (ETDEWEB)

    Wyatt, D.

    2000-01-04

    A siting and reconnaissance geotechnical program has been completed in S-Area at the Savannah River Site in South Carolina. This program investigated the subsurface conditions for the area known as ``Salt Disposition Facility (SDF), Site B'' located northeast of H-Area and within the S-Area. Data acquired from the Site B investigation includes both field exploration and laboratory test data.

  3. Lakeview, Oregon, Disposal Site

    Energy Technology Data Exchange (ETDEWEB)

    Linard, Joshua [USDOE Office of Legacy Management (LM), Washington, DC (United States); Hall, Steve [Navarro Research and Engineering, Inc., Oak Ridge, TN (United States)

    2016-03-01

    9.1 Compliance Summary The Lakeview, Oregon, Uranium Mill Tailings Radiation Control Act (UMTRCA) Title I Disposal Site was inspected September 16 and 17, 2015. Other than some ongoing concern with erosion-control rock riprap degradation, the disposal cell was in good condition. Some minor fence repairs and vegetation removal, and minor erosion repair work along the west site fence is planned. Inspectors identified no other maintenance needs or cause for a follow-up or contingency inspection. Disposal cell riprap is evaluated annually to ensure continued long-term protection of the cell from erosion during a severe precipitation event. Degradation of the rock riprap was first observed at the site in the mid-1990s. Rock gradation monitoring of the riprap on the west side slope has been performed as part of the annual inspection since 1997 to determine the mean diameter (D50) value. As prescribed by the monitoring procedure, the rock monitoring is routinely conducted at random locations. However, at the U.S. Nuclear Regulatory Commission’s (NRC’s) request, the 2015 rock monitoring approach deviated from the normal procedure by using a pre-established monitoring grid in a subset area of the west side slope. This changed the monitoring approach from random sampling to biased sampling. The D50 value measured during the 2015 gradation monitoring is 2.39 inches, which falls below the original D50 design size range of 2.7–3.9 inches for the Type B size side slope riprap. At NRC’s request, rock durability monitoring was added to the gradation monitoring in 2009 to monitor durability by rock type. Results of the 2015 durability monitoring showed that74 percent of the total rock sampled is durability class code A rock with an assigned durability class of “highly durable” or durability class code B “durable” rock, and that over 90 percent of the 3-inch or larger rock is durability class code A or B. The rock durability

  4. 2006 SITE ENVIRONMENTAL REPORT

    Energy Technology Data Exchange (ETDEWEB)

    BROOKHAVEN NATIONAL LABORATORY; RATEL,K.

    2007-10-01

    Each year, Brookhaven National Laboratory (BNL) prepares an annual Site Environmental Report (SER) in accordance with DOE Order 231.1A, Environment, Safety and Health Reporting of the U.S. Department of Energy. The report is written to inform the public, regulators, employees, and other stakeholders of BNL's environmental performance during the calendar year in review. The SER summarizes environmental data; environmental management performance; compliance with applicable DOE, federal, state, and local regulations; and compliance, restoration, and surveillance monitoring program performance. BNL has prepared annual SERs since 1971 and has documented nearly all of its environmental history since the Laboratory's inception in 1947. The report is available in print and as a downloadable file on the BNL web page at http://www.bnl.gov/ewms/ser/. A summary of the SER is also prepared each year to provide a general overview of the report, and is distributed with a CD of the full report.

  5. 2009 Site Environmental Report

    Energy Technology Data Exchange (ETDEWEB)

    Ratel, K.M.; Brookhaven National Laboratory

    2010-09-30

    Each year, Brookhaven National Laboratory (BNL) prepares an annual Site Environmental Report (SER) in accordance with DOE Order 231.1A, Environment, Safety and Health Reporting of the U.S. Department of Energy. The report is written to inform the public, regulators, employees, and other stakeholders of BNL's environmental performance during the calendar year in review. The SER summarizes environmental data; environmental management performance; compliance with applicable DOE, federal, state, and local regulations; and compliance, restoration, and surveillance monitoring program performance. BNL has prepared annual SERs since 1971 and has documented nearly all of its environmental history since the Laboratory's inception in 1947. The report is available in print and as a downloadable file on the BNL web page at http://www.bnl.gov/ewms/ser/. A summary of the SER is also prepared each year to provide a general overview of the report, and is distributed with a CD of the full report.

  6. Web Site Development Support

    Science.gov (United States)

    Abdul, Hameed

    2016-01-01

    This summer I assisted the RPT Program Office in developing a design plan to update their existing website to current NASA web standards. The finished website is intended for the general public, specifically potential customers interested in learning about NASA's chemical rocket test facility capabilities and test assignment process. The goal of the website is to give the public insight about the purpose and function of the RPT Program. Working on this project gave me the opportunity to learn skills necessary for effective project management. The RPT Program Office manages numerous facilities so they are required to travel often to other sites for meetings throughout the year. Maneuvering around the travel schedule of the office and the workload priority of the IT Department proved to be quite the challenge. I overcame the travel schedule of the office by frequently communicating and checking in with my mentor via email and telephone.

  7. IOs as Social Sites

    DEFF Research Database (Denmark)

    Park, Susan M.; Vetterlein, Antje

    Norms research has made significant inroads into examining their emergence and influence in international relations, while recognizing international organizations (IOs) as key social sites for norms to be created and/or disseminated. This paper interrogates how IOs as “organizational platforms......” (Finnemore 1996) influence the norm building process. Going beyond state-centric approaches to norm construction, it argues that the process of taking up a norm by an IO does affect the norm’s power. A norm’s strength is determined by the extent to which it is uncontested and taken for granted as appropriate...... for actors with a given identity, which becomes institutionalized and internalized over time. Building on recent work that details how a norm’s strength is also derived from its specificity, the article assesses how the different ways an IO adopts norms may affect the norm’s power. The article provides...

  8. Sprucing up the site

    CERN Multimedia

    2009-01-01

    From the Globe to restaurants and meeting rooms, feverish activity is under way on both of the CERN sites to replace old equipment, carry out maitenance on existing facilities and buildings and increase their energy efficiency. Work being carried out on the Globe of Science and Innovation.The visual landmark of CERN, the Globe, has been undergoing maintenance work since July. The 40 m diameter sphere, made entirely of wood, is currently being sanded down and new treatments are being applied to the wood to protect the whole building. The work will continue until the beginning of October. Major work is also under way on some of the most emblematic rooms of the Lab, such as the Conference Room in Building 60 and the Council Chamber: while the first has been completely refurbished, with around 15 extra seats added and new audiovisual facilities installed, in the latter the air conditioning and the main electrical switchboards have been r...

  9. Faculty pilot sites announced.

    Science.gov (United States)

    2000-11-01

    From a total of 33 submissions, four pilot sites for the Faculty of Emergency Nursing have now been announced by the RCN A&E Nursing Association. They are the University of Hospital Wales, Cardiff, Royal Gwent Hospital, Newport, Neville Hall, Abergavenny, and Royal Glamorgan Hospital, Llantrisant (linked with University of Wales College of Medicine); City Hospital, Sunderland, Queen Elizabeth Hospital, Gateshead and Dryburn Hospital, Durham (linked with University of Sunderland); Altnagalvin Hospital Health and Social Services Trust, Belfast City Hospital, Craigavon Area Hospitals Trust, Royal Hospitals Trust, Belfast and Ulster Community and Hospitals Trust (linked with University of Ulster); and Bart's and London NHS Trust, Newham Healthcare and Homerton Hospital NHS Trust (linked with City University). Rob Crouch, Chair, Faculty Project Management Group said 'This is an exciting step for the Faculty concept where we can begin to turn the work of the last five years into reality'.

  10. Target sites of anthelmintics.

    Science.gov (United States)

    Martin, R J; Robertson, A P; Bjorn, H

    1997-01-01

    This paper reviews sites of action of anthelmintic drugs including: (1) levamisole and pyrantel, which act as agonists at nicotinic acetylcholine receptors of nematodes; (2) the avermectins, which potentiate or gate the opening of glutamategated chloride channels found only in invertebrates; (3) piperazine, which acts as an agonist at GABA gated chloride channels on nematode muscle; (4) praziquantel, which increases the permeability of trematode tegument to calcium and results in contraction of the parasite muscle; (5) the benzimidazoles, like thiabendazole, which bind selectively to parasite beta-tubulin and prevents microtubule formation; (6) the proton ionophores, like closantel, which uncouple oxidative phosphorylation; (7) diamphenethide and clorsulon, which selectively inhibit glucose metabolism of Fasciola and; (8) diethylcarbamazine, which appears to interfere with arachidonic acid metabolism of filarial parasites and host. The review concludes with brief comments on the development of anthelmintics in the future.

  11. 1999 Rose Site 10P

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Underwater Site 10P was established off Rose Atoll, American Samoa by Dr. James Maragos, U.S. Fish & Wildlife Service, on July 31, 1999. The site was originally...

  12. 2002 Rose Site 10P

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Underwater Site 10P was established off Rose Atoll, American Samoa by Dr. James Maragos, U.S. Fish & Wildlife Service, on July 31, 1999. The site was originally...

  13. 2002 Rose Site 8P

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Underwater Site 8P was established off Rose Atoll, American Samoa by Dr. James Maragos, U.S. Fish & Wildlife Service, on July 29, 1999. The site was originally...

  14. 1999 Rose Site 27P

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Underwater Site 27P was established off Rose Atoll, American Samoa by Dr. James Maragos, U.S. Fish & Wildlife Service, on August 24, 1999. The site was...

  15. 2002 Rose Site 9P

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Underwater Site 9P was established off Rose Atoll, American Samoa by Dr. James Maragos, U.S. Fish & Wildlife Service, on July 31, 1999. The site was originally...

  16. 2004 Rose Site 10P

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Underwater Site 10P was established off Rose Atoll, American Samoa by Dr. James Maragos, U.S. Fish & Wildlife Service, on July 31, 1999. The site was originally...

  17. 1999 Rose Site 13P

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Underwater Site 13P was established off Rose Atoll, American Samoa by Dr. James Maragos, U.S. Fish & Wildlife Service, on August 25, 1999. The site was...

  18. 2004 Rose Site 13P

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Underwater Site 13P was established off Rose Atoll, American Samoa by Dr. James Maragos, U.S. Fish & Wildlife Service, on August 25, 1999. The site was...

  19. 2006 Rose Site 13P

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Underwater Site 13P was established off Rose Atoll, American Samoa by Dr. James Maragos, U.S. Fish & Wildlife Service, on August 25, 1999. The site was...

  20. 2004 Rose Site 9P

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Underwater Site 9P was established off Rose Atoll, American Samoa by Dr. James Maragos, U.S. Fish & Wildlife Service, on July 31, 1999. The site was originally...

  1. 2006 Rose Site 31P

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Underwater Site 31P was established off Rose Atoll, American Samoa by Dr. James Maragos, U.S. Fish & Wildlife Service, on August 22, 1999. The site was...

  2. 2012 Rose Site 25P

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Underwater Site 25P was established off Rose Atoll, American Samoa by Dr. James Maragos, U.S. Fish & Wildlife Service, on July 30, 1999. The site was originally...

  3. Site compare scripts and output

    Data.gov (United States)

    U.S. Environmental Protection Agency — Monthly site compare scripts and output used to generate the model/ob plots and statistics in the manuscript. The AQS hourly site compare output files are not...

  4. 2012 Rose Site 10P

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Underwater Site 10P was established off Rose Atoll, American Samoa by Dr. James Maragos, U.S. Fish & Wildlife Service, on July 31, 1999. The site was originally...

  5. 2012 Rose Site 27P

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Underwater Site 27P was established off Rose Atoll, American Samoa by Dr. James Maragos, U.S. Fish & Wildlife Service, on August 24, 1999. The site was...

  6. 2006 Rose Site 10P

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Underwater Site 10P was established off Rose Atoll, American Samoa by Dr. James Maragos, U.S. Fish & Wildlife Service, on July 31, 1999. The site was originally...

  7. 1999 Rose Site 9P

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Underwater Site 9P was established off Rose Atoll, American Samoa by Dr. James Maragos, U.S. Fish & Wildlife Service, on July 31, 1999. The site was originally...

  8. 2012 Rose Site 31P

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Underwater Site 31P was established off Rose Atoll, American Samoa by Dr. James Maragos, U.S. Fish & Wildlife Service, on August 22, 1999. The site was...

  9. 2012 Rose Site 9P

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Underwater Site 9P was established off Rose Atoll, American Samoa by Dr. James Maragos, U.S. Fish & Wildlife Service, on July 31, 1999. The site was originally...

  10. 1999 Rose Site 31P

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Underwater Site 31P was established off Rose Atoll, American Samoa by Dr. James Maragos, U.S. Fish & Wildlife Service, on August 22, 1999. The site was...

  11. 2006 Rose Site 9P

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Underwater Site 9P was established off Rose Atoll, American Samoa by Dr. James Maragos, U.S. Fish & Wildlife Service, on July 31, 1999. The site was originally...

  12. 2006 Rose Site 27P

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Underwater Site 27P was established off Rose Atoll, American Samoa by Dr. James Maragos, U.S. Fish & Wildlife Service, on August 24, 1999. The site was...

  13. 1999 Rose Site 25P

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Underwater Site 25P was established off Rose Atoll, American Samoa by Dr. James Maragos, U.S. Fish & Wildlife Service, on July 30, 1999. The site was originally...

  14. 1999 Rose Site 8P

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Underwater Site 8P was established off Rose Atoll, American Samoa by Dr. James Maragos, U.S. Fish & Wildlife Service, on July 29, 1999. The site was originally...

  15. Refined mapping and YAC contig construction of the X-linked cleft palate and ankyloglossia locus (CPX) including the proximal X-Y homology breakpoint within Xq21.3

    Energy Technology Data Exchange (ETDEWEB)

    Forbes, S.A.; Brennan, L.; Richardson, M. [Queen Charlotte`s Hospital, London (United Kingdom)] [and others

    1996-01-01

    The gene for X-linked cleft palate (CPX) has previously been mapped in an Icelandic kindred between the unordered proximal markers DXS1002/DXS349/DXS95 and the distal marker DXYS1X, which maps to the proximal end of the X-Y homology region in Xq21.3. Using six sequence-tagged sites (STSs) within the region, a total of 91 yeast artificial chromosome (YAC) clones were isolated and overlapped in a single contig that spans approximately 3.1 Mb between DXS1002 and DXYS1X. The order of microsatellite and STS markers in this was established as DXS1002-DXS1168-DXS349-DXS95-DXS364-DXS1196-DXS472-DXS1217-DXYS1X. A long-range restriction map of this region was created using eight nonchimeric, overlapping YAC clones. Analysis of newly positioned polymorphic markers in recombinant individuals from the Icelandic family has enabled us to identify DXS1196 and DXS1217 as the flanking markers for CPX. The maximum physical distance containing the CPX gene has been estimated to be 2.0 Mb, which is spanned by a minimum set of five nonchimeric YAC clones. In addition, YAC end clone and STS analyses have pinpointed the location of the proximal boundary of the X-Y homology region within the map. 40 refs., 2 figs., 2 tabs.

  16. A hemicentric inversion in the maize line knobless Tama flint created two sites of centromeric elements and moved the kinetochore-forming region.

    Science.gov (United States)

    Lamb, Jonathan C; Meyer, Julie M; Birchler, James A

    2007-06-01

    A maize line, knobless Tama flint (KTF), was found to contain a version of chromosome 8 with two spatially distinct regions of centromeric elements, one at the original genetic position and the other at a novel location on the long arm. The new site of centromeric elements functions as the kinetochore-forming region resulting in a change of arm length ratio. Examination of fluorescence in situ hybridization markers on chromosome 8 revealed an inversion between the two centromere sites relative to standard maize lines, indicating that this chromosome 8 resulted from a hemicentric inversion with one breakpoint approximately 20 centi-McClintocks (cMc) on the long arm (20% of the total arm length from the centromere) and the other in the original cluster of centromere repeats. This inversion moved the kinetochore-forming region but left the remainder of the centromere repeats. In a hybrid between a standard line (Mo17) and KTF, both chromosome 8 homologues were completely synapsed at pachytene despite the inversion. Although the homologous centromeres were not paired, they were always correctly oriented at anaphase and migrated to opposite poles. Additionally, recombination on 8L was severely repressed in the hybrid.

  17. SHAREPOINT SITE CREATING AND SETTING

    Directory of Open Access Journals (Sweden)

    Oleksandr V. Tebenko

    2011-02-01

    Full Text Available Tools for sites building that offer users the ability to work together, an actual theme in information society and modern Web technologies. This article considers the SharePoint system, which enables to create sites of any complexity, including large portals with a complex structure of documents. Purpose of this article is to consider the main points of site creating and its setting with tools of SharePoint system, namely: a site template creating and configuring, web application environment to create and configure Web applications, change of existing and creation of new theme site, a web part setting.

  18. 2002 SITE ENVIRONMENTAL REPORT.

    Energy Technology Data Exchange (ETDEWEB)

    BROOKHAVEN NATIONAL LABORATORY

    2003-10-01

    The 2002 Site Environmental Report (SER) is prepared in accordance with DOE Order 231.1, ''Environment, Safety and Health Reporting'', and summarizes the status of Brookhaven National Laboratory's (BNL) environmental programs and performance and restoration efforts, as well as any impacts, both past and present, that Laboratory operations have had on the environment. The document is intended to be technical in nature. A summary of the report is also prepared as a separate document to provide a general overview and includes a CD version of the full report. Operated by Brookhaven Science Associates (BSA) for the Department of Energy (DOE), BNL manages its world-class scientific research with particular sensitivity to environmental and community issues. BNL's motto, ''Exploring Life's Mysteries...Protecting its Future'', reflects BNL's management philosophy to fully integrate environmental stewardship into all facets of its missions, with a health balance between science and the environment.

  19. 2007 Site Environmental Report

    Energy Technology Data Exchange (ETDEWEB)

    Ratel,K.

    2008-10-01

    Brookhaven National Laboratory (BNL) prepares an annual Site Environmental Report (SER) in accordance with DOE Order 231.1A, Environment, Safety and Health Reporting of the U.S. Department of Energy. The report is written to inform the public, regulators, employees, and other stakeholders of the Laboratory's environmental performance during the calendar year in review. Volume I of the SER summarizes environmental data; environmental management performance; compliance with applicable DOE, federal, state, and local regulations; and performance in restoration and surveillance monitoring programs. BNL has prepared annual SERs since 1971 and has documented nearly all of its environmental history since the Laboratory's inception in 1947. Volume II of the SER, the Groundwater Status Report, also is prepared annually to report on the status of and evaluate the performance of groundwater treatment systems at the Laboratory. Volume II includes detailed technical summaries of groundwater data and its interpretation, and is intended for internal BNL users, regulators, and other technically oriented stakeholders. A brief summary of the information contained in Volume II is included in this volume in Chapter 7, Groundwater Protection. Both reports are available in print and as downloadable files on the BNL web page at http://www.bnl.gov/ewms/ser/. An electronic version on compact disc is distributed with each printed report. In addition, a summary of Volume I is prepared each year to provide a general overview of the report, and is distributed with a compact disc containing the-length report.

  20. Generic Site Safety Report

    CERN Document Server

    International Atomic Energy Agency. Vienna. ITER Joint Central Team

    2001-01-01

    The ITER Engineering Design Activities (EDA) are being conducted jointly by Euratom, Japan, and the Russian Federation, as Parties to the ITER EDA Agreement signed on 21 July 1992 and subsequently extended until July 20th 2001. (The United States of America was an ITER Party until September 30th 1999). The activities are conducted under the auspices of the IAEA by the ITER Joint Central Team and by the Home Teams (HT). The JCT is composed of qualified persons made available by each of the Parties in approximately equal numbers. The JCT members are located at the ITER Joint Work Sites (JWS) in Naka (Japan), Garching (Germany), and formerly in San Diego (USA). The Home Teams are established and organized by each Party for performing the tasks of the work programme for the EDA, assigned to them in approximately equal shares. Home Teams in each of the Parties perform specific design tasks, and perform research and development in technology (physics R&D is contributed voluntarily). The Home Team Leaders (HTL) ...

  1. 2005 SITE ENVIRONMENTAL REPORT

    Energy Technology Data Exchange (ETDEWEB)

    BROOKHAVEN NATIONAL LABORATORY

    2006-08-29

    Each year, Brookhaven National Laboratory (BNL) prepares an annual Site Environmental Report (SER) in accordance with DOE Order 231.1A, Environment, Safety and Health Reporting of the U.S. Department of Energy (DOE). The report is written to inform the public, regulators, employees, and other stakeholders of BNL's environmental performance during the calendar year in review. The SER summarizes environmental data; environmental management performance; compliance with applicable DOE, federal, state, and local regulations; and compliance, restoration, and surveillance monitoring program performance. BNL has prepared annual SERs since 1971 and has documented nearly all of its environmental history since the Laboratory's inception in 1947. The report is available in print and as a downloadable file on the BNL web page at http://www.bnl.gov/ewms/ser/. A summary of the SER is also prepared each year to provide a general overview of the report, and is distributed with a CD of the full report.

  2. 2004 SITE ENVIRONMENTAL REPORT

    Energy Technology Data Exchange (ETDEWEB)

    BROOKHAVEN NATIONAL LABORATORY; SER TEAM; ENVIRONMENTAL INFORMATION MANAGEMENT SERVICES GROUP; ENVIROMENTAL AND WASTE MANAGEMENT SERVICES DIVISION FIELD SAMPLING TEAM; (MANY OTHER CONTRIBUTORS)

    2005-08-22

    Each year, Brookhaven National Laboratory (BNL) prepares an annual Site Environmental Report (SER) in accordance with DOE Order 231.1A, Environment, Safety and Health Reporting of the U.S. Department of Energy (DOE). The SER is written to inform the public, regulators, Laboratory employees, and other stakeholders of BNL's environmental performance during the calendar year in review. The report summarizes BNL's environmental data; environmental management performance; compliance with applicable DOE, federal, state, and local regulations; and restoration and surveillance monitoring programs. BNL has prepared annual SERs since 1971 and has documented nearly all of its environmental history since the Laboratory's inception in 1947. The SER is intended to be a technical document. It is available in print and as a downloadable file on the BNL web page at http://www.bnl.gov/esd/SER.htm. A summary of the SER is also prepared each year to provide a general overview of the report, and is distributed with a CD version of the full report. The summary supports BNL's educational and community outreach program.

  3. Site Management Guide (Blue Book)

    Energy Technology Data Exchange (ETDEWEB)

    None

    2014-03-01

    The U.S. Department of Energy (Department) Office of Legacy Management (LM), established in 2003, manages the Department’s postclosure responsibilities and ensures the future protection of human health and the environment. During World War II and the Cold War, the Federal government developed and operated a vast network of industrial facilities for the research, production, and testing of nuclear weapons, as well as other scientific and engineering research. These processes left a legacy of radioactive and chemical waste, environmental contamination, and hazardous facilities and materials at well over 100 sites. Since 1989, the Department has taken an aggressive accelerated cleanup approach to reduce risks and cut costs. At most Departmental sites undergoing cleanup, some residual hazards will remain at the time cleanup is completed due to financial and technical impracticality. However, the Department still has an obligation to protect human health and the environment after cleanup is completed. LM fulfills DOE’s postclosure obligation by providing long-term management of postcleanup sites which do not have continuing missions. LM is also responsible for sites under the Formerly Utilized Sites Remedial Action Program (FUSRAP). Currently, the U.S. Army Corps of Engineers (USACE) is responsible for site surveys and remediation at FUSRAP sites. Once remediation is completed, LM becomes responsible for long-term management. LM also has responsibility for uranium processing sites addressed by Title II of the Uranium Mill Tailings Radiation Control Act (UMTRCA). UMTRCA Title II sites are sites that were commercially owned and are regulated under a U.S. Nuclear Regulatory Commission (NRC) license. For license termination, the owner must conduct an NRC-approved cleanup of any on-site radioactive waste remaining from former uranium ore-processing operations. The site owner must also provide full funding for inspections and, if necessary, ongoing maintenance. Once site

  4. SITE-94. Site specific base data for the performance assessment

    Energy Technology Data Exchange (ETDEWEB)

    Geier, J. [ed.] [Clearwater Hardrock Consulting, Monmouth, OR (United States); Tiren, S. [Geosigma AB, Uppsala (Sweden); Dverstorp, B. [Swedish Nuclear Power Inspectorate, Stockholm (Sweden); Glynn, P. [U.S. Geological Survey, Reston, VA (United States)

    1996-06-01

    This report documents the site specific base data that were available, and the utilization of these data within SITE-94. A brief summary is given of SKB`s preliminary site investigations for the Aespoe Hard Rock Laboratory (HRL), which were the main source of site-specific data for SITE-94, and an overview is given of the field methods and instrumentation for the preliminary investigations. A compilation is given of comments concerning the availability and quality of the data for Aespoe, and specific recommendations are given for future site investigations. It was found that the HRL pre-investigations produced a large quantity of data which were, for the most part, of sufficient quality to be valuable for a performance assessment. However, some problems were encountered regarding documentation, procedural consistency, positional information, and storage of the data from the measurements. 77 refs, 4 tabs.

  5. 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/

  6. SITE COMPREHENSIVE LISTING (CERCLIS) (Superfund) - Non-NPL Sites

    Data.gov (United States)

    U.S. Environmental Protection Agency — Non-NPL Sites - The Comprehensive Environmental Response, Compensation and Liability Information System (CERCLIS) (Superfund) Public Access Database contains a...

  7. SITE COMPREHENSIVE LISTING (CERCLIS) - Contaminants at CERCLIS (Superfund) Sites

    Data.gov (United States)

    U.S. Environmental Protection Agency — Contaminants at Comprehensive Environmental Response, Compensation and Liability Information System (CERCLIS) (Superfund) Sites - The CERCLIS Public Access Database...

  8. SITE COMPREHENSIVE LISTING (CERCLIS) (Superfund) - Responsible Parties at CERCLIS Sites

    Data.gov (United States)

    U.S. Environmental Protection Agency — Responsible Parties at CERCLIS Sites - The Comprehensive Environmental Response, Compensation and Liability Information System (CERCLIS) (Superfund) Public Access...

  9. 2010 Site Environmental Report

    Energy Technology Data Exchange (ETDEWEB)

    Ratel, K.; Lee, R; Remien, J; Hooda, B; Green, T; Williams, J; Pohlot, P; Dorsch, W; Paquette, D; Burke, J

    2011-10-01

    Brookhaven National Laboratory (BNL) prepares an annual Site Environmental Report (SER) in accordance with DOE Order 231.1A, Environment, Safety and Health Reporting of the U.S. Department of Energy. The report is written to inform the public, regulators, employees, and other stakeholders of the Laboratory's environmental performance during the calendar year in review. Volume I of the SER summarizes environmental data; environmental management performance; compliance with applicable DOE, federal, state, and local regulations; and performance in restoration and surveillance monitoring programs. BNL has prepared annual SERs since 1971 and has documented nearly all of its environmental history since the Laboratory's inception in 1947. Volume II of the SER, the Groundwater Status Report, also is prepared annually to report on the status of and evaluate the performance of groundwater treatment systems at the Laboratory. Volume II includes detailed technical summaries of groundwater data and its interpretation, and is intended for internal BNL users, regulators, and other technically oriented stakeholders. A brief summary of the information contained in Volume II is included in Chapter 7, Groundwater Protection, of this volume. Both reports are available in print and as downloadable files on the BNL web page at http://www.bnl.gov/ewms/ser/. An electronic version on compact disc is distributed with each printed report. In addition, a summary of Volume I is prepared each year to provide a general overview of the report, and is distributed with a compact disc containing the full report. BNL is operated and managed for DOE's Office of Science by Brookhaven Science Associates (BSA), a partnership formed by Stony Brook University and Battelle Memorial Institute. For more than 60 years, the Laboratory has played a lead role in the DOE Science and Technology mission and continues to contribute to the DOE missions in energy resources, environmental quality, and

  10. Tapping Site Planning and Design

    Science.gov (United States)

    2010-06-17

    US Army Corps of Engineers BUILDING STRONG® Tapping Site Planning and Design Kevin S. Holden, RLA, ASLA Landscape Architecture Community of Practice...PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) US Army Corps of Engineers,Community of Practice Leader for Landscape ,Rock Island,IL,61204-2004 8...STRONG® Site Planning and Design 1. How is Site Planning and Design foundational to sustainable development? 2. What role does the Landscape Architect

  11. 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.

  12. Early Site Permit Demonstration Program: Siting Guide, Site selection and evaluation criteria for an early site permit application. Revision 1

    Energy Technology Data Exchange (ETDEWEB)

    1993-03-24

    In August 1991, the Joint Contractors came to agreement with Sandia National Laboratories (SNL) and the Department of Energy (DOE) on a workscope for the cost-shared Early Site Permit Demonstration Program. One task within the scope was the development of a guide for site selection criteria and procedures. A generic Siting Guide his been prepared that is a roadmap and tool for applicants to use developing detailed siting plans for their specific region of the country. The guide presents three fundamental principles that, if used, ensure a high degree of success for an ESP applicant. First, the site selection process should take into consideration environmentally diverse site locations within a given region of interest. Second, the process should contain appropriate opportunities for input from the public. Third, the process should be applied so that it is clearly reasonable to an impartial observer, based on appropriately selected criteria, including criteria which demonstrate that the site can host an advanced light water reactor (ALWR). The Siting Guide provides for a systematic, comprehensive site selection process in which three basic types of criteria (exclusionary, avoidance, and suitability) are presented via a four-step procedure. It provides a check list of the criteria for each one of these steps. Criteria are applied qualitatively, as well as presented numerically, within the guide. The applicant should use the generic guide as an exhaustive checklist, customizing the guide to his individual situation.

  13. Standardized UXO Technology Demonstration Site

    National Research Council Canada - National Science Library

    Overbay, Larry

    2005-01-01

    ...) utilizing the YPG Standardized UXO Technology Demonstration Site Blind Grid. The scoring record was coordinated by Larry Overbay and the by the Standardized UXO Technology Demonstration Scoring Committee...

  14. Region 9 Removal Sites 2012

    Data.gov (United States)

    U.S. Environmental Protection Agency — Point geospatial dataset representing locations of CERCLA (Superfund) Removal sites. CERCLA (Comprehensive Environmental Response, Compensation, and Liability Act)...

  15. UST/LUST Site Information

    Data.gov (United States)

    U.S. Environmental Protection Agency — This asset contains all Underground Storage Tank (UST) site information. It includes details such as property location, acreage, identification and characterization,...

  16. Nevada Test Site Environmental Report 2005, Attachment A - Site Description

    Energy Technology Data Exchange (ETDEWEB)

    Cathy A. Wills

    2006-10-01

    This appendix to the ''Nevada Test Site Environmental Report 2005'', dated October 2006 (DOE/NV/11718--1214; DOE/NV/25946--007) expands on the general description of the Nevada Test Site (NTS) presented in the Introduction. Included are subsections that summarize the site?s geological, hydrological, climatological, and ecological setting. The cultural resources of the NTS are also presented. The subsections are meant to aid the reader in understanding the complex physical and biological environment of the NTS. An adequate knowledge of the site's environment is necessary to assess the environmental impacts of new projects, design and implement environmental monitoring activities for current site operations, and assess the impacts of site operations on the public residing in the vicinity of the NTS. The NTS environment contributes to several key features of the site which afford protection to the inhabitants of adjacent areas from potential exposure to radioactivity or other contaminants resulting from NTS operations. These key features include the general remote location of the NTS, restricted access, extended wind transport times, the great depths to slow-moving groundwater, little or no surface water, and low population density. This appendix complements the annual summary of monitoring program activities and dose assessments presented in the main body of this report.

  17. Site locality identification study: Hanford Site. Volume II. Data cataloging

    Energy Technology Data Exchange (ETDEWEB)

    1980-07-01

    Data compilation and cataloging for the candidate site locality identification study were conducted in order to provide a retrievable data cataloging system for the present siting study and future site evaluation and licensng processes. This task occurred concurrently with and also independently of other tasks of the candidate site locality identification study. Work in this task provided the data utilized primarily in the development and application of screening and ranking processes to identify candidate site localities on the Hanford Site. The overall approach included two steps: (1) data acquisition and screening; and (2) data compilation and cataloging. Data acquisition and screening formed the basis for preliminary review of data sources with respect to their probable utilization in the candidate site locality identification study and review with respect to the level of completeness and detail of the data. The important working assumption was that the data to be used in the study be based on existing and available published and unpublished literature. The data compilation and cataloging provided the basic product of the Task; a retrievable data cataloging system in the form of an annotated reference list and key word index and an index of compiled data. The annotated reference list and key word index are cross referenced and can be used to trace and retrieve the data sources utilized in the candidate site locality identification study.

  18. Region 9 NPL Sites (Superfund Sites 2013) Polygons

    Science.gov (United States)

    NPL site POLYGON locations for the US EPA Region 9. NPL (National Priorities List) sites are hazardous waste sites that are eligible for extensive long-term cleanup under the Superfund program. Eligibility is determined by a scoring method called Hazard Ranking System. Sites with high scores are listed on the NPL. Area covered by this data set include Arizona, California, Nevada, Hawaii, Guam, American Samoa, Northern Marianas and Trust Territories. Attributes include NPL status codes, NPL industry type codes and environmental indicators. Related table, NPL_Contaminants contains information about contaminated media types and chemicals. This is a one-to-many relate and can be related to the feature class using the relationship classes under the Feature Data Set ENVIRO_CONTAMINANT. Generally, each NPL polygon has a separate source. Information about sources for each polygon can be found in the related table, NPL_POLY_METADATA. This table contains a record for each site that has information about the source. Polygons for non-Federal Facility sites were updated in January, 2007 for the Superfund Work Load Models project. Each polygon was approved by the site RPM. Where available, the majority of these polygons represent the surface expression of the extent of the contamination. All Federal Facilities are represented by the facility boundary. The following sites currently have no polygon data available at this time: Alameda Naval Air Station, Jet Pr

  19. Bedrock hydrogeology Forsmark. Site descriptive modelling, SDM-Site Forsmark

    Energy Technology Data Exchange (ETDEWEB)

    Follin, Sven (SF GeoLogic AB, Taeby (Sweden))

    2008-12-15

    The Swedish Nuclear Fuel and Waste Management Company (SKB) has conducted site investigations at two different locations, the Forsmark and Laxemar-Simpevarp areas, with the objective of siting a final repository for spent nuclear fuel according to the KBS-3 concept. Site characterisation should provide all data required for an integrated evaluation of the suitability of the investigated site and an important component in the characterisation work is the development of a hydrogeological model. The hydrogeological model is used by repository engineering to design the underground facility and to develop a repository layout adapted to the site. It also provides input to the safety assessment. Another important use of the hydrogeological model is in the environmental impact assessment. This report presents the understanding of the hydrogeological conditions of the bedrock at Forsmark reached following the completion of the surface-based investigations and provides a summary of the bedrock hydrogeological model and the underlying data supporting its development. It constitutes the main reference on bedrock hydrogeology for the site descriptive model concluding the surface-based investigations at Forsmark, SDM-site, and is intended to describe the hydraulic properties and hydrogeological conditions of the bedrock at the site and to give the information essential for demonstrating understanding

  20. The Hermes nominal landing sites

    Science.gov (United States)

    Romero, E.; Perez de Laborda, A.; Erce, I.; Aldamiz, A.

    1992-08-01

    The functions, installations, and main operational aspects that have been defined for the Hermes nominal landing sites are discussed. The landing site infrastructures, landing aids, and facilities for payload, crew, reception, operations, communications, logistics, and SAR are outlined. The typical milestones and tasks performed during each of five operational phases of a typical Hermes mission are described.

  1. Site environmental report for 1996

    Energy Technology Data Exchange (ETDEWEB)

    Holland, R.C.

    1997-08-01

    To help verify effective protection of public safety and preservation of the environment, Sandia National Laboratories (SNL)/California maintains an extensive, ongoing environmental monitoring program. This program monitors all significant airborne and liquid effluents and the environment at the SNL/California site perimeter. Lawrence Livermore National Laboratory (LLNL) performs off-site environmental monitoring for both sites. These monitoring efforts ensure that emission controls are effective in preventing contamination of the environment. As part of SNL/California`s Environmental Monitoring Program, an environmental surveillance system measures the possible presence of radioactive and hazardous materials in ambient air, surface water, groundwater, sewage, soil, vegetation, and locally produced food-stuffs. The program also includes an extensive environmental dosimetry program, which measures external radiation levels around the Livermore site and nearby vicinity. Each year, the results of the Environmental Monitoring Program are published in this report, the Site Environmental Report. This executive summary focuses on impacts to the environment and estimated radiation doses to the public from site emissions. Chapter 3, {open_quotes}Compliance Summary,{close_quotes} reviews the site`s various environmental protection activities and compliance status, with applicable environmental regulations. The effluent monitoring and environmental surveillance results for 1996 show that SNL/California operations had no harmful effects on the environment or the public. 37 figs., 12 tabs.

  2. Hanford site sodium management plan

    Energy Technology Data Exchange (ETDEWEB)

    Guttenberg, S.

    1995-09-25

    The Hanford Site Sodium Management Plan, Revision 1, provides changes to the major elements and management strategy to ensure an integrated and coordinated approach for disposition of the more than 350,000 gallons of sodium and related sodium facilities located at the DOE`s Hanford Site

  3. Site Environmental Report for 2013

    Energy Technology Data Exchange (ETDEWEB)

    Pauer, Ron [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Baskin, David [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Borglin, Ned [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Fox, Robert [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Harvey, Zachary [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Jelinski, John [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Thorson, Patrick [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Wahl, Linnea [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Wehle, Petra [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Xu, Suying [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

    2014-09-01

    This report, prepared by LBNL for the U.S. Department of Energy, Berkeley Site Office provides a comprehensive summary of the environmental program activities at LBNL for calendar year 2013 SERS are prepared annually for all DOE sites with significant environmental activities, and distributed to relevant external regulatory agencies and other interested organizations or individual.

  4. Birch soil-site requirements

    Science.gov (United States)

    Boyd W. Post; Willard H. Carmean; Robert O. Curtis

    1969-01-01

    Yellow birch is among our more valued hardwood species. Yet only meager information about site requirements is available for this tree and for paper birch. Site studies for yellow birch and paper birch and for other northern hardwood species have been completed for the Green Mountains of Vermont by Curtis and Post (1962a, 1962b). A similar study for northern hardwoods...

  5. Search Our Site With Google

    African Journals Online (AJOL)

    PROMOTING ACCESS TO AFRICAN RESEARCH. AFRICAN JOURNALS ONLINE (AJOL) · Journals · Advanced Search · USING AJOL · RESOURCES. Search Our Site With Google. Journal Home > Search Our Site With Google. Log in or Register to get access to full text downloads.

  6. Hanford Site technical baseline database

    Energy Technology Data Exchange (ETDEWEB)

    Porter, P.E., Westinghouse Hanford

    1996-05-10

    This document includes a cassette tape that contains the Hanford specific files that make up the Hanford Site Technical Baseline Database as of May 10, 1996. The cassette tape also includes the delta files that delineate the differences between this revision and revision 3 (April 10, 1996) of the Hanford Site Technical Baseline Database.

  7. Hanford Site technical baseline database

    Energy Technology Data Exchange (ETDEWEB)

    Porter, P.E.

    1996-09-30

    This document includes a cassette tape that contains the Hanford specific files that make up the Hanford Site Technical Baseline Database as of September 30, 1996. The cassette tape also includes the delta files that dellinate the differences between this revision and revision 4 (May 10, 1996) of the Hanford Site Technical Baseline Database.

  8. Nevada Test Site Environmental Report 2007 Attachment A: Site Description

    Energy Technology Data Exchange (ETDEWEB)

    Cathy Wills

    2008-09-01

    This appendix expands on the general description of the Nevada Test Site (NTS) presented in the Introduction to the Nevada Test Site Environmental Report 2007 (U.S. Department of Energy [DOE], 2008). Included are subsections that summarize the site's geological, hydrological, climatological, and ecological setting. The cultural resources of the NTS are also presented. The subsections are meant to aid the reader in understanding the complex physical and biological environment of the NTS. An adequate knowledge of the site's environment is necessary to assess the environmental impacts of new projects, design and implement environmental monitoring activities for current site operations, and assess the impacts of site operations on the public residing in the vicinity of the NTS. The NTS environment contributes to several key features of the site which afford protection to the inhabitants of adjacent areas from potential exposure to radioactivity or other contaminants resulting from NTS operations. These key features include the general remote location of the NTS, restricted access, extended wind transport times, the great depths to slow-moving groundwater, little or no surface water, and low population density. This attachment complements the annual summary of monitoring program activities and dose assessments presented in the main body of this report.

  9. Introduction to the Hanford Site

    Energy Technology Data Exchange (ETDEWEB)

    Cushing, C.E.

    1995-06-01

    This section of the 1994 Hanford Site Environmental Report discusses the Site mission and provides general information about the site. The U.S. DOE has established a new mission for Hanford including: Management of stored wastes, environmental restoration, research and development, and development of new technologies. The Hanford Reservation is located in south central Washington State just north of the confluence of the Snake and Yakima Rivers with the Columbia River. The approximately 1,450 square kilometers which comprises the Hanford Site, with restricted public access, provides a buffer for the smaller areas within the site which have historically been used for the production of nuclear materials, radioactive waste storage, and radioactive waste disposal.

  10. Web sites that work secrets from winning web sites

    CERN Document Server

    Smith, Jon

    2012-01-01

    Leading web site entrepreneur Jon Smith has condensed the secrets of his success into 52 inspiring ideas that even the most hopeless technophobe can implement. The brilliant tips and practical advice in Web sites that work will uplift and transform any website, from the simplest to the most complicated. It deals with everything from fundamentals such as how to assess the effectiveness of a website and how to get a site listed on the most popular search engines to more sophisticated challenges like creating a community and dealing with legal requirements. Straight-talking, practical and humorou

  11. Tidal energy site - Tidal energy site mammal/bird survey

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — A vessel-based line visual transect survey was conducted for birds and marine mammals near the proposed Snohomish County PUD Admiralty Inlet tidal energy site...

  12. Comparison of site evaluation methods

    Energy Technology Data Exchange (ETDEWEB)

    Rowe, M.D.; Pierce, B.L.

    1979-08-01

    This report presents results of tests of different final site selection methods used for siting large-scale facilities such as nuclear power plants. Test data are adapted from a nuclear power plant siting study conducted on Long Island, New York. The purpose of the tests is to determine whether or not different final site selection methods produce different results, and to obtain some understanding of the nature of any differences found. Decision rules and weighting methods are included. Decision rules tested are Weighting Summation, Power Law, Decision Analysis, Goal Programming, and Goal Attainment; weighting methods tested are Categorization, Ranking, Rating Ratio Estimation, Metfessel Allocation, Indifferent Tradeoff, Decision Analysis lottery, and Global Evaluation. Results show that different methods can, indeed, produce different results, but that the probability that they will do so is controlled by the structure of differences among the sites being evaluated. Differences in weights and suitability scores attributable to methods have reduced significance if the alternatives include one or two sites that are superior to all others in many attributes. The more tradeoffs there are among good and bad levels of different attributes at different sites, the more important are the specifics of methods to the final decision. 5 refs., 14 figs., 19 tabs.

  13. 1992 Fernald Site Environmental Report

    Energy Technology Data Exchange (ETDEWEB)

    1993-06-01

    The Fernald site is a Department of Energy (DOE) owned facility that produced high-quality uranium metals for military defense for nearly 40 years. DOE suspended production at the Fernald site in 1989 and formally ended production in 1991. Although production activities have ceased, the site continues to examine the air and liquid pathways as possible routes through which pollutants from past operations and current remedial activities may leave the site. This report covers the reporting period from January 1, 1992, through December 31, 1992, with the exception of Chapter Three, which provides information from the first quarter of 1993 as well as calendar year 1992 information. This 1992 report provides the general public as well as scientists and engineers with the results from the site`s ongoing Environmental Monitoring Program. Use included in this report are summary data of the sampling conducted to determine if the site complies with DOE, US Environmental Protection Agency (USEPA), and Ohio EPA (OEPA) requirements. Finally, this report provides general information on the major waste management and environmental restoration activities during 1992.

  14. Confidence assessment. Site-descriptive modelling SDM-Site Laxemar

    Energy Technology Data Exchange (ETDEWEB)

    2008-12-15

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

  15. State Cancer Profiles Web site

    Data.gov (United States)

    U.S. Department of Health & Human Services — The State Cancer Profiles (SCP) web site provides statistics to help guide and prioritize cancer control activities at the state and local levels. SCP is a...

  16. Topical Day on Site Remediation

    Energy Technology Data Exchange (ETDEWEB)

    Vandenhove, H. [ed.

    1996-09-18

    Ongoing activities at the Belgian Nuclear Research Centre relating to site remediation and restoration are summarized. Special attention has been paid to the different phases of remediation including characterization, impact assessment, evaluation of remediation actions, and execution of remediation actions.

  17. 2000 Johnston Site 4P

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Underwater Site 4P was established at Johnston Atoll by Dr. James Maragos, U.S. Fish & Wildlife Service, on July 1, 2000. With a start point (meter 0) at...

  18. Hanford Site Environmental Report 1999

    Energy Technology Data Exchange (ETDEWEB)

    TM Poston; RW Hanf; RL Dirkes

    2000-09-28

    This Hanford Site environmental report is prepared annually to summarize environmental data and information, to describe environmental management performance, to demonstrate the status of compliance with environmental regulations, and to highlight major environmental programs and efforts. The report is written to meet requirements and guidelines of the U.S. Department of Energy (DOE) and to meet the needs of the public. This summary has been written with a minimum of technical terminology. Individual sections of the report are designed to: (1) describe the Hanford Site and its mission; (2) summarize the status of compliance with environmental regulations; (3) describe the environmental programs at the Hanford Site; (4) discuss the estimated radionuclide exposure to the public from 1999 Hanford Site activities; (5) present the effluent monitoring, environmental surveillance, groundwater protection and monitoring information; and (6) discuss the activities to ensure quality.

  19. SMEX03 Site Photographs, Alabama

    Data.gov (United States)

    National Aeronautics and Space Administration — The SMEX03 Site Photographs data set includes photographs of the regional study areas of Alabama, Georgia, and Oklahoma, USA as part of the 2003 Soil Moisture...

  20. Drug Establishments Current Registration Site

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Drug Establishments Current Registration Site (DECRS) is a database of current information submitted by drug firms to register establishments (facilities) which...

  1. 2004 Rose Site 4P

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Underwater Site 4P was established off Rose Atoll, American Samoa by Dr. James Maragos, U.S. Fish & Wildlife Service, on February 9, 2004. With a start point...

  2. Sensitive Sites - OSPR [ds358

    Data.gov (United States)

    California Department of Resources — The data was created by reviewing the information contained in the Site Summaries of the Area Contingency Plan (ACP) section 9800. A summary of the document is: "The...

  3. 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.

  4. Allegheny County Summer Food Sites

    Data.gov (United States)

    Allegheny County / City of Pittsburgh / Western PA Regional Data Center — This data set shows the Summer Food Sites located within Allegheny County for children (18 years and younger) for breakfast and lunch during summer recess. OPEN...

  5. 2005 Rose Site 26P

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Underwater Site 26P was established off Rose Atoll, American Samoa by Dr. James Maragos, U.S. Fish (5) = between meters 4 and 5). Quantitative analysis of the...

  6. 2006 Rose Site 26P

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Underwater Site 26P was established off Rose Atoll, American Samoa by Dr. James Maragos, U.S. Fish & Wildlife Service, on July 29, 2004. With a start point...

  7. 2004 Rose Site 23P

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Underwater Site 23P was established off Rose Atoll, American Samoa by Dr. James Maragos, U.S. Fish & Wildlife Service, on February 10, 2004. With a start point...

  8. 2005 Rose Site 27P

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Underwater Site 27P was established off Rose Atoll, American Samoa by Dr. James Maragos, U.S. Fish (5) = between meters 4 and 5). Quantitative analysis of the...

  9. 2012 Rose Site 4P

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Underwater Site 4P was established off Rose Atoll, American Samoa by Dr. James Maragos, U.S. Fish & Wildlife Service, on February 9, 2004. With a start point...

  10. Site AVIRIS Images, 1992 (ACCP)

    Data.gov (United States)

    National Aeronautics and Space Administration — AVIRIS image scenes were acquired in 1992 over ACCP sites. Pixels that coincided with field study plots were extracted and reflectance values were correlated with...

  11. Site AVIRIS Images, 1992 (ACCP)

    Data.gov (United States)

    National Aeronautics and Space Administration — ABSTRACT: AVIRIS image scenes were acquired in 1992 over ACCP sites. Pixels that coincided with field study plots were extracted and reflectance values were...

  12. Runway Arrested Landing Site (RALS)

    Data.gov (United States)

    Federal Laboratory Consortium — The Runway Arrested Landing Site includes an underground complex located on a Mod 2, Mod 3, and Mod 3+ arresting gear and are located under the runway and accurately...

  13. Antimicrobial Pesticide Use Site Index

    Science.gov (United States)

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

  14. Hanford Site 1998 Environmental Report

    Energy Technology Data Exchange (ETDEWEB)

    RL Dirkes; RW Hanf; TM Poston

    1999-09-21

    This Hanford Site environmental report is prepared annually to summarize environmental data and information, to describe environmental management performance, to demonstrate the status of compliance with environmental regulations, and to highlight major environmental programs and efforts. The report is written to meet requirements and guidelines of the U.S. Department of Energy (DOE) and to meet the needs of the public. This summary has been written with a minimum of technical terminology. Individual sections of the report are designed to: describe the Hanford Site and its mission; summarize the status of compliance with environmental regulations; describe the environmental programs at the Hanford Site; discuss the estimated radionuclide exposure to the public from 1998 Hanford Site activities; present the effluent monitoring, environmental surveillance, and groundwater protection and monitoring information; and discuss the activities to ensure quality.

  15. The Table Mountain Field Site

    Data.gov (United States)

    Federal Laboratory Consortium — The Table Mountain Field Site, located north of Boulder, Colorado, is designated as an area where the magnitude of strong, external signals is restricted (by State...

  16. 2004 Rose Site 14P

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Underwater Site 14P was established off Rose Atoll, American Samoa by Dr. James Maragos, U.S. Fish & Wildlife Service, on February 25, 2002. With a start point...

  17. 2005 Rose Site 13P

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Underwater Site 13P was established off Rose Atoll, American Samoa by Dr. James Maragos, U.S. Fish (5) = between meters 4 and 5). Quantitative analysis of the...

  18. 2000 Johnston Site 6P

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Underwater Site 6P was established at Johnston Atoll by Dr. James Maragos, U.S. Fish & Wildlife Service, on July 3, 2000. With a start point (meter 0) at...

  19. 2000 Johnston Site 5P

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Underwater Site 5P was established at Johnston Atoll by Dr. James Maragos, U.S. Fish & Wildlife Service, on July 2, 2000. With a start point (meter 0) at...

  20. 2002 Rose Site 7P

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Underwater Site 7P was established off Rose Atoll, American Samoa by Dr. James Maragos, U.S. Fish & Wildlife Service, on February 24, 2002. With a start point...

  1. 2006 Rose Site 29P

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Underwater Site 29P was established off Rose Atoll, American Samoa by Dr. James Maragos, U.S. Fish & Wildlife Service, on July 31, 2004. With a start point...

  2. 2004 Rose Site 32P

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Underwater Site 32P was established off Rose Atoll, American Samoa by Dr. James Maragos, U.S. Fish & Wildlife Service, on August 2, 2004. With a start point...

  3. 2002 Rose Site 5P

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Underwater Site 5P was established off Rose Atoll, American Samoa by Dr. James Maragos, U.S. Fish & Wildlife Service, on February 20, 2002. With a start point...

  4. 2004 Rose Site 26P

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Underwater Site 26P was established off Rose Atoll, American Samoa by Dr. James Maragos, U.S. Fish & Wildlife Service, on July 29, 2004. With a start point...

  5. Site Environmental Report for 2014

    Energy Technology Data Exchange (ETDEWEB)

    Pauer, Ronald O. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Baskin, David [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Borglin, Ned [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Fox, Robert [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Harvey, Zachary [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Jelinski, John [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Thorson, Patrick [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Wehle, Petra [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Xu, Suying [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

    2015-09-01

    The annual Site Environmental Report documents Lawrence Berkeley National Laboratory’s performance in reducing its environmental impacts, progress toward cleaning up groundwater contamination, and compliance with applicable Department of Energy, federal, state, and local environmental regulations.

  6. Discovery of Genomic Breakpoints Affecting Breast Cancer Progression and Prognosis

    Science.gov (United States)

    2010-10-01

    19a. NAME OF RESPONSIBLE PERSON USAMRMC a. REPORT U b. ABSTRACT U c. THIS PAGE U UU 34 19b. TELEPHONE NUMBER (include area code...Predki, P., Martin, C., Wernick , M., et al. 2001. Comprehensive genome sequence analysis of a breast cancer amplicon. Genome Res. 11: 1034–1042. Hahn, Y

  7. Nearshore bars and the break-point hypothesis

    Science.gov (United States)

    Sallenger, A.H.; Howd, P.A.

    1989-01-01

    The set of hypotheses calling for bar formation at the break point was tested with field data. During two different experiments, waves were measured across the surf zone coincident with the development of a nearshore bar. We use a criterion, based on the wave height to depth ratio, to determine the offshore limit of the inner surf zone. During the first experiment, the bar became better developed and migrated offshore while remaining well within the inner surf zone. During the second experiment, the surf zone was narrower and we cannot rule out the possibility of break point processes contributing to bar development. We conclude that bars are not necessarily coupled with the break point and can become better developed and migrate offshore while being in the inner surf zone landward from initial wave breaking in the outer surf zone. ?? 1989.

  8. Site environmental report for 1994

    Energy Technology Data Exchange (ETDEWEB)

    Brekke, D.D.; Holland, R.C.; Gordon, K.W. [ed.

    1995-12-01

    Sandia National Laboratories (SNL) is committed to conducting its operations in an environmentally safe and sound manner. It is mandatory that activities at SNL/California comply with all applicable environmental statutes, regulations, and standards. Moreover, SNL/California continuously strives to reduce risks to employees, the public, and the environment to the lowest levels reasonably possible. To help verify effective protection of public safety and preservation of the environment, SNL/California maintains an extensive, ongoing environmental monitoring program. This program monitors all significant airborne and liquid effluents and the environment at the SNL/California site perimeter. Lawrence Livermore National Laboratory (LLNL) performs off-site environmental monitoring for both sites. These monitoring efforts ensure that emission controls are effective in preventing contamination of the environment. As part of SNL/California`s Environmental Monitoring Program, an environmental surveillance system measures the possible presence of radioactive and hazardous materials in ambient air, surface water, groundwater, sewage, soil, vegetation, and locally-produced food-stuffs. The program also includes an extensive environmental dosimetry program, which measures external radiation levels around the Livermore site and nearby vicinity. Each year, the results of the Environmental Monitoring Program are published in this report, the Site Environmental Report This executive summary focuses on impacts to the environment and estimated radiation doses to the public from site emissions. Chapter 3, {open_quotes}Compliance Summary,{close_quotes} reviews the site`s various environmental protection activities and compliance status with applicable environmental regulations. The effluent monitoring and environmental surveillance results for 1994 show that SNL/California operations had no harmful effects on the environment or the public. A summary of the findings is provided below.

  9. Site Environmental Report for 1998

    Energy Technology Data Exchange (ETDEWEB)

    Holland, R.C.

    1999-06-01

    Sandia National Laboratories (SNL) is committed to conducting its operations in an environmentally safe and sound manner. It is mandatory that activities at SNL/California comply with all applicable environmental statutes, regulations, and standards. Moreover, SNL/California continuously strives to reduce risks to employees, the public, and the environment to the lowest levels reasonably possible. To help verify effective protection of public safety and preservation of the environment, SNL/California maintains an extensive, ongoing environmental monitoring program. This program monitors all significant effluents and the environment at the SNL/California site perimeter. Lawrence Livermore National Laboratory (LLNL) performs off-site external radiation monitoring for both sites. These monitoring efforts ensure that emission controls are effective in preventing contamination of the environment. As part of SNL/California's Environmental Monitoring Program, an environmental surveillance system measures the possible presence of hazardous materials in groundwater, stormwater, and sewage. The program also includes an extensive environmental dosimetry program, which measures external radiation levels around the Livermore site and nearby vicinity. Each year, the results of the Environmental Monitoring Program are published in this report, the Site Environmental Report. This executive summary focuses on impacts to the environment. Chapter 3, ''Compliance Summary,'' reviews the site's various environmental protection activities and compliance status with applicable environmental regulations. The effluent monitoring and environmental surveillance results for 1998 show that SNL/California operations had no harmful effects on the environment or the public.

  10. Hanford Site environmental management specification

    Energy Technology Data Exchange (ETDEWEB)

    Grygiel, M.L.

    1998-06-10

    The US Department of Energy, Richland Operations Office (RL) uses this Hanford Site Environmental Management Specification (Specification) to document top-level mission requirements and planning assumptions for the prime contractors involved in Hanford Site cleanup and infrastructure activities under the responsibility of the US Department of Energy, Office of Environmental Management. This Specification describes at a top level the activities, facilities, and infrastructure necessary to accomplish the cleanup of the Hanford Site and assigns this scope to Site contractors and their respective projects. This Specification also references the key National Environmental Policy Act of 1969 (NEPA), Comprehensive Environmental Response, Compensation, and Liability Act of 1980 (CERCLA), and safety documentation necessary to accurately describe the cleanup at a summary level. The information contained in this document reflects RL`s application of values, priorities, and critical success factors expressed by those involved with and affected by the Hanford Site project. The prime contractors and their projects develop complete baselines and work plans to implement this Specification. These lower-level documents and the data that support them, together with this Specification, represent the full set of requirements applicable to the contractors and their projects. Figure 1-1 shows the relationship of this Specification to the other basic Site documents. Similarly, the documents, orders, and laws referenced in this specification represent only the most salient sources of requirements. Current and contractual reference data contain a complete set of source documents.

  11. The Hanford Site focus, 1994

    Energy Technology Data Exchange (ETDEWEB)

    Peterson, J.M.

    1994-03-01

    This report describes what the Hanford Site will look like in the next two years. We offer thumbnail sketches of Hanford Site programs and the needs we are meeting through our efforts. We describe our goals, some recent accomplishments, the work we will do in fiscal year (FY) 1994, the major activities the FY 1995 budget request covers, and the economic picture in the next few years. The Hanford Site budget shows the type of work being planned. US Department of Energy (DOE) sites like the Hanford Site use documents called Activity Data Sheets to meet this need. These are building blocks that are included in the budget. Each Activity Data Sheet is a concise (usually 4 or 5 pages) summary of a piece of work funded by the DOE`s Environmental Restoration and Waste Management budget. Each sheet describes a waste management or environmental restoration need over a 5-year period; related regulatory requirements and agreements; and the cost, milestones, and steps proposed to meet the need. The Hanford Site is complex and has a huge budget, and its Activity Data Sheets run to literally thousands of pages. This report summarizes the Activity Data Sheets in a less detailed and much more reader-friendly fashion.

  12. Nevada Test Site Environmental Report 2009, Attachment A: Site Description

    Energy Technology Data Exchange (ETDEWEB)

    Cathy Wills, ed.

    2010-09-13

    This attachment expands on the general description of the Nevada Test Site (NTS) presented in the Introduction to the Nevada Test Site Environmental Report 2009. Included are subsections that summarize the site’s geological, hydrological, climatological, and ecological setting. The cultural resources of the NTS are also presented. The subsections are meant to aid the reader in understanding the complex physical and biological environment of the NTS. An adequate knowledge of the site’s environment is necessary to assess the environmental impacts of new projects, design and implement environmental monitoring activities for current site operations, and assess the impacts of site operations on the public residing in the vicinity of the NTS. The NTS environment contributes to several key features of the site that afford protection to the inhabitants of adjacent areas from potential exposure to radioactivity or other contaminants resulting from NTS operations. These key features include the general remote location of the NTS, restricted access, extended wind transport times, the great depths to slow-moving groundwater, little or no surface water, and low population density. This attachment complements the annual summary of monitoring program activities and dose assessments presented in the main body of this report.

  13. Nevada Test Site Environmental Report 2008 Attachment A: Site Description

    Energy Technology Data Exchange (ETDEWEB)

    Cathy A. Wills

    2009-09-01

    This attachment expands on the general description of the Nevada Test Site (NTS) presented in the Introduction to the Nevada Test Site Environmental Report 2008 (National Security Technologies, LLC [NSTec], 2009a). Included are subsections that summarize the site’s geological, hydrological, climatological, and ecological setting. The cultural resources of the NTS are also presented. The subsections are meant to aid the reader in understanding the complex physical and biological environment of the NTS. An adequate knowledge of the site’s environment is necessary to assess the environmental impacts of new projects, design and implement environmental monitoring activities for current site operations, and assess the impacts of site operations on the public residing in the vicinity of the NTS. The NTS environment contributes to several key features of the site that afford protection to the inhabitants of adjacent areas from potential exposure to radioactivity or other contaminants resulting from NTS operations. These key features include the general remote location of the NTS, restricted access, extended wind transport times, the great depths to slow-moving groundwater, little or no surface water, and low population density. This attachment complements the annual summary of monitoring program activities and dose assessments presented in the main body of this report.

  14. Carnegie Science Academy Web Site

    Science.gov (United States)

    Kotwicki, John; Atzinger, Joe; Turso, Denise

    1997-11-01

    The Carnegie Science Academy is a professional society "For Teens...By Teens" at the Carnegie Science Center in Pittsburgh. The CSA Web Site [ http://csa.clpgh.org ] is designed for teens who have an interest in science and technology. This online or virtual science academy provides resources for teens in high school science classes. The Web site also allows students around the world to participate and communicate with other students, discuss current events in science, share opinions, find answers to questions, or make online friends. Visitors can enjoy the main components of the site or sign up for a free membership which allows access to our chat room for monthly meeting, online newsletter, members forum, and much more. Main components to the site include a spot for cool links and downloads, available for any visitor to download or view. Online exhibits are created by students to examine and publish an area of study and also allow teachers to easily post classroom activities as exhibits by submitting pictures and text. Random Access, the interactive part of the academy, allows users to share ideas and opinions. Planet CSA focuses on current events in science and the academy. In the future the CSA Web site will become a major resource for teens and science teachers providing materials that will allow students to further enhance their interest and experiences in science.

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

    Energy Technology Data Exchange (ETDEWEB)

    2009-12-15

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

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

    Energy Technology Data Exchange (ETDEWEB)

    2008-12-15

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

  17. SMAD5 Gene Expression, Rearrangements, Copy Number, Amplification at Fragile Site FRA5C in Human Hepatocellular Carcinoma

    Directory of Open Access Journals (Sweden)

    Drazen B. Zimonjic

    2003-09-01

    Full Text Available Signaling by the transforming growth factor (TGFfamily members is transduced from the cell surface to the nucleus by the Smad group of intracellular proteins. Because we detected alterations on the long arm of chromosome 5, we examined the status of the SMAD5 gene in human hepatocellular carcinoma (HCC cell lines and primary HCC. In 16 cell lines, chromosome alterations of chromosome 5 were observed in nine cell lines by fluorescence in situ hybridization (FISH, an increase in SMAD5 gene copy number relative to the ploidy level was found in eight lines. The breakpoints in unbalanced translocations and deletions frequently occurred near the SMAD5 locus, but apparently did not cause loss of SMAD5. In one cell line, where comparative genomic hybridization showed DNA copy number gain confined to the region 5831, we detected by FISH high-level amplification of the SMAD5 gene located within the fragile site FRA5C. Semiquantitative polymerase chain reaction did not reveal changes in SMAD5 DNA levels in 15 of 17 primary HCC specimens. In 17 HCC cell lines, SMAD5 mRNA levels were either maintained or upregulated by an increase in gene dosage or another mechanism. Collectively, our results show that SMAD5 undergoes copy number gain and increased expression, rather than loss of expression, therefore suggest that this gene does not act as a tumorsuppressor gene in HCC. The Hep-40 HCC cell line with high-level amplification and significant overexpression of SMAD5 may be useful in studying the interaction of SMAD5 with other genes.

  18. Optimum windmill-site matching

    Energy Technology Data Exchange (ETDEWEB)

    Salameh, Z.M.; Safari, I. (Dept. of Electrical Engineering, Univ. of Massachusetts, Lowell, Lowell, MA (United States))

    1992-12-01

    In this paper a methodology for the selection of the optimum windmill for a specific site is developed. The selection windmill for a specific site is developed. The selection is based on finding the capacity factors (CF) of the available windmills. This is done by using long term wind speed data recorded at different hours of the day for many years. This data is then used to generate mean wind speeds for a typical day in a month. Probability density functions for the mean wind speeds for the different hours of the day are generated with the manufacturer's specifications on windmills used to calculate the capacity factors for the windmills. The windmill with the highest average capacity factor for the specific site is the optimum one and to be recommended.

  19. Hanford Site Environmental Report 1993

    Energy Technology Data Exchange (ETDEWEB)

    Dirkes, R.L.; Hanf, R.W.; Woodruff, R.K. [eds.

    1994-06-01

    The Hanford Site Environmental Report is prepared annually to summarize environmental data and information, describe environmental management performance, and demonstrate the status of compliance with environmental regulations. The report also highlights major environmental programs and efforts. The report is written to meet reporting requirements and Guidelines of the U.S. Department of Energy (DOE) an to meet the needs of the public. This summary has been written with a minimum of technical terminology. Individual sections of the report are designed to (a) describe the Hanford Site and its mission, (b) summarize the status in 1993 of compliance with environmental regulations, (c) describe the environmental programs at the Hanford Site, (d) discuss estimated radionuclide exposure to the public from 1993 Hanford activities, (e) present information on effluent monitoring and environmental surveillance, including ground-water protection and monitoring, (f) discuss activities to ensure quality. More detailed information can be found in the body of the report, the appendixes, and the cited references.

  20. Proteoglycan: site mapping and site-directed mutagenesis.

    Science.gov (United States)

    Hagen, Fred K

    2012-01-01

    Identification of proteoglycan chain modification sites cannot yet be reliably predicted from primary amino acid sequence data. A number of studies have shown that serine is the predominant amino acid that is modified and it is frequently flanked by a C-terminal glycine and proximal N-terminal acidic amino acids; however, not all simple Ser-Gly motifs constitute a modification site. Here we present a rapid method for cloning small, defined segments of putative proteoglycan attachment sites and expressing them as a mini-reporter protein in an insect tissue culture system that is expandable to high throughput analysis. Reporter proteins with attached proteoglycans can be readily discerned from their unmodified form, by a simple gel-shift assay and Western blot detection for an epitope tag engineered into the reporter. Unmodified proteins are generated as a reference standard by treating cells with dsRNA to knock down the endogenous polypeptide xylose transferase, which is responsible for initiating proteoglycan site attachment. Examination of proteoglycan attachment by different metazoan organisms can be studied in the same cell line by cotransfecting a polypeptide xylose transferase expression plasmid and reporter construct from human, mouse, frog, or worm, for example. Reporter proteins engineer with point mutations can be rapidly generated with this system to pinpoint the exact residue that is glycosylated, to verify the mapping data.

  1. Construction site chaos : an edutainment game for construction site workers

    NARCIS (Netherlands)

    Boer, de J. (Johannes)

    2014-01-01

    This paper describes a demo for the Persuasive Conference 2014 (21-23 May, Padua, Italy) which shows the result of a design project in the edutainment field. The tries to raise safety awareness among construction site workers. The purpose of the demo is to raise safety awareness amongst

  2. Linking snow depth to avalanche release area size: measurements from the Vallée de la Sionne field site

    Science.gov (United States)

    Veitinger, Jochen; Sovilla, Betty

    2016-08-01

    One of the major challenges in avalanche hazard assessment is the correct estimation of avalanche release area size, which is of crucial importance to evaluate the potential danger that avalanches pose to roads, railways or infrastructure. Terrain analysis plays an important role in assessing the potential size of avalanche releases areas and is commonly based on digital terrain models (DTMs) of a snow-free summer terrain. However, a snow-covered winter terrain can significantly differ from its underlying, snow-free terrain. This may lead to different, and/or potentially larger release areas. To investigate this hypothesis, the relation between avalanche release area size, snow depth and surface roughness was investigated using avalanche observations of artificially triggered slab avalanches over a period of 15 years in a high-alpine field site. High-resolution, continuous snow depth measurements at times of avalanche release showed a decrease of mean surface roughness with increasing release area size, both for the bed surface and the snow surface before avalanche release. Further, surface roughness patterns in snow-covered winter terrain appeared to be well suited to demarcate release areas, suggesting an increase of potential release area size with greater snow depth. In this context, snow depth around terrain features that serve as potential delineation borders, such as ridges or trenches, appeared to be particularly relevant for release area size. Furthermore, snow depth measured at a nearby weather station was, to a considerable extent, related to potential release area size, as it was often representative of snow depth around those critical features where snow can accumulate over a long period before becoming susceptible to avalanche release. Snow depth - due to its link to surface roughness - could therefore serve as a highly useful variable with regard to potential release area definition for varying snow cover scenarios, as, for example, the avalanche

  3. Site investigations: Strategy for rock mechanics site descriptive model

    Energy Technology Data Exchange (ETDEWEB)

    Andersson, Johan [JA Streamflow AB, Aelvsjoe (Sweden); Christiansson, Rolf [Swedish Nuclear Fuel and Waste Management Co., Stockholm (Sweden); Hudson, John [Rock Engineering Consultants, Welwyn Garden City (United Kingdom)

    2002-05-01

    As a part of the planning work for the Site Investigations, SKB has developed a Rock Mechanics Site Descriptive Modelling Strategy. Similar strategies are being developed for other disciplines. The objective of the strategy is that it should guide the practical implementation of evaluating site specific data during the Site Investigations. It is also understood that further development may be needed. This methodology enables the crystalline rock mass to be characterised in terms of the quality at different sites, for considering rock engineering constructability, and for providing the input to numerical models and performance assessment calculations. The model describes the initial stresses and the distribution of deformation and strength properties of the intact rock, of fractures and fracture zones, and of the rock mass. The rock mass mechanical properties are estimated by empirical relations and by numerical simulations. The methodology is based on estimation of mechanical properties using both empirical and heroretical/numerical approaches; and estimation of in situ rock stress using judgement and numerical modelling, including the influence of fracture zones. These approaches are initially used separately, and then combined to produce the required characterisation estimates. The methodology was evaluated with a Test Case at the Aespoe Hard Rock Laboratory in Sweden. The quality control aspects are an important feature of the methodology: these include Protocols to ensure the structure and coherence of the procedures used, regular meetings to enhance communication, feedback from internal and external reviewing, plus the recording of an audit trail of the development steps and decisions made. The strategy will be reviewed and, if required, updated as appropriate.

  4. 2011 ANNUAL SITE ENVIRONMENTAL REPORT

    Energy Technology Data Exchange (ETDEWEB)

    Meyer, A.; Eddy, T.; Jannik, T.; Terry, B.; Cauthen, K.; Coward, L.; Dunaway-Ackerman, J.; Wilson, M.; Hutchison, J.; O' Quinn, S.

    2012-10-01

    The Savannah River Site Environmental Report for 2011 (SRNS-STI-2012-00200) is prepared for the U.S. Department of Energy (DOE) according to requirements of DOE Order 231.1 B, “Environment, Safety and Health Reporting." The annual SRS Environmental Report has been produced for more than 50 years. Several hundred copies are and interested individuals. The report’s purpose is to: present summary environmental data that characterize site environmental management performance; describe compliance status with respect to environmental standards and requirements; highlight significant programs and efforts.

  5. SITE DESIGN SETTING IN SHAREPOINT

    Directory of Open Access Journals (Sweden)

    Oleksii V. Tebenko

    2010-10-01

    Full Text Available Creation and promotion of the site is one of way to implement of ICT in education. To build modern sites and large portals, to avoid the process of content creation and management tools, when new content is added, dynamic model for page building is used. The article deals with means and methods of dynamic page template in SharePoint. Purpose of the article is to analyze the key components of SharePoint for dynamic pages, such as setting and changing master pages, standard types of spaceholders master pages, setting aggregates content and consideration of standard types of SharePoint spaceholders.

  6. From Measurements to Site Approval

    DEFF Research Database (Denmark)

    Toft, Henrik Stensgaard; Svenningsen, Lasse; Sørensen, John Dalsgaard

    2014-01-01

    In the present paper the influence of natural variations in turbulence, wind shear and air density on the fatigue damage equivalent loads during power production are investigated. In site suitability analysis it is normally assumed that the fatigue loads can be estimated based on a 90% quantile...... for the turbulence and average values for the wind shear and air density. The analysis in the present paper shows that wind shear variations can have a significant influence on fatigue loads for some wind turbine sensors (components). The natural variation in shear should therefore be taken into account in site...

  7. Knowledge for Web Site Development.

    Science.gov (United States)

    Taylor, Mark J.; England, David; Gresty, David

    2001-01-01

    Examines the results of a research exercise involving case studies in 20 United Kingdom organizations aimed at investigating: the skills and knowledge required for Web site development work, how such skills and knowledge are used in actual practice, and the mechanisms by which such skills and knowledge can be acquired and improved. (Author/AEF)

  8. Young Child. [SITE 2001 Section].

    Science.gov (United States)

    Yelland, Nicola, Ed.; DeVoogd, Glenn, Ed.

    This document contains the following papers on the young child from the SITE (Society for Information Technology & Teacher Education) 2001 conference: (1) "Young Children and Technology: Building Computer Literacy" (Michael J. Bell and Caroline M. Crawford); (2) "Integrating Technology into the Young Child Lesson Plan"…

  9. Young Child. [SITE 2002 Section].

    Science.gov (United States)

    Yelland, Nicola, Ed.; DeVoogd, Glenn, Ed.

    This document contains the following papers on the young child from the SITE (Society for Information Technology & Teacher Education) 2002 conference: (1) "Young Children's Computer Use: Perspectives of Early Childhood Teacher Educators" (Mehmet Buldu); (2) "Using Technology To Support Preschool Teachers' Professional Development" (Julie Hirschler…

  10. Pin site metastasis of meningioma.

    Science.gov (United States)

    Ozer, Ercan; Kalemci, Orhan; Acar, Umit Dursun; Canda, Serafettin

    2007-10-01

    Metastasis of meningiomas due to iatrogenic implantation of tumour cells is extremely rare and only four cases have been reported to date. In this study, we report a 45-year-old female patient who presented with meningioma metastasis at the pin site of head holder applied in the original operation.

  11. Hanford Site Ecological Quality Profile

    Energy Technology Data Exchange (ETDEWEB)

    Bilyard, Gordon R.; Sackschewsky, Michael R.; Tzemos, Spyridon

    2002-02-17

    This report reviews the ecological quality profile methodology and results for the Hanford Site. It covers critical ecological assets and terrestrial resources, those in Columbia River corridor and those threatened and engdangered, as well as hazards and risks to terrestrial resources. The features of a base habitat value profile are explained, as are hazard and ecological quality profiles.

  12. Interactive Web Sites for Teens

    Science.gov (United States)

    Haycock, Ken

    2005-01-01

    Eighty-three percent of teenagers are online. The average teen spends 5 to 10 hours a week on the Web. When using Web sites, teenagers are easily bored. Teenagers are also not nearly as skilled as adults at navigating the Web and do not really care for glitzy graphics. Insufficient reading skills, immature research strategies, and unwillingness to…

  13. World's finest tech sites immortalised

    CERN Multimedia

    2008-01-01

    They may have transformed man's understanding of the universe but the monumental impact of the world's first large radio telescope and the planet's largest particle physics lab has never been fully recognised. Now both Jodrell Bank and CERN are among the technological landmarks that could be immortalised alongside the pyramids of Egypt and Taj Mahal on UNESCO's World Heritage Site (WHS) list.

  14. Desert Test Site Uniformity Analysis

    Science.gov (United States)

    Kerola, Dana X.; Bruegge, Carol J.

    2009-01-01

    Desert test sites such as Railroad Valley (RRV) Nevada, Egypt-1, and Libya-4 are commonly targeted to assess the on-orbit radiometric performance of sensors. Railroad Valley is used for vicarious calibration experiments, where a field-team makes ground measurements to produce accurate estimates of top-of-atmosphere (TOA) radiances. The Sahara desert test sites are not instrumented, but provide a stable target that can be used for sensor cross-comparisons, or for stability monitoring of a single sensor. These sites are of interest to NASA's Atmospheric Carbon Observation from Space (ACOS) and JAXA's Greenhouse Gas Observation SATellite (GOSAT) programs. This study assesses the utility of these three test sites to the ACOS and GOSAT calibration teams. To simulate errors in sensor-measured radiance with pointing errors, simulated data have been created using MODIS Aqua data. MODIS data are further utilized to validate the campaign data acquired from June 22 through July 5, 2009. The first GOSAT vicarious calibration experiment was conducted during this timeframe.

  15. Anilortem: A Siting Simulation Game.

    Science.gov (United States)

    Canipe, Stephen L.

    This siting game is based on the assumption that students will become involved in research required to determine the need for a power plant. Once the need is established, students must determine the location and type of plant to be built. There are brief character sketches which describe the key actors in the simulation. It is suggested that…

  16. Step sites in syngas catalysis

    DEFF Research Database (Denmark)

    Rostrup-Nielsen, J.; Nørskov, Jens Kehlet

    2006-01-01

    Step sites play an important role in many catalytic reactions. This paper reviews recent results on metal catalysts for syngas reactions with emphasis on steam reforming. Modern characterization techniques (STEM, HREM...) and theoretical calculations (DFT) has allowed a more quantitative explanat...

  17. Site Environmental Report for 2015

    Energy Technology Data Exchange (ETDEWEB)

    Pauer, Ron O. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Baskin, David A. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Borglin, Ned K. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Fox, Robert A. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Harvey, Zachary R. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Jelinski, John A. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Kassis, Maram M. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Muhlholland, Brendan J. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Thorson, Patrick A. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Xu, Suying Y. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Sutherland, Nancy L. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Wehle, Petra C. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

    2016-09-30

    The annual Site Environmental Report documents Lawrence Berkeley National Laboratory’s performance in reducing its environmental impacts, progress toward cleaning up groundwater contamination, and compliance with applicable Department of Energy, federal, state, and local environmental regulations. The report is required by DOE Order 231.1B, Environment, Safety, and Health Reporting.

  18. NGNP SITE 2 HAZARDS ASSESSMENT

    Energy Technology Data Exchange (ETDEWEB)

    Wayne Moe

    2011-10-01

    The Next Generation Nuclear Plant (NGNP) Project initiated at Idaho National Laboratory (INL) by the U.S. Department of Energy pursuant to the 2005 Energy Policy Act, is based on research and development activities supported by the Generation IV Nuclear Energy Systems Initiative. The principal objective of the NGNP Project is to support commercialization of the high temperature gas-cooled reactor (HTGR) technology. The HTGR is a helium-cooled and graphite-moderated reactor that can operate at temperatures much higher than those of conventional light water reactor (LWR) technologies. Accordingly, it can be applied in many industrial applications as a substitute for burning fossil fuels, such as natural gas, to generate process heat in addition to producing electricity, which is the principal application of current LWRs. Nuclear energy in the form of LWRs has been used in the U.S. and internationally principally for the generation of electricity. However, because the HTGR operates at higher temperatures than LWRs, it can be used to displace the use of fossil fuels in many industrial applications. It also provides a carbon emission-free energy supply. For example, the energy needs for the recovery and refining of petroleum, for the petrochemical industry and for production of transportation fuels and feedstocks using coal conversion processes require process heat provided at temperatures approaching 800 C. This temperature range is readily achieved by the HTGR technology. This report summarizes a site assessment authorized by INL under the NGNP Project to determine hazards and potential challenges that site owners and HTGR designers need to be aware of when developing the HTGR design for co-location at industrial facilities, and to evaluate the site for suitability considering certain site characteristics. The objectives of the NGNP site hazard assessments are to do an initial screening of representative sites in order to identify potential challenges and restraints

  19. Sacrifical sites, types and function

    Directory of Open Access Journals (Sweden)

    Örnulv Vorren

    1987-01-01

    Full Text Available Much has been written and said about Saami mythology and pre-Christian religion. There is, however, considerably less documentation of concrete cultural elements in scholarly descriptions. These investigations are considered important not only because they aim to provide documentation that can be used for studies of Saami mythology and pre-Christian religion. They also provide material that can throw light on the function of the holy places in a social context through analysis of their origin, their connections with certain families and persons, their associations with the siidas, their location within the areas where the Saamis from these siidas gained their livelihood, etc. The materials collected about the sacrificial sites also play an important role in studying the course of events leading up to the differentiation of Saami hunting and gathering culture. A question that has frequently arisen in the course of this work is with what powers or deities the different sacrificial sites were associated. This is naturally connected with their origin and their form. This, in turn, is reflected in the traditions and legends recounted concerning them. It is also reflected in their location in the physical environment and in the kinds of offerings that have been found. In the materials so far collected it is possible to distinguish between about eight different types of sacrificial site and holy mountain or fell according to their form and location: holy fells, rock formations, stone boulders, holes, cracks in fells, springs, lakes, ring-shaped sacrificial sites. Missionaries were urged to destroy the offering sites.

  20. Suitability of oyster restoration sites along the Louisiana coast: Examining site and stock × site interaction

    Science.gov (United States)

    Schwarting Miller, Lindsay; La Peyre, Jerome F.; LaPeyre, Megan K.

    2017-01-01

    Recognition of the global loss of subtidal oyster reefs has led to a rise in reef restoration efforts, including in the Gulf of Mexico. Created reef success depends entirely on selecting a location that supports long-term oyster growth and survival, including the recruitment and survival of on-reef oysters. Significant changes in estuarine salinity through management of freshwater inflows and through changed precipitation patterns may significantly impact the locations of optimal oyster restoration sites. These rapid shifts in conditions necessitate a need to better understand both impacts to on-reef oyster growth and population development, and variation in oyster stock performance. Oyster growth, mortality, condition, and disease prevalence were examined in three different stocks of oysters located in protected cages, as well as oyster recruitment and mortality on experimental reef units in three different locations representing a salinity gradient, along the Louisiana Gulf coast in 2011 and 2012. Over a 2-y period, the high-salinity site had highest oyster growth rate in protected cages but demonstrated the least likelihood for reef development based on on-reef oyster population failure, likely because of predation-related mortality (high recruitment and 100% mortality). In contrast, the midsalinity site with moderate oyster growth and on-reef recruitment and low mortality demonstrated a higher likelihood for reef development. The lowest salinity site exhibited extreme variability in all oyster responses between years because of extreme variation in environmental conditions during the study, indicating a low likelihood of long-term reef development. Whereas limited differences in stock performance between sites were found, the range of site environmental conditions tested was ultimately much lower than expected and may not have provided a wide enough range of conditions. In areas with limited, low recruitment, or rapidly changing environmental conditions

  1. Savannah River Site's Site Specific Plan

    Energy Technology Data Exchange (ETDEWEB)

    1991-08-01

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

  2. Basic Information About School Siting Guidelines

    Science.gov (United States)

    EPA's voluntary school siting guidelines provide recommendations for local school districts and community members on how to evaluate environmental factors to make the best possible school siting decisions.

  3. SNF Site Characterization Data: C.Jarvis

    Data.gov (United States)

    National Aeronautics and Space Administration — Site characterization parameters (canopy density, litter components, soil characterization: color, moisture, components) for selected sites within the Superior...

  4. 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.

  5. 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.

  6. Nevada Test Site annual site environmental report, 1989

    Energy Technology Data Exchange (ETDEWEB)

    Wruble, D T; McDowell, E M [eds.

    1990-11-01

    Prior to 1989 annual reports of environmental monitoring and assessment results for the Nevada Test Site (NTS) were prepared in two separate parts. Onsite effluent monitoring and environmental monitoring results were reported in an onsite report prepared by the US Department of Energy, Nevada Operations Office (DOE/NV). Results of the offsite radiological surveillance program conducted by the US Environmental Protection Agency (EPA), Environmental Monitoring Systems Laboratory, Las Vegas, Nevada, were reported separately by that Agency. Beginning with this 1989 annual Site environmental report for the NTS, these two documents are being combined into a single report to provide a more comprehensive annual documentation of the environmental protection program conducted for the nuclear testing program and other nuclear and non-nuclear activities at the Site. The two agencies have coordinated preparation of this combined onsite and offsite report through sharing of information on environmental releases and meteorological, hydrological, and other supporting data used in dose-estimate calculations. 57 refs., 52 figs., 65 tabs.

  7. Searching your site`s management information systems

    Energy Technology Data Exchange (ETDEWEB)

    Marquez, W.; Rollin, C. [S.M. Stoller Corp., Boulder, CO (United States)

    1994-12-31

    The Department of Energy`s guidelines for the Baseline Environmental Management Report (BEMR) encourage the use of existing data when compiling information. Specific systems mentioned include the Progress Tracking System, the Mixed-Waste Inventory Report, the Waste Management Information System, DOE 4700.1-related systems, Programmatic Environmental Impact Statement (PEIS) data, and existing Work Breakdown Structures. In addition to these DOE-Headquarters tracking and reporting systems, there are a number of site systems that will be relied upon to produce the BEMR, including: (1) site management control and cost tracking systems; (2) commitment/issues tracking systems; (3) program-specific internal tracking systems; (4) Site material/equipment inventory systems. New requirements have often prompted the creation of new, customized tracking systems. This is a very time and money consuming process. As the BEMR Management Plan emphasizes, an effort should be made to use the information in existing tracking systems. Because of the wealth of information currently available from in-place systems, development of a new tracking system should be a last resort.

  8. Environmental assessment, Deaf Smith County site, Texas

    Energy Technology Data Exchange (ETDEWEB)

    1986-05-01

    The Nuclear Waste Policy Act of 1982 (42 USC sections 10101-10226) requires the environmental assessment of a proposed site to include a statement of the basis for nominating a site as suitable for characterization. Volume 2 provides a detailed statement evaluating the site suitability of the Deaf Smith County Site under DOE siting guidelines, as well as a comparison of the Deaf Smith County Site to the other sites under consideration. The evaluation of the Deaf Smith County Site is based on the impacts associated with the reference repository design, but the evaluation will not change if based on the Mission Plan repository concept. The second part of this document compares the Deaf Smith County Site to Davis Canyon, Hanford, Richton Dome and Yucca Mountain. This comparison is required under DOE guidelines and is not intended to directly support subsequent recommendation of three sites for characterization as candidate sites. 259 refs., 29 figs., 66 refs. (MHB)

  9. Environmental assessment, Richton Dome site, Mississippi (US)

    Energy Technology Data Exchange (ETDEWEB)

    none,

    1986-05-01

    The Nuclear Waste Policy Act of 1982 (42 USC Sections 10101-10226) requires the environmental assessment of a potential site to include a statement of the basis for the nomination of a site as suitable for characterization. Volume 2 of this environmental assessment provides a detailed evaluation of the Richton Dome Site and its suitability as the site for a radioactive waste disposal facility under DOE siting guidelines, as well as a comparison of the Richton Dome site with other proposed sites. Evaluation of the Richton Dome site is based on the reference repository design, but the evaluation will not change if based on the Mission Plan repository concept. The comparative evaluation of proposed sites is required under DOE guidelines, but is not intended to directly support the subsequent recommendation of three sites for characterization as candidate sites. 428 refs., 24 figs., 62 tabs. (MHB)

  10. Confidence assessment. Site descriptive modelling SDM-Site Forsmark

    Energy Technology Data Exchange (ETDEWEB)

    2008-09-15

    The objective of this report is to assess the confidence that can be placed in the Forsmark site descriptive model, based on the information available at the conclusion of the surface-based investigations (SDM-Site Forsmark). In this exploration, an overriding question is whether remaining uncertainties are significant for repository engineering design or long-term safety assessment and could successfully be further reduced by more surface based investigations or more usefully by explorations underground made during construction of the repository. The confidence in the Forsmark site descriptive model, based on the data available at the conclusion of the surface-based site investigations, have been assessed by exploring: Confidence in the site characterisation data base; Key remaining issues and their handling; Handling of alternative models; Consistency between disciplines; and, Main reasons for confidence and lack of confidence in the model. It is generally found that the key aspects of importance for safety assessment and repository engineering of the Forsmark site descriptive model are associated with a high degree of confidence. Because of the robust geological model that describes the site, the overall confidence in Forsmark site descriptive model is judged to be high. While some aspects have lower confidence this lack of confidence is handled by providing wider uncertainty ranges, bounding estimates and/or alternative models. Most, but not all, of the low confidence aspects have little impact on repository engineering design or for long-term safety. Poor precision in the measured data are judged to have limited impact on uncertainties on the site descriptive model, with the exceptions of inaccuracy in determining the position of some boreholes at depth in 3-D space, as well as the poor precision of the orientation of BIPS images in some boreholes, and the poor precision of stress data determined by overcoring at the locations where the pre

  11. Efficient on-site construction

    DEFF Research Database (Denmark)

    Thuesen, Christian Langhoff; Hvam, Lars

    2011-01-01

    selected market – optimising cost and value. Based on the platform, the company has managed to create a high-quality product at low cost. In fact, they have managed to reduce costs by more than 30 per cent, enabling the company to sell houses to people that normally would not be able to afford a house...... from the German platform such as: platform does not imply that “off-site manufacturing” is the most optimal production method, rather it is a matter of handling complexity; strong commitment and loyalty from the whole organization is needed; importance of having a specific customer focus (target...... costing); and incremental rather than radical innovation. Originality/value – The findings challenge the predominant understanding of industrialisation of the construction processes, illustrating how substantial improvements can be achieved through platform thinking, on-site production and traditional...

  12. Y-12 Site Sustainability Plan

    Energy Technology Data Exchange (ETDEWEB)

    Spencer, Charles G

    2012-12-01

    The accomplishments to date and the long-range planning of the Y-12 Energy Management and Sustainability and Stewardship programs support the U.S. Department of Energy (DOE) and the National Nuclear Security Administration (NNSA) vision for a commitment to energy effi ciency and sustainability and to achievement of the Guiding Principles. Specifi cally, the Y-12 vision is to support the Environment, Safety and Health Policy and the DOE Strategic Sustainability Performance Plan, while promoting overall sustainability and reduction of greenhouse gas emissions. The mission of the Y-12 Energy Management program is to incorporate energy-effi cient technologies site-wide and to position Y-12 to meet NNSA energy requirement needs through 2025 and beyond. The plan addresses greenhouse gases, buildings, fleet management, water use, pollution prevention, waste reduction, sustainable acquisition, electronic stewardship and data centers, site innovation and government-wide support.

  13. Nevada Test Site closure program

    Energy Technology Data Exchange (ETDEWEB)

    Shenk, D.P.

    1994-08-01

    This report is a summary of the history, design and development, procurement, fabrication, installation and operation of the closures used as containment devices on underground nuclear tests at the Nevada Test Site. It also addresses the closure program mothball and start-up procedures. The Closure Program Document Index and equipment inventories, included as appendices, serve as location directories for future document reference and equipment use.

  14. Preliminary site characterization - final report

    Energy Technology Data Exchange (ETDEWEB)

    Clark, D.; Smith, L.B.

    1993-12-01

    This report summarizes the ecological unit reconnaissance conducted at the F-Area Burning/Rubble Pit(s) RCRA/CERCLA Unit (F-Area BRP) on August 30 and 31, 1993 as part of the RFI/RI baseline risk assessment for the waste unit The baseline risk assessment will assess the potential endangerment to human health and the environment associated with the unit and will be used to evaluate remediation criteria, if needed. The information presented in this report will be used in subsequent stages of the ecological risk assessment to refine the conceptual site model, assist in the selection of contaminants of concern, identify potential ecological receptors, and evaluate trophic relationships and other exposure pathways. The unit reconnaissance survey was conducted in accordance with Specification No. E-18272, Rev. 1 dated August 5, 1993, and the Draft {open_quotes}Ecological Risk Assessment Program Plan for Evaluation of Waste Sites on the Savannah River Site{close_quotes}. The objectives of the site reconnaissance were to: Assess the general characteristics of on-unit biological communities including mammals, birds, reptiles, amphibians, and any aquatic communities present. Determine the location, extent, and characteristics of on-unit ecological resources, such as forested areas and wetlands, that could serve as important wildlife habitat or provide other ecological functions. Identify any overt effects of contamination on biological communities. The field investigations included mapping and describing all wetland and terrestrial habitats; recording wildlife observations of birds, mammals, and reptiles; and investigating ecological resources in nearby downgradient and downstream areas which could be affected by mobile contaminants or future remedial actions. In preparation for the field investigation, existing unit information including aerial photographs and reports were reviewed to help identify and describe ecological resources at the waste unit.

  15. The SARA REU Site Program

    Science.gov (United States)

    Wood, M. A.; Oswalt, T. D.; SARA Collaboration

    2000-12-01

    We present an overview of the Research Experiences for Undergraduates (REU) Site Program hosted by the Southeastern Association for Research in Astronomy (SARA) for the past 6 years. SARA is a consortium of the six universities: Florida Institute of Technology, East Tennessee State University, Florida International University, The University of Georgia, Valdosta State University, and Clemson University. We host 10-11 student interns per year out of an application pool of ~150-200. Recruiting flyers are sent to the ~3400 undergraduate institutions in the United States, and we use a web-based application form and review process. We are a distributed REU Site, but come together for group meetings at the beginning and end of the summer program and stay in contact in between using email list manager software. Interns complete a research project working one-on-one with a faculty mentor, and each intern travels to observe at the SARA Observatory at Kitt Peak National Observatory. Interns give both oral and display presentations of their results at the final group meeting. In addition, all interns write a paper for publication in the IAPPP Communications, an international amateur-professional journal, and several present at professional meetings and in refereed publications. We include in the group meetings a ``how-to'' session on giving talks and posters, an Ethics Session, and a session on Women in Astronomy. This work was supported by the NSF Research Experiences for Undergraduates (REU) Site Program through grant AST 96169939 to The Florida Institute of Technology.

  16. Site maps and facilities listings

    Energy Technology Data Exchange (ETDEWEB)

    1993-11-01

    In September 1989, a Memorandum of Agreement among DOE offices regarding the environmental management of DOE facilities was signed by appropriate Assistant Secretaries and Directors. This Memorandum of Agreement established the criteria for EM line responsibility. It stated that EM would be responsible for all DOE facilities, operations, or sites (1) that have been assigned to DOE for environmental restoration and serve or will serve no future production need; (2) that are used for the storage, treatment, or disposal of hazardous, radioactive, and mixed hazardous waste materials that have been properly characterized, packaged, and labelled, but are not used for production; (3) that have been formally transferred to EM by another DOE office for the purpose of environmental restoration and the eventual return to service as a DOE production facility; or (4) that are used exclusively for long-term storage of DOE waste material and are not actively used for production, with the exception of facilities, operations, or sites under the direction of the DOE Office of Civilian Radioactive Waste Management. As part of the implementation of the Memorandum of Agreement, Field Offices within DOE submitted their listings of facilities, systems, operation, and sites for which EM would have line responsibility. It is intended that EM facility listings will be revised on a yearly basis so that managers at all levels will have a valid reference for the planning, programming, budgeting and execution of EM activities.

  17. Rulison Site corrective action report

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-09-01

    Project Rulison was a joint US Atomic Energy Commission (AEC) and Austral Oil Company (Austral) experiment, conducted under the AEC`s Plowshare Program, to evaluate the feasibility of using a nuclear device to stimulate natural gas production in low-permeability gas-producing geologic formations. The experiment was conducted on September 10, 1969, and consisted of detonating a 40-kiloton nuclear device at a depth of 2,568 m below ground surface (BGS). This Corrective Action Report describes the cleanup of petroleum hydrocarbon- and heavy-metal-contaminated sediments from an old drilling effluent pond and characterization of the mud pits used during drilling of the R-EX well at the Rulison Site. The Rulison Site is located approximately 65 kilometers (40 miles) northeast of Grand Junction, Colorado. The effluent pond was used for the storage of drilling mud during drilling of the emplacement hole for the 1969 gas stimulation test conducted by the AEC. This report also describes the activities performed to determine whether contamination is present in mud pits used during the drilling of well R-EX, the gas production well drilled at the site to evaluate the effectiveness of the detonation in stimulating gas production. The investigation activities described in this report were conducted during the autumn of 1995, concurrent with the cleanup of the drilling effluent pond. This report describes the activities performed during the soil investigation and provides the analytical results for the samples collected during that investigation.

  18. Off-sites that work.

    Science.gov (United States)

    Frisch, Bob; Chandler, Logan

    2006-06-01

    Of all the meetings top executives go to in a year, none is more important than the strategy off-site, where the most essential conversations for the future of the business occur. Yet it is the rare management team that can say its strategy off-site truly changed the way the business is run. At best, participants do some vague direction setting and work on team-building skills; at worst, they write off the retreat as a waste of time and resources. It needn't be like that. From their two decades of experience designing and facilitating strategy off-sites in companies large and small around the world, the authors have distilled a set of best practices that businesses can use to make the most of this annual opportunity. Essentially, the problem with most strategy off-sites is that they're insufficiently structured. People think that if you schedule a meeting, invite top leaders (and perhaps an outside expert), and block off units of time to discuss big subjects, the rest will take care of itself. In reality, formlessness leads to aimlessness. Oddly enough, only rigorously designed meetings give rise to truly candid strategy discussions. That rigor starts before the meeting, when the scope of the matters discussed must be limited, the participant list drawn up accordingly, the relevant materials (and only those) sent out and absorbed, and a detailed agenda established. During the meeting, the pace and quality of the conversation can be managed through attention to politics and by using carefully tailored frameworks, decision points, and group exercises. After the meeting, an action plan ensures clear accountability and follow-through. If you and your executive team spend four days a year rafting down rivers together, you'll eventually get good at rafting down rivers. Spend four days a year having well -designed strategy conversations together, and you will transform your annual off-site from a meaningless junket into a genuine turning point for your business.

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

    Energy Technology Data Exchange (ETDEWEB)

    1991-08-01

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

  20. SFR site investigation. Bedrock Hydrogeochemistry

    Energy Technology Data Exchange (ETDEWEB)

    Nilsson, Ann-Chatrin [Geosigma AB, Uppsala (Sweden); Tullborg, Eva-Lena [Terralogica AB, Graabo (Sweden); Smellie, John [Conterra AB, Uppsala (Sweden); Gimeno, Maria J.; Gomez, Javier B.; Auque, Luis F. [Univ. of Zaragoza, Zaragoza (Spain); Sandstroem, Bjoern [WSP Sverige AB, Goeteborg (Sweden); Pedersen, Karsten [Micans AB, Moelnlycke (Sweden)

    2011-11-15

    There are plans that the final repository for low and intermediate level radioactive waste, SFR, located about 150 km north of Stockholm, will be extended. Geoscientific studies to define and characterise a suitable bedrock volume for the extended repository have been carried out from 2007 to 2011, and have included the drilling and evaluation of seven new core drilled and four percussion boreholes. These new data, together with existing data extending back to 1985, have been interpreted and modelled in order to provide the necessary information for safety assessment and repository design. This report presents the final hydrogeochemical site description for the SFR site, and will constitute a background report for the integrated site description (the SFR Site Descriptive Model version 1.0) together with corresponding reports from the geological and hydrogeological disciplines. Most of the hydrogeochemical data from the field investigations consist of major ions and isotopes together with sporadic gas, microbe and measured redox data. Despite the close proximity of the Forsmark site, few data from this source are of relevance because of the shallow nature of the SFR site, the fact that SFR is located beneath the Baltic Sea and also the drawdown/upconing impacts of its construction on the hydrogeochemistry. This artificially imposed dynamic flow system is naturally more prevalent along major deformation fracture zones of higher transmissivity, whilst lower transmissive fractures together with the less transmissive bedrock masses between major deformation zones, still retain some evidence of the natural groundwater mixing patterns established prior to the SFR construction. The groundwaters in the SFR dataset cover a depth down to -250 m.a.s.l. with single sampling locations at -300 and -400 m.a.s.l. and represent a relatively limited salinity range (1,500 to 5,500 mg/L chloride). However, the {delta}{sup 18}O values show a wide variation (-15.5 to -7.5 per mille V